Author Index - symposium.cshlp.orgsymposium.cshlp.org/content/58/local/back-matter.pdfAuthor Index A...

Author Index

A

Aboussekhra, A., 625 Ainscough, R., 367 Allen, S., 767 Almouzni, G., 225 Alroy, I., 133 Anderson, K., 367 Antoniou, M., 7 Archer, T.K., 63 Arents, G., 273 Ariel, M., 307

B

Barnes, D.E., 619 Bartolomei, M.S., 287 Baum, M., 687 Beard, C., 297 Beese, L.S., 495 Bell, S.P., 435 Bellann6-Chantelot, C., 377 Benson, F.E., 525 Berks, M., 367 Berry, M., 7 Bestor, T.H., 297 Bienz-Tadmor, B., 487 Biggerstaff, M., 625 Bird, A.P., 281 Blackburn, E.H., 707 Blair, D., 367 Blow, J.J., 475 Blundell, P.A., 105 Bonaduce, M.J., 457 Bonifer, C., 37 Borst, P., 105 Botchan, M.R., 403 Bradley, J., 707 Brandeis, M., 307 Bresnick, E.H., 63 Brewer, B.J., 425 Briot, A., 645 Brown, C.J., 315 Brunkow, M.E., 287 Burley, S.K., 123

C

Canfield, T.K., 633 Carbon, J., 669 Carlson, M., 257 Carrel, L., 315 Carter, K.C., 807 Cedar, H., 307 Chapman, L., 141 Cheng, X., 331 Choy, B., 199 Chumakov, I., 377 Chung, J., 1 Cisek, L.J., 187 Clark, D., 1 Clark, K.L., 123 Clarke, L., 687 Cleary, M.A., 167 Cohen, D., 377

Collins, I., 415 Connell, M., 367 Cooper, J., 367 Cooper, J.P., 237 Corden, J.L., 187 Coulson, A., 367 Craxton, M., 367 Cremer, C., 777 Cremer, T., 777 Crothers, D.M., 115

D

Daly, G., 619 Davis, I., 793 de Boer, E., 7 Dear, S., 367 DePamphilis, M.L., 475 Dershowitz, A., 415 Deshpande, A.M., 415 Deufel, A., 505 DiBartolomeis, S.M., 487 Dietzel, S., 777 Dijkwel, P.A., 467 Di Leonardo, A., 655 Diller, J.D., 425 Dillon, N., 7 Du, W., 73 Du, Z., 367 Dujon, B., 357 Durbin, R., 367 DutnaU, R.N., 141

E

Earnshaw, W.C., 697 Egelman, E.H., 567 Elgin, S.C.R., 83 Ellis, J., 7 Emmerich, P., 777

F

Fairall, L., 141 Fang, W.-H., 597 Fangman, W.L., 425 Farkas, G., 45 Faust, N., 37 Favello, A., 367 Felsenfeld, G., 1 Ferr6-D'Amar6, A., 123 Fertitta, A., 767 Finch, J.T., 141 Forrester, W., 97 Forsburg, S.L., 637 Forster, A.C., 297 Foss, M.A., 443 Fouts, E., 403 Fox, C.A., 443 Fragoso, G., 63 Francis-Lang, H., 793 Fraser, P., 7 Freedman, L.F., 133 Friedman, J.M., 495

Friedman, K.L., 425 Fulton, L., 367

G

Gall, J.G., 747 Gallagher, R.C., 707 Galloni, M., 45 Garrett-Engele, P.W., 323 Gartler, S.M., 633 Gasser, S.M., 733 Gaszner, M., 45 Gausz, J., 45 Georgiev, G.P., 25 Gerbi, S.A., 487 Gilbert, D.M., 475 Gilson, E., 733 Gommers-Ampt, J.H., 105 Granok, H., 83 Green, M.R., 199 Green, P., 349, 367 Greenfeder, S.A., 415 Greider, C.W., 719 Griffin, L.A., 199 Gromova, I., 25 Grosschedl, R., 97 Grosveld, F., 7 Grunstein, M., 247 Guacci, V., 677 Gyurkovics, H., 45

H

Hager, G.L., 63 Hagstrom, K., 45 Hall, I., 645 Halloran, N., 367 Hamlin, J.L., 467 Hancock, R., 25 Hansen, R.S., 633 Hawkins, T., 367 Hayes, J.J., 225 Hecht, A., 37 Hecht, A., 247 Hendrich, B., 315 Henikoff, S., 577 Herr, W., 167 Hillier, L., 367 Hiom, K., 525 Hogan, E., 677 Hogga, I., 45 Holmes, J., 597 Hood, L., 339 Hurst, J., 7 Huynh, C., 367

Iarovaia, O., 25 Ikeya, T., 567 Imam, A., 7 Ish-Horowicz, D., 793

J

Jacob, F., 383 Jaenisch, R., 297 J~iger, J., 495 Jauch, A., 777 Jenuwein, T., 97 Jiang, W., 669 Jim6nez-Garcia, L.F., 799 John, S., 63 Johnston, L., 367 Jonczyk, P., 645 Jones, C.J., 625 Juan, L.-J., 213

K

Kadonaga, J.T., 205 Kafri, T., 307 Kahmann, R., 505 Kahn, J.D., 115 Kamakaka, R.T., 205 Karch, F., 45 Karzai, A.W., 389 Kelly, T.J., 637 Kelsey, G., 55 Kershaw, J., 367 Kershisnik, E.O., 577 Keshet, I., 307 Kieft, R., 105 Kim, J.L., 123 Kingsbury, J., 677 Kingston, R.E., 213 Kirsten, J., 367 Kitsberg, D., 307 Kladde, M.P., 237 Klar, A.J.S., 457 Kleckner, N., 553 Klimasauskas, S., 331 Kohlstaedt, L.A., 495 Kolor, K.M., 425 Koop, B.F., 339 Koshland, D., 677 Kozono, Y., 367 Kumar, S., 331 Kurz, A., 777

L

Laemmli, U.K., 755 Lai, J.-S., 167 Laird, C.D., 633 Laister, N., 367 LaMarco, K., 167 Lamb, M.M., 633 Lande, R., 543 Larin, Z., 55 Laroche, T., 733 Latreille, P., 367 Laurent, B.C., 257 Lawrence, J.B., 807 Learn, B., 389 Lee, E., 1 Lee, M.S., 707 LeGall, I., 377

837

838 AUTHOR INDEX

Lehmann, A.R., 619 Lehrach, H., 55 Leighton, P.A., 287 Li, E., 297 Li, G.-M., 597 L1, R., 403 Liang, C., 487 Llchter, E, 55, 777 Ligtenberg, M.J.L., 105 Lin, H.-B., 467 Lindahl, T.. 619 Linke, S.P., 655 Livanos, E., 645 Longley, M., 597 Loo. S., 443 Loughney, K., 577 Lu, H., 187 Lu, Q., 83 Luger, K., 265

M

Mackay, A.M., 697 Maniatis, T., 73 Marahrens, Y., 435 Marschall, L.G., 687 Martin-Morris, L.E., 577 Massa, H., 767 Mathieu, U., 777 McMacken, R., 389 Meijer, D., 7 Meluh, P., 677 Merker, P., 505 Miao, V., 323 Miller, A.P., 315 Miyazawa, H., 475 Mizuuchi, K., 515 Mizuuchi, M., 515 Modrich, E, 597 Montoliu, L., 55 Morse, R.H., 237 Mortimore, B., 367 Mosca, P.J., 467 Moudrianakis, E.N., 273 Mialler, H.-P., 533 Muller, M., 45 Murphy, C., 747 Murphy, M., 237 Muskhelishvili, G., 505

N

Nabetani, A., 567 Nallaseth, F.S., 475 Nash, R.A., 619 Newlon, C.S., 415 Ngan, V.K., 687 Nikolov, D.B., 123 Nurse, P., 637

O

O'Donovan, A., 625 O'Keefe, R.T., 799

Ogawa, H., 567 Ogawa, T., 567 Olson, M.V., 349 Ong, L.Y., 415 Ortega, J,M., 475

P

Palladino, F., 733 Panussis, D., 367 Patterton, H.-G., 237 Percy, C., 367 Peterson, M.G., 167 Pfeifer, K., 287 Philipsen, S., 7 Pillus, L., 733 Poortinga, G., 577 Poulose, B., 645 Prigent, C., 619 Pruss, D., 225 Pruzina, S., 7 Pryciak, P.M., 533

R

Raghuraman, M.K., 425 Rao, H., 435 Razin, A., 307 Razin, S.V., 25 Reardon, J.T., 605 Rechsteiner, T., 265 Reinberg, D., 187 Reitman, M., 1 Rhodes, D., 141 Rice, P.A,, 495 Richardson, G.A., 323 Richmond, T.J., 265 Ried, T., 777 Rifkin, L., 367 Rine, J., 443 Rinke, B., 777 Rivier, D.H., 443 Roberts, E., 619 Roberts, R.J., 331 Roberts, S.G.E., 199 Robins, R, 619 Roelofs, H., 645 Roopra, A., 367 Roth, S.Y., 237 Rowen, L., 339 Rudenko, G., 105 Rusch, K., 505

Saam, J., 287 Sachs, R., 767 Sage, M., 645 Saltoh, Y.. 755 Sancar, A., 605 Sanchez, J., 645 Satoh, M,S, 619 Saueressig, H., 37 Schafer, G., 37

Schaefer, D., 645 Schedl, A., 55 Schedl, P., 45 Scherthan, H., 777 Schrock, E., 777 Schutz, G., 55 Schwabe, J.W.R., 141 Selig, S., 307 Selker, E.U., 323 Shimizu, M., 237 Shinohara, A., 567 Shivji, M.K.K., 625 Shownkeen, R., 367 Sigler, P.B., 133 Simpson, R.T., 237 Singer, M.J., 323 Sipos, L., 45 Sippel, A.E., 37 Smaldon, N., 367 Smerdon, S., 495 Smith, A., 367 Smith, C.L., 63 Smith, H.S., 487 Smith, M.. 367 Spector, D.L., 799 Speicher, M.R., 777 Spradling, A.C., 585 Staden, R., 367 Stahl, F.W., 543 Steiner, N.C., 687 Steitz. T.A., 495 Stillman, B., 435 Strouboulis, J., 7 Strunnikov, A., 677 Studltsky, V., 1 Sulston, J., 367 Szymkowskl, D.E., 625

T

Tanese, N., 179 Taylor, I.C.A., 213 Taylor, M.C., 105 Thanos, D., 73 Theis, J.F., 415 Thierry-Mieg, J., 367 Thilly, W., 597 Thomas, J.O., 15 Thompson, J.S., 247 Thompson, L.H., 605 Tilghman. S.M., 287 Tjian, R., 179 Tlsty, T.D.. 645 Trask, B.J., 767 Treich, I., 257 Tsaneva, I.R., 525 Tsukagoshi, Y., 63 Tsvetkov, A., 747

Udvardy, A., 45 Ura, K., 225 Urnov, F.D., 487

V

van den Engh, G., 767 van Leeuwen, F., 105 Varmus, H.E., 533 Vaudin, M., 367 Vaughan, K., 367 Vazquez, J., 45 Verreault, A., 15

W

Wahl, G.M., 655 Wallrath, L.L., 83 Walter, P.P., 213 Wang, J., 495 Wang, K., 339 Waterston, R., 367 Webber, A.L., 287 Weiner, B.M., 553 Weinstock, L., 367 Wemtraub, H., 819 Weiss, A., 307 Wellinger, R.J., 725 West, S.C., 525 Westergaard, O., 25 Westphal, H., 1 White, A., 645 Whyatt, D., 7 Willard, H.F., 315 Wilson, A.C., 167 Wilson, R., 367 Wohldmann, P., 367 Wolberger, C., 159 Wolf, A.J., 725 Wolffe, A.P., 225 Wood, R.D., 625 Workman, J.L., 213 Wu, C.-H.H., 747 Wu, M., 767 Wu, N., 487 Wu, Z., 747 Wfithrich, K., 149

X

Xing, X., 807 Xu, W., 133

Y

Yamamoto, A., 677 Yang, L., 403 Yin, Y., 655 Yu, X., 567

Z

Zakian, V.A., 725 Zawel, L., 187 Zemel, S., 287 Zirbel, R., 777

Subject Index

A

37A5 antigen, 699. See also IN- CENPs

87A7, 45-48 (A)BC excinuclease, 613-614. See

also UvrABC excision repair enzymes

abd-A and Abd-B genes. See Bithorax complex

Abfl/ABF1 (ARS binding factor 1), 250, 409, 419, 436-437, 444, 448-450, 452. See also ARS

a-Cell-specific gene. See STE6 gene

Acentric structures, 656-657, 663 Acetylation of histones. See H3;

H4; Histones Achiasmatic chromosomes,

segregation, 563 ACS. See ARS, consensus se-

quence Actinomycin D, 816 Activators. See GAL4; Replication

of DNA; Transcription ADE gene, telomeric repression,

250, 733 S-Adenosyl-L-methionine

(AdoMet), crystal structure with HhaI, 331-337

Adenovirus and splicing, 802, 817 Adh and positioned nucleosomes,

94 AdoMet. See S-Adenosyl-L-

methionine A element. See Lysozyme gene Alkylation tolerance and mis-

match repair, 600-601 Allele-specific gene expression,

methylation, and replication timing. See Imprint- ing

c~-Amanitin, 800-801, 816 ct-Globin. See Globin genes c~-TIF. See VP16 a2 repressor

and chromatin structure in gene expression, 237-244

and retroviral DNA integration, 533, 537

Alu-PCR hybridization, YAC to YAC, for mapping, 378- 382

am gene. See Neurospora crassa 3-Aminobenzamide, 622-623 Amplifiable YACs, 55, 57-58 Amplification of DNA. See Gene

amplification; Puffs

Anaphase. See Chromosome, segregation

spindle stability and INCENPs, 697-705

Aneuploidy, 645, 650-652 Antennapedia homeodomain, 159,

163 Antp(C39S)-DNA complex,

hydration and structure, 150, 152, 155-156, 827

Antigenic variation in trypanosomes, 105-112

Antigens as chromosome passenger proteins, 697-705

Antimetabolites, cell cycle arrest, 659-661. See also Methotrexate; PALA

Antirepression. See Replication of DNA; Transcription

Antisense RNA pairing, 554-556 Antp(C39S). See Antennapedia

homeodomain Aphidicolin, 471,480, 599 Arab~dopsis thaliana TBP-2, X-ray

crystallographic studies, 123-126

ARS (autonomously replicating sequence), 249, 363, 475, 477. See also Abfl/ABF1

ARS1 domains and function, 409, 435-436

ARS307 domains and function, 418-419, 435-436

consensus sequence (ACS), 418- 419, 435,444

in HM loci, 447-448 ORC binding to, 437-441

function at HMR-E, 449-450 origin interference of ARS1 and

ARS501, 428-431, 433 rDNA, 428 replication origin function, 415-

422, 425-433, 435-436 replication timing of ARS1,

ARS305, ARS501, and KEX ARS, 426-427

Assembly of preinitiation complex. See Preinitiation complex

Assembly of splicing complex. See Lampbrush chromosomes; Snur- posomes

Ataxia telangiectasia, 658 ATF-2 and virus induction of IFN-

[3 gene, 75-79, 834 ATP

and disassembly of preinitiation complex at orig., 389, 393

and ORC binding, 437 and transposition target im-

munity, 516, 520-522 ATPase

DNA-stimulated in SNF2, 260- 262

of RecA and Rad51 proteins, 567, 569

of RuvB protein, 526-528 A tracts in DNA bending, 115-117,

121, 538-539 att sites and retroviral DNA in-

tegration, 533-534 Autonomously replicating se-

quence. See ARS Autosomal recessive disease. See

Xeroderma pigmentosum Autosomes and imprinting, 287.

See also Imprinting 5-Azacytidine (azaC), 283, 297,

323

B

Bacterial o factors, 179, 188, 821- 822, 833

Bacteriophage k clones in mapping, 349, 351 replication in vitro, direc-

tionality and effect of transcription, 389-400, 828

repressor, 821 Bacteriophage Mu. See Phage Mu Band assignments. See

Chromosome, banding Barr body, 320, 782, 810, 831 Basal replication machinery. See

Replication of DNA Basal transcription factors and

machinery. See RNA polymerase; Transcrip- tion factors

B asic/helix-loop-helix/leucine zipper (b/HLH/Z) form of Max, 123, 126-128

Basic pancreatic trypsin inhibitor. See BPTI

bcd gene. See Bicoid Benomyl resistance (Bml) marker.

See Neurospora crassa [3-Galactosidase. See also lacZ

expression from bluetail transposon, 52

[3-Globin. See Globin genes [3-D-Glucosyl-hydroxymethyluracil

and [3-glucosyl transferase, 108-109

839

840 SUBJECT INDEX

~-Thalassemias. See Thalassemias b/HLH/Z. See Basic/helix-loop-

helix/leucine zipper form of Max

Bicoid (bcd) transcriptional activator, 258 transcript localization, 793-794

Bidirectional replication and mapping of origins. See

Mapping and unidirectional replication in

~., 389-400 Biotinylated dUTP to visualize

repair event, 626 Bithorax complex, cis-regulatory

units and pairing- sensitive elements, 48- 53

Bloom's syndrome, 621-622 bluetail transposon, 51-52 Bml marker. See Neurospora

crassa Bombyx and chromosome pairing,

560-561 "Bouquet formation," 557, 741 Bovine papillomavirus. See BPV BPTI (basic pancreatic trypsin in-

hibitor), hydration and structure, 149-150, 152- 154, 827

BPV (bovine papillomavirus) chimeric episomes and mobiliza-

tion of MMTV LTR, 63- 70

problems as model for replication, 482-484

-1 replication and enhancers, 404-412

Branch migration, RuvAB- mediated, 525-530

Breakage-fusion-bridge cycle, 653, 657

Bromodomain, 259 brown gene. See Drosophila Brownian movements in inter-

chromosome domain compartment, 787-788

Budding yeast. See Yeast, Sac- charomyces cerevisiae

C

C1. See HCF CAD gene amplification, 647-652,

656, 662 Caenorhabditis elegans, genomic

sequencing and mapping, 367-374

cAMP-binding protein (CAP), DNA bending role, 115-117

Cancer and loss of genomic integrity.

See Gene amplification and telomere length, 721-722

CAP. See cAMP-binding protein;

Catabolite activator protein

Carbamyl synthase, aspartate transcarbamylase, and dihydrooratase activity. See CAD gene amplification

Carboxy-terminal domain (CTD) of RNA polymerase II, phosphorylation of, 187, 190-197

Casein kinase II. See CKII Catabolite activator protein (CAP),

DNA bending and retroviral DNA integration target, 537

C-bands, 756, 758 CBF1, 669 CBF2 gene and CBF3 suhunits,

669-675, 682 CBF5, 674 CCG1, 182, 827-828 CCGG methylation, 323 CCG repeats and methylation in

fragile X syndrome, 633- 634

cdaA1 mutants, macronuclear division and telomeric sequences, 709-711

cdc mutations, genes, and proteins cdc2-Cln kinase, 820-821 cdc2 and phosphorylation

in control of replication and mitotic checkpoint, 638, 640

RNA polymerase II, 193 CDC7 gene, 444 cdcl O+-dependent transcrip-

tional control, 639-640 CDC17 and telomere length, 720 cdc18 +, DNA replication and

coordination with mitosis, 639-642, 832

CDC46 gene, 439-440 in study of sister chromatid pair-

ing and chromosome condensation in mitosis, 679-680

Cell cycle. See also cdc mutations, genes, and proteins; Replication of DNA

arrest by antimetabolites, 659-661.

See also Methotrexate; PALA

and DNA replication proteins, 437

in response to DNA damage. See p53; RAD proteins, RAD9

checkpoint control, 412, 683, 698, 832. See also DSC1; p53; RAD proteins, RAD9

mitotic checkpoint, 639-642 control proteins and

phosphorylation, 193, 638, 640

coordination with replication, 384-386, 487, 637-642. See also Replication of DNA, timing

S phase, 439, 441, 444 and chromosome breakage,

657 nuclei in CHO cells and

Xenopus extracts, replication initiation, 479-481

premeiotic vs. mitotic, ARS element role, 421

replication timing of ARSs, 426-427

-specific genes, 638-640 Cell membrane and replication

control, 384-385 cen/ CEN locus, 669-675, 682,

687-694. See also Centromere

CENP-E, 699, 704-705. See also INCENPs

Centromere, 421,432, 563-564. See also Genomic sequencing; INCENPs

and ARS308, 428 assembly and function in S.

cerevisiae, 681-683 CBF3 subunits and function in

S. cerevisiae, 669-675, 682

conditional, for amplifiable YACs, 55, 57

and FISH effect on nuclear topography, 781-782

gene conversions at, distribution of exchange models, 545-550

heterochromatin, 756, 758 position effects in S. pombe, 249 structure, function, and K

repeats in S. pombe, 687-694

CFF. See HCF CFP (circular form of plasmid) and

yeast telomere replication, 727-730

Chiasma interference, 543-550 Chicken globin genes, chromatin

structure, 1-3, 15-22 Chicken INCENPs, 697, 699-705 Chicken lysozyme locus, 3, 37-43,

823 Chicken RAD51 gene, 573-575 Chimerisms in YACs, 377-379 Chinese hamster ovary (CHO)

cells complementation groups and ex-

cision repair, 605-615 S-phase nuclei, replication in-

itiation, 479-481 CHO cells. See Chinese hamster

ovary cells

SUBJECT INDEX 841

Chromatid interference, 543 Chromatid pairing and attach-

ment. See Sister chromatids

Chromatin. See also Acentric structures; Heterochromatin; Histones; Loops; Nucleosomes; scs and S C S t

assembly and replication, 233, 408-409, 411-412

and nuclear organization, 478- 482, 484

compacting in nucleus, structure and organization, 1, 15- 22, 45, 83, 92, 94, 248, 273-275, 692-694, 758, 782, 810. See also DNA; Domains; Heterochromatin; Nucleosomes; Scaffold

10-nm fiber, 22, 63, 254 30-nm fiber, 1, 15, 22, 45, 63,

130, 248, 758, 810 and electric forces of inter-

chromosome domain compartment, 786-788

and imprinting defect, 461,463 in interphase, 247-248, 771-

772, 774 movements within nucleus, 788-

789 and nuclear membrane interac-

tion. See Nuclear envelope

nuclease sensitivity. See DNase I sensitivity of chromatin

structure alterations by SNF/SWI

proteins, 262 and centromere function, 692-

694 (CT) n elements, 89, 94 and DNA repair, 623, 630 effect on retroviral DNA in-

tegration, 533-540 effect on transcriptional com-

petence and control. See DNase I sensitivity of chromatin; Domains; Transcription

effect on transcription factor access to binding sites. See Transcription factors

of H19 imprinted gene and DNA methylation, 289- 291, 293, 311

HMG I(Y) role in, 79 mapping, 84-85 -mediated transcription

repression. See Tran- scription, repression and silencing

preset gene configuration vs. remodeling, 83, 88

hsp26 as preset gene, 83-95 and X inactivation, 320

and transcript export, 794-796 Chromatosome-like complexes of

Hi on nucleosome cores, 214, 217, 221

Chromomycin, 29 Chromosomal control elements

and X inactivation. See Chromosome, X

Chromosomal in situ suppression hybridization. See CISS hybridization

Chromosomal origin of replication. See Mapping; Replica- tion of DNA

Chromosome. See also Centromere; DNA; Mini- chromosomes; Telomere; YACs

7 (mouse) imprinted genes. See H19

gene; Igf2 and receptor genes; snRNA and snRNPs

tyrosinase gene, 55-56 21 (human), physical mapping,

377-382 I, II, III (S. pombe) centromere,

687-694 III (C. elegans), sequencing,

367-374 III (yeast), 248

ARS elements, replication origin function. See ARS

sequencing and mapping, 357- 359, 362-365

IV (yeast), ARS1, 426-431, 433 V (yeast)

ARS501, 426-433 replication terminus, 431

XI (yeast), sequencing and mapping, 357-362

XIV (yeast), KEX2 ARS, 426- 427

achiasmatic, chromosome segregation, 563

arrangements, cell-type-specific, 788-789

autosomes and imprinting, 287. See also Imprinting

banding by FISH, 768 and SARs, 755-764

breakage and gene amplification, 656-657. See also Gene amplification

condensation, 703-704, 782 failure and breakage. See

Fragile X syndrome and loop/scaffold model. See

Loops for mitosis, 680-681,697 at time of homologous pairing,

562 cytogenetic analysis of ab-

normalities by FISH, 772-774

dicentric, 652-653, 656-657, 663 domains and structure. See

Chromatin; Domains double minute (DMs), 656-657,

663 interphase and metaphase, map-

ping, 767-774 lampbrush, 45, 747-749, 752 pairing of homologous, unstable

interactions in, 553-564 passenger proteins, 697-705 polytene, 45,487, 491,544 rearrangements. See Deletions;

Dicentric chromosomes; Duplication; Gene amplification; Inver- sions; Mating-type interconversion; Retroviral DNA integration; Trans- locations; Transposition

segregation, 385-386, 549, 563, 677, 680-681, 697-698, 705. See also Centromere; INCENPs; Kinetochore; Mitotic spindle and spindle pole bodies; Strand- segregation model

site-specific replication initiation, 475-484

-specific sublibraries for mapping human genome, 379-380

territories. See Domains X

dystrophin gene chromatin condensation, 810 localization, 782-784, 808

fragile sites (fragile X syndrome), replication timing and methylation, 633-634, 832

inactivation, 311,315, 782 epigenetic and chromosomal

control of gene expression, 315-321, 831

inactivation center (X/C), 315, 318-321

and methy]ation, 282, 312, 319, 831

and replication timing, 307- 308, 311

and X/ST /X i s t gene, 294, 303, 317-321,831

X (Drosophila), chiasma interference and linkage map distance, 543-550

Y (Drosophila), imprinting and position-effect variegation, 593-594

Y (human), 381-382 STS-content mapping,

resolution-completeness profile, 352-353

842 SUBJECT INDEX

Ciliate telomerase, 707-717, 719- 720, 725, 832

Circle-to-circle replication. See Replication of DNA

cis-Acting elements and expression of homeotic

genes, 48-53 for lysozyme gene, 37, 39-42

"concerted action model" for transcription regulation, 38, 42-43

and replication timing, 307, 311 and silencing of mating loci,

248-249 and silencing of trypanosome

genes, 107-108 and transcription, 32

cis-Limited inactivation in X chromosome. See Chromosome, X

CISS (chromosomal in situ suppression) hybridization, 779, 782-784

CKII (casein kinase II), 619, 621 Cleavage furrow, 697-700, 705 Clonal evolution model of

tumorigenesis, 655 Clonal position effects. See Gene

expression Clone fingerprinting and overlap.

See Mapping Cloning large DNA fragments. See

YACs Coactivators of transcription and

TAFs, 179-184, 202 Cockayne's syndrome (CS) and ex-

cision repair, 606, 612- 613, 63O

Coefficient of coincidence, 543- 544, 547, 549-550

Coiled bodies, 785-786, 813 and RNA processing, 749-753

Coilin and related proteins, 749, 752-753

ColE 1 antisense RNA pairing, 555-556

Colocalization of homologous chromosomes, 553-564

Comparative genomic hybridization (CGH), 646

Complementation groups and excision repair, 605-615, 625-631

Concerted evolution. See Evolution Condensation of chromatin and

chromosomes. See Chromatin; Chromosome

Confocal microscopy, 782-785, 789. See also Chromosome, banding, and SARs

Conservation of sequence. See Evolution

Constant (C) region of TCR. See TCR

Contigs. See Mapping

Conversion. See Gene conversion Copy number. See also Compara-

tive genomic hybridization

dependence. See Gene expression; Methylation of DNA

increase. See Gene amplification regulation in transposons, 592-

594 Core histones. See H2; H3; H4;

Histones, octamer Core promoter element, 123, 187.

See also TATA box Cosmid clones in mapping and se-

quencing. See Genomic sequencing; Mapping

CP1,669 CpG methylation. See Methylation

of DNA CpG to TpG transitions, 622 C (constant) region of TCR. See

TCR Cross-linking

histone/DNA, 226-227, 267 interstrand, by mitomycin C,

612 pyridoxyl 5 r phosphate to

reverse transcriptase and Klenow fragment, 497-498

UV-mediated H1 and MMTV LTR promoter,

65-67 H5/DNA in ~-globin, 15-22

Crossovers accompanying gene conversion.

See Chiasma interference

and homologous chromosome pairing, 556

Crystal-packing effects on protein surface, 149

Crystal structure. See X-ray crystal structure

CS. See Cockayne's syndrome and excision repair

CT-binding protein. See GAGA factor

CTD. See Carboxy-terminal domain of RNA polymerase II

(CT) n elements, role in transcriptional activation, 89, 94

CTF13, 674 Cyclization kinetics and DNA

bending, 115-122 Cys2-His 2 and Cys2-Cys 2. See Zinc

fingers and zinc- stabilized motifs

Cytogenetic analysis in interphase and metaphase chromosomes by FISH, 772-774. See also Chromosome, banding

Cytokinesis and INCENPs, 697- 705

Cytoplasmic localization of pair- rule transcripts. See Drosophila

Cytosine methylation. See Methylation of DNA

Cytoskeleton and chromosome passenger proteins, 698, 703

D

dam methylase and replication control, 384-385 in study of yeast chromatin

structure, 251 Daunomycin staining of

chromosome bands and SARs, 756, 758-764

Debye-Hfickel forces on chromosome territories, 787-788

D (diversity) gene segment. See TCR

Deletions, FISH for cytogenetic analysis, 772-773

De novo methylation, 283, 324- 325, 328

Deoxyadenosine methylation. See dam methylase

DHFR (dihydrofolate reductase) locus, 664

and gene amplification, 648, 651, 657

replication initiation in, 467- 472, 476-477, 480, 488

Dicentric chromosomes, 652-653, 656-657, 663

Dihydrofolate reductase. See DHFR locus

Directionality of replication fork movement and 2-D gel anal-

ysis of replication intermediates. See Mapping

k, 389-400 Distamycin, 28 Diversity (D) gene segment. See

TCR Dmcl, 573-575 DMs (double minute

chromosomes), 656-657, 663

DNA. See also Chromosome; Cross-linking; Genomic sequencing; Loops; Map- ping; Methylation of DNA; Minicircle DNA

amplification, intra- and extrachromosomal, 487. See also Gene amplification; Puffs

attachment to nuclear matrix. See MARs; Scaffold, -associated regions

bending, 65, 78, 505

SUBJECT INDEX 843

A tracts in, 115-117, 121,538- 539

free energy of, 120-122 and HMG I(Y), 75, 79 mechanisms, 115 and retroviral DNA integra-

tion target at major groove, 537-539

and synergistic action of transcription initiation proteins, 115-122

-binding proteins. See c~2 repressor; Catabolite activator protein; DNA, bending; Domains; Enhancer; GAGA factor; GAL4; HhaI crystal structure; Histones; Homeodomain proteins; lac repressor; LexA; ORC; PARP; Rapl/RAP1; RecA; RNA polymerase; RPA; RuvABC proteins; Tran- scription factors; Zinc fingers and zinc- stabilized motifs

cleavage. See DNase I sensitivity of chromatin; Double- stranded DNA break; Recombination; Topoisomerase

cloning large fragments. See YACs

compacting in nucleus. See Chromatin

concerted evolution of double helix and core histones, 278

damage and cell cycle arrest. See p53;

RAD proteins, RAD9 and repair. See Repair of DNA

domains and structure. See Chromatin; Domains; Heterochromatin

electrostatic charge and hydration in compaction of double helix, 274

fragile sites. See Fragile X syndrome

gapped, 525, 528-529. See also Recombination; Repair of DNA

hydration water in recognition, 155-156

incision mechanism, 626-628 insertion. See Retroviral DNA

integration; Transposi- tion

invertase. See Inversions joining. See DNA ligases; PARP;

Repair of DNA modified nucleoside in silencing

ofVSG gene, 108-109 nicked circular, RNA polymerase

binding to, 118-122

nicking and transcription sensitivity, 32

rearrangements and elimina- tion. See Genome, stability

-stimulated ATPase in SNF2, 260-262

strand exchange or transfer. See Recombination

supercoiling, 274 and Gin/FIS-mediated recom-

bination, 505-506, 511 and replication templates. See

Bacteriophage k; BPV and RNA polymerase binding,

120 and transcription, 4, 32

synthesis. See Replication of DNA; Telomere, and telomerase

telomeric, 707. See also Telomere

transcription factor access to. See Transcription factors

-typing screen for brown + deletions. See Drosophila, brown gene

unwinding. See DNA helicase; Topoisomerase, II

element (DUE), 419 and strand exchange. See

Recombination dnaA protein. See Replication of

DNA DnaB protein. See DNA helicase DNA-dependent RNA

polymerases. See RNA polymerase

DNA fluorochromes in chromosome banding, 756-764

DNA helicase, 398, 630, 717. See also Mismatch repair

DnaB and k replication, 389- 390, 397-398, 400

El, 405-406, 411-412 of ERCC proteins, 629-630 and excision repair, 629-631 -like domain of SNF2, 259-260 of RuvAB, 527-528 T antigen, 411-412 of TFIIH, 193, 197, 262

DnaJ and DnaK. See Heat shock genes

DNA ligases, I, II, and III, 619- 622

DNA methyltransferases. See Methyltransferases

DNA polymerases, 725 accessory factor. See PCNA a, 642, 720

inhibitor. See Aphidicolin :primase, 412, 637

5 or e, 615, 626, 629, 631,637 III holoenzyme

subunit ofE. coli, 629

and ~. replication. See Bac- teriophage

and repair. See Mismatch repair

reverse transcriptase and Klenow fragment, mechanism, nucleotide misincorporation, and structure, 495- 5O3

DNA primase. See Primase DNA puffs. See Puffs DNase I sensitivity of chromatin,

37, 248, 437, 550 hypersensitivity regions, 37, 51,

83 in centromeric repeat, 693 gene remodeling to form, 83 in globin, 1-3, 5, 7, 18, 21,822 in hsp26, 87

role of (CT) n elements, 89 and insulator elements, 3, 22,

32, 45-48 in lysozyme gene, 37, 39, 42 MARs and cryptic promoters

in generating, 97-102 in M A T loci, 250 in regulation of replication and

transcription, 492 and retroviral DNA integra-

tion targets, 534, 537, 539

and steroid-receptor binding to nucleosome B, 63-64, 66

and topoisomerase II, 26-28 in regulatory unit for lysozyme

gene transcription, 38- 39, 42

and transcriptional competence of ~-globin domain, 15- 22

DNA topoisomerase. See Topoisomerase

Domains a-globin, 25-26, 31 ARS1, 435-436 ARS307, 418-419, 435-436 ~-globin, 15-22 border regions in lysozyme gene,

37-39, 41-42 bromodomain, 259 of chromatin structure for

repression of yeast genes, 237-244

linkage to replication initiation, 452-454

of chromosome, functional com- partmentalization of nucleus, 777-789

transcript domains and splicing, 799, 813-817

coiled-coil and INCENP binding to micro-

tubules, 697, 700, 705 of lamins A and C, homology

with SIR4, 743-744

844 SUBJECT INDEX

Domains (continued) communication within and be-

tween, 33 containing rRNA genes,

26-29 containing single-copy genes,

29-31 DNA-binding, in steroid recep-

tors and transcription factors, 123-130, 133- 139, 141-146, 826-827. See also Homeodomain proteins; Zinc fingers and zinc-stabilized motifs

of DNA ligases, 619-621 of DNA methyltransferase, 297 DNase-sensitive chromatin,

regulatory unit for lysozyme gene transcription, 37-43

domain fragments for use in YACs, 31-32

and enhancer trapping, 795 helicase-like, SNF2, 259-260 of histone amino terminus, tran-

scription repression, 238, 252

of HMR-E silencer, 444 oflgf2-H19, allele-specific struc-

tures in, 307-312 in interphase nuclei, 771 joint-pairing. See Chromosome,

pairing of homologous ligand-binding, in steroid recep-

tor, 133 methylation, allele-specific, 289-

294 positive regulatory (PRDs), IFN-

gene, 73-80 POU, 169. See also Oct-1 and

Oct-2 homeodomain proteins

in protein/protein interactions of Gin/FIS-mediated recombination, 505-512

putative boundary elements 87A7 heat shock locus, 45-48.

See also scs and scs ~ bithorax complex, 48-53

in recombination/repair proteins, 569, 574-575

and replication control, 32 activation, 404, 409-411 timing and allele-specific ex-

pression, 307-308, 310- 311

RNA polymerase II carboxy- terminal, 187, 190-197

Smclp and NTP-binding motif of mechanochemical motors, 681

and subdomains of reverse transcriptase and Klenow fragment, 495- 498, 5O3

target recognition, HhaI, 331, 334-335

templating, of telomerase RNA, 715-716

topological organization and zeste protein, 33

and transcription control, 32-33, 37

activation, 167-169, 171, 179- 181, 183, 199, 822, 825

alleviating nucleosome- or HI- mediated repression in GAL4 derivatives, 213, 220-222

in yeast centromeres, 669, 682- 683, 687

Dominant variegation, 577. See also Drosophila, brown gene

Donnan potentials and chromosome territories, 788

Double minute chromosomes (DMs), 656-657, 663

Double-stranded DNA break (DSB), 550, 659

and cell cycle checkpoint control, 657, 832

imprinting event in mating-type interconversion, 458-464

joining. See DNA ligases; PARP. See also Repair of DNA

and recombination. See Recom- bination

Drosophila, 591, 829, 833. See also GAGA factor; Heat shock genes; Heterochromatin; Homeodomain proteins; Homeotic genes; In- sulator elements; P element

brown gene, trans-inactivation and dominant variegation, 577-583, 822

chorion gene and amplification, 487-488, 490, 492

DNA ligase I in, 619 enhancer-trap transposons. See

Enhancer, trapping and excision repair, 611 and pairing of homologous

chromosomes, 553 pairing-sensitive elements and

cis-regulatory units, 48- 53

pair-rule transcript localization and export, 793-797

Tramtrack, 141-143, 146 transvection and domain com-

munication, 33 white gene, 359

and enhancer blocking, 47-48 pairing-sensitive repression,

52-53 position effect of reporter gene

in euchromatin, 46

and topological organization of domains, 33

variegating phenotype in heterochromatin, 84, 93- 95, 247, 577

X chromosome, chiasma interference and linkage map distance, 543-550

Y chromosome, imprinting and position-effect variegation, 593-594

yellow gene, genomic instability and position-effect variegation, 585-590

DSB. See Double-stranded DNA break

DSC1 (or MCBF), 638-639, 679- 680, 683

DUE (DNA unwinding element), 419

Duplication FISH for cytogenetic analysis,

772-773 in retroviral DNA integration,

533 Dystrophin gene

chromatin condensation, 810 localization, 782-784, 808

E

E-box recognition by transcription factors, 127-128

E1 helicase. See DNA helicase E2 and E1 in replication, 404-412 E2F, 664 EBV (Epstein-Barr virus), nuclear

RNA tracks, 784-785, 811,815

Ecdysone, role in transcription and DNA amplification, 488, 491-493

Electric forces acting on chromosomal territories, 786-789

Electron microscopy to visualize repair event, 626

Electrophoresis. See Mapping Electrostatic charge in compaction

of double helix, 274 Elongation. See also Processivity

cycling with transcription initiation, role of RNA polymerase phosphory]a- tion, 187-197

inhibitor. See Aphidicolin Embryonic development and

methylation. See Im- printing; Methylation of DNA

Endonuclease for dual incision in excision repair, 627

Engrailed homeodomain, 159, 162-163

Enhancer, 123, 821-822. See also

SUBJE CT INDEX 845

Gene expression; Tran- scription

-binding factors in antirepression, 210-211

-binding HNF-3/fork head, 124, 128-130

blocking, 47-48, 52 cell-stage specific activation in

myeloid cells, 39-40 in Gin/FIS-mediated recombina-

tion, 505-506, 511 and globin LCR, 1-3, 5, 18, 822-

823 immunoglobulin K, 346 and imprinting of H19 and Igf2

genes, 288, 291,293-294 and looping, 823 in ]ysozyme cells, 42 ~, and factor access in

chromatin, 97-102 in replication initiation in BPV-

1,403-412 sequences in TCR loci, 346 structural role of proteins in

function of, 78-79 TCR-a gene, 78 and topological organization of

domains, 33 trapping, 586, 590, 795-796 virus-inducible complex of IFN-~

gene, HMG I(Y) and combinatorial control, 73-80, 834

Epigenetic inheritance and control, 444-445, 829-832. See also Chromosome, X; Imprinting; Transcrip- tion, repression and silencing

Epipodophyllotoxin. See VM-26 Episomal replication. See ARS Episomes, 656, 663 e-Globin. See Globin gene switch-

ing Epstein-Barr virus. See EBV ERCC (excision repair cross-

complementing) genes and proteins, 606, 609, 611-613, 625-631

Erythroid cells, 1, 37. See also Globin gene switching; Globin genes

ESAGs. See Expression-site associated genes

Escherichia coh enzymes, genes, and proteins.

See dam methylase; Heat shock genes; HU protein; Klenow fragment of DNA polymerase I; lacZ; LexA; RNA polymerase

in recombination/repair, 597- 598. See also (A)BC excinuclease; FIS; mfd gene product; RecA;

RuvABC proteins; Uv- rABC excision repair enzymes

oriC. See Replication of DNA, origin

E silencers, 444. See also HM loci and repression

EST1 and telomerase, 720 Estrogen receptor

DNA-binding domain, 133-139, 141,143-146

in transcriptional activation and regulation, 94

Ethidium bromide, 118, 756 Euchromatin, 46, 84, 247, 577,

585-594, 758, 782. See also Chromatin

Euplotes telomerase, 707, 719 Evolution

concerted, 347 for double helix and core

histones, 278 and conserved sequences in C.

elegans, 373 of heterochromatin, transposon

role, 594 TCR loci in mouse and human,

343-346 trypsinogen gene, 346-347

Excinuclease (excision nuclease) in DNA repair, 605-615

Excision (bidirectional) in mismatch repair, 597-600

Excision and gap repair, 528, 578, 581,598, 625-631

human/rodent excision nuclease and excision assay, 605- 615

PARP role, 622-623 Excision of transposons, 593 3 ' ,5 ' -Exonuclease activity of

Klenow fragment, 495, 499-502

Exonuclease in mismatch repair, 597-598

Export of transcripts. See Nucleus Expression of genes. See Gene ex-

pression Expression-site associated genes

(ESAGs), 110 Extrachromosomal elements and

chromosome breakage, 656-657, 663

e(y) genes and zeste protein, 33

F

Fab-7, 51-52 Fibrillarin, 750, 752-753 Fibronectin RNA, 811-813, 815-

816 Fibrous corona, 675 Fingerprinting. See Mapping FIS, Gin-mediated recombination

and genetic mapping, 505-512

FISH (fluorescence in situ hybridization), 784

for banding assignments, 768 for cytogenetic analysis of

chromosomal ab- normalities, 772-774

in localization of RNA tracks, 810-813

in mapping human genome using YAC contigs, 377- 379, 382

in mapping metaphase and interphase chromosomes, 767-774

in measuring chromatin condensation, 810

and nuclear topography, 781- 782, 789, 808-810

replication patterns of lgf2-H19 region, 307-308

technique, 767-768 for YAC DNA integration in gen-

erating transgenic mice, 58-59

for yeast chromosomes in mitosis, 678-681

for yeast meiotic chromosome pairing, 553-554

Fission yeast. See Yeast, Schizosaccharomyces pombe

Flow cytometry in measuring amplification fre-

quency, 648, 651 and ORC role, 439

Fluorescence in situ hybridization. See FISH

Fluorochromes. See also FISH in chromosome banding, 756-

764 Footprinting

on DNA-binding surface of histone octamer, 276- 277

of MuB at transposition target, 520-521

nucleosome cores, 65 Fragile X syndrome, replication

timing and methylation, 633-634, 832

FRAXA. See Fragile X syndrome Free energy of DNA bending, 120-

122 ftz. See fushi tarazu fushi tarazu, 795

transcriptional regulator. See Tramtrack

Fusion-bridge-breakage cycle, 653, 657

G

GAGA factor, role in transcription, 85-86, 89, 91, 94-95, 205-207

846 SUBJECT INDEX

GAL4 derivatives and transcriptional

activation/reactivation, 180, 200-201,213-222

GAL4-VP16, 206-207, 209- 211,213-214, 219-222

LexA-GAL4 fusion protein, 437

and function of SNF/SWI proteins, 258

and DNA replication, GAL4- p53(1-73) and GAL4- VP16, 409-412

y-Globin. See Globin gene switching

y-Irradiation and DNA damage. See p53

Gapped DNA. See DNA; Repair of DNA

GATA1, 8 G-bands, 756, 758 GC periodicity in yeast

chromosomes, 363, 365 Gel electrophoresis. See Mapping Gene amplification

FISH for cytogenetic analysis, 772-774

as genetic instability marker, 645-653, 655-665

Gene conversion. See also Chiasma interference; Drosophila, brown gene; Mating-type interconversion

in yeast telomeric DNA replication, 725, 731

Gene disruption in yeast chromosomes, 359, 364

Gene domain transfer, 40-43 Gene expression, 33. See also

Transcription allele-specific and developmen-

tal regulation. See Im- printing

and DNase sensitivity. See DNase I sensitivity of chromatin

and enhancer trapping. See En- hancer, trapping

epigenetic control, 829-832. See also Chromosome, X; Im- printing; Transcription, repression and silencing

and genome organization, 808, 815-816

globin chromatin structure role, 1-5,

15-22 copy number dependence, 7 developmental regulation and

gene switching, 7-12 position independence, 3, 7-10

homeotic genes in bithorax complex, 48-53, 788

hormone inducible. See Estrogen receptor; Glucocorticoid

receptor; Progesterone receptor; Steroid receptor

immediate early. See VP16 and interchromosome domain

compartment, 786-788 long-range control. See Enhan-

cer; Insulator elements; LCR; Transcription

lysozyme control by chromatin

regulatory units, 37-43 position effects and copy num-

ber dependence, 41-43 methylation role. See Methyla-

tion of DNA mouse RAD51 gene, 575 pairing-sensitive repression, 52-

53 position effect of reporter gene

integration, 37, 46 position-effect variegation. See

Heterochromatin preset genes vs. remodeling, 83,

88 hsp26 as preset gene, 83-95

recombination in regulation. See Recombination

regulation of genes for DNA replication, 638-639

repression and silencing. See Transcription, repression and silencing

segmentation genes, 48-53, 793- 794

and "trans-sensing effects," 577 tyrosinase (YAC-borne), copy-

number dependence and position independence, 56, 60

virus inducible in IFN-[~, 73-80 X-linked. See Chromosome, X yeast, 437, 441,585, 829-830

a-cell- or mating-type-specific. See a2 repressor; HM loci and repression

chromatin structure in transcription repression and replication, 237-244, 250-255, 443-444, 450- 454, 743-744

copy number of S1R4 gene and HM repression, 738-740

and coupling replication to cell cycle, 638-639

position effects, 248-250, 253- 254, 421-422, 427, 443- 444, 733, 743-744

SNF/SWI proteins in, 257-262 Gene-gating model of export, 794-

796 General transcription factors

(GTFs). See Transcrip- tion factors

Gene replacement. See Antigenic variation in

trypanosomes Gene switching. See Globin gene

switching; Mating-type interconversion

Genetic complementation groups. See Complementation groups and excision repair

Genetic distance and chiasma interference, 543-550

Genetic mapping. See Mapping Genome

integration of structure with RNA metabolism, 807- 817

mapping and analysis. See Map- ping; YACs

methylation density, 281-283 stability, 832. See also

Aneuploidy; Deletions; Chromosome, X; Dicentric chromosomes; Duplication; Gene amplification; Inver- sions; Mating-type interconversion; Transloca- tions

and cell cycle checkpoint control. See Cell cycle

integration of DNA into. See Heterochromatin; Retroviral DNA integration; Transposition

and mismatch repair, 597-602 SIR3, SIR4, and RAP1 in, 734,

740-741,744-745 Genomic imprinting. See Imprint-

ing Genomic sequencing, 835

of C. elegans, shotgun and directed strategies, 367- 374

large-scale comparative analyses of mouse and human TCR loci, 339-347

ofNeurospora, methylation, 323, 328

ofS. cerevisiae, 357-365 and transcript mapping of brown

gene, 578-580 Germinal vesicle (GV) of

amphibian oocytes. See Xenopus

Giemsa staining of chromosome bands and SARs, 756, 758-759, 763

Gin/FIS-mediated site-specific recombination, genetic mapping of interaction domains, 505-512

gix inverted repeat, 505-506 Globin genes

a-globin, 25-26, 31 ~-globin. See also LCR

chromatin structure and

SUBJECT INDEX 847

DNase I sensitivity, 15- 22

gene domain and replication timing in Igf2-H19, 307, 311

insulator element, 3, 823 chromatin structure role in ex-

pression, 1-5 developmental regulation of ex-

pression. See Globin gene switching

Globin gene switching, 7-12 Glucocorticoid receptor, transcrip-

tional activation and regulation, 64, 68, 825. See also Steroid receptor

DNA-binding domain, 133-139, 143-146

Glucosyl transferase and VSG gene, 108-109

Glycoprotein (surface) gene of trypanosome, 106-112

G6PD and X inactivation, 316-317 GrpE. See Heat shock genes GTFs (general transcription fac-

tors). See Transcription factors

GV (germinal vesicle). See Xenopus

gypsy, 3, 52

H

H1, 5, 15, 18-22, 69, 130, 193, 233-234, 248, 680, 825. See also Histones

association in nucleosome structure, 217, 228-232, 265- 266, 270-271

cross-linking assay and MMTV LTR promoter activation, 65-67

and factor access to nucleosomal DNA, 217-218, 233-234

-mediated repression, 94, 206- 222, 825

and SARs, 79, 755 H2, octamer structure, 265, 267-

270, 275-279. See also Histones

H3. See also Histones acetylation, 253 octamer structure, 265-270,

275-279 and regulation of silencing in

yeast, 252, 824 H4, 83, 733. See also Histones

acetylation, 247-248, 251-253 in chromatin structure, a-cell-

specific gene expression, 238-239

octamer structure, 265-270, 275-279

and regulation of silencing in yeast, 252-254, 443, 824

H5, 5, 15. See also Histones

globular domain structure, 130 H5/DNA interactions in ~-globin

domain, 17-22 H19 gene, 287,831

Igf2-H19 domain, differential replication timing and allele-specific expression, 307-312

methylation and imprinting, 282, 287-294, 297-298, 300-301, 303-304, 309- 312

hairy (h) gene, 795-796 Handshake motif of histone oc-

tamer, 276 Haploid mating function, 248 Haploid-specific genes, repression

of, 241 HCF (host-cell factor), structure

and role in Oct-1/VP16 association, 169-176

Heat shock genes Drosophila

87A7, putative domain boundary elements, 45-48

hsp26 as preset gene, chromatin structure role in expression, 83-95

hsp70 insulator elements. See scs and scs '

E. coli, DnaJ, DnaK, and GrpE in ~. replication in vitro, 389-400

Helical repeats and discontinuity of nucleosoma] core DNA, 226, 228, 231-232

Helicase. See DNA helicase Helix-loop-helix (HLH) transcrip-

tion factors, 126-127. See also Basic/helix-loop- helixfleucine zipper form of Max; Transcription factors

Helix-turn-helix (HTH) motif in FIS, 505 in homeodomains, 159, 161, 169

Hematopoietic system. See Erythroid cells; Macro- phages; Myelomonocytic lineage

Hepatocyte nuclear factor-3),. See HNF-3/fork head

Herpes simplex virus VP16. See VP16

Heterochromatin, 247-248, 443, 733, 735, 743, 788

histone role in repression of gene expression

Drosophda, 247-248 yeast mating-type, 250-255

and LCR function, 3 of loop base and chromosome

bands, 755-756, 758 and pairing of sister chromatids,

679 and variegating phenotype, 92-

95, 247, 250, 577 dominant variegation and

trans-inactivation of brown gene, 577-583, 822

role of genomic instability and transposable elements, 585-594

trans-acting repressors of variegation and heterochromatin dosage, 593

and X inactivation, 320, 782 Heterodimers and combinatorial

control, 833 Heteroduplex joint. See Holliday

junctions Heterogeneous nuclear RNA

(hnRNA). See Poly(A) RNA and pre-mRNA metabolism

HhaI crystal structure, 331-337 1H-1H nuclear Overhauser effects.

See NOEs High mobility group proteins. See

HMG-1; HMG I(Y) Histones, 4-5, 63, 115, 623, 680.

See also Chromatin; H1; H3; H4; H5; Nucleosomes

acetylation, 232-233. See also H3; H4

role of Sir2, 253-254 amino-terminal tails, 265,267-

270, 277 and factor access, 225, 227-

228, 232-233 and repression at silent

mating loci and telomeres, 252-253

competitors and nucleosome dis- placement, 222

concerted evolution of core and double helix, 278

cross-linking to DNA, 226-227, 267. See also H1

dimer/tetramer interface, 278- 279

fold, handshake motif, labile termini, protein supercoil, and parallel !3 bridge and paired ends of helices motifs, 276- 279, 827

genes and methylation, 282-283 -like protein. See HU protein linker, 15-22, 130, 225, 228-231.

See also H1; H5 octamer, 45, 228, 233, 273,405,

408-409, 475 core position for translation,

226-228, 231-232 structure and function, 265-

271, 273-279 and retroviral DNA integration

targets, 537

848 SUBJECT INDEX

Histones (continued) role in transcription regulation

and chromatin structure, 242-244, 825-826. See also H4

factor access, 102, 225-234 repression by

heterochromatin, 247- 248, 250-255

tetramer, 226, 228, 232-233, 252, 267, 275-276, 278- 279

transcription of genes and pre- mRNA processing, 747, 749, 752-753

HIV (human immunodeficiency virus). See also Reverse transcriptase

integrase, 535, 537-538 HLH. See Helix-loop-helix tran-

scription factors HMG-1, 74-75 HMG I(Y)

and binding to SARs, 79, 755, 763

role in virus induction of IFN-~ gene, 74-80, 834

HM loci and repression, 248-255, 421,437, 733, 737, 740, 743-744, 829-830. See also Sir/SIR proteins

linkage to replication initiation, 443-454

HNF (hepatocyte nuclear factor)- 3~fork head, X-ray crystallographic studies, 124, 128-130, 826-827

hnRNA (heterogenous nuclear RNA). See Poly(A) RNA and pre-mRNA metabolism

HO endonuclease accessibility, SIR-dependence, 450- 452

Holliday junctions, branch migration and resolution, 525- 530

Homeodomain proteins Antennapedia, 159, 163

Antp(C39S)-DNA complex, 150, 152, 155-156

engrailed, 159, 162-163 MAT(~2, 159-165 Oct-1 and Oct-2, 167-176

Homeotic genes, 247, 788, 823, 831 in bithorax complex, 48-53 fork head, 128

HOM homeobox cluster in C. elegans, 370

Homologous recombination of DNA methyltransferase gene.

See Methyltransferases for inserting I-Sce I sites. See I-

Sce I sites Homology

in C. elegans sequence, 370

-dependent chromosome pairing, unstable interactions in, 553-564

in DNA ligases, 619-621 in excision repair genes. See

Complementation groups and excision repair

in human/mouse TCR loci, 343- 346

to RecA proteins, 567, 569, 573- 575

in telomeric sequences, 707-708, 719

and yeast orphan genes, 359, 361

Hormone receptors in transcriptional activation and regulation, 73. See also Estrogen receptor; Glucocorticoid receptor; Progesterone receptor; Steroid receptor; Thyroid hormone receptor

Hormone response elements, stereochemistry of targeting by receptors, 133-139

Host-cell factor. See HCF HPRT gene, 316 HPV (human papillomavirus) type

16 E6/E7 and gene amplification, 648, 651- 652

HS2, HS3, and HS4 and LCR function, 3, 7-10

hsp26 and hsp70. See Heat shock genes

HSV (herpes simplex virus) VP16. See VP16

HTH. See Helix-turn-helix motif HU protein

in phage Mu transposition, 515- 517

transcription and replication coupling in ~., 390, 395- 396, 399-400

Human chromosomes. See Chromosome

Human excision nuclease, 605-615 Human genome mapping. See

Mapping Human immunodeficiency virus.

See HIV Human mismatch repair, 597-602 Human papillomavirus. See HPV

type 16 E6/E7 and gene amplification

Human RAD51 gene, 573-575 Human telomerase, 722 hus mutants, 639 Hybridization. See Alu-PCR

hybridization; CISS hybridization; Compara- tive genomic hybridization; FISH

Hydration in compaction of double

helix, 274 Hydration of proteins in solution,

NMR and X-ray diffraction studies, 149-156

Hydroxyl radical cleavage patterns of nucleosomal DNA, 226-232

Hypersensitive regions. See DNase I sensitivity of chromatin

Hypervariable regions of trypanosome ESAGs, 110-111

I

ICD compartment. See Inter- chromosome domain compartment

ICP25. See VP16 IE promoter. See Immediate early

promoter of HSV IFN-~. See Interferon-~ gene Igf2 (insulin-like growth factor 2)

and receptor genes, 831 Igf2-H19 domain, differential

replication timing and allele-specific expression, 307-312

methylation and imprinting, 282-283, 287, 293-294, 297-298, 301-303, 309- 312

Immediate early (IE) promoter of HSV, VP16 and Oct-1 in activation, 167-169, 176

Immune system. See also TCR and antigenic variation in

trypanosomes, 106, 110 Immunoglobulin K enhancer, 346 Immunoglobulin ~ enhancer, 97-

102 Immunolocalization of Sir3, Sir4,

and RAP1, 735-737, 741-744

Imprinting, 830-831 and DNA methylation, 282-283,

287-294, 297-304, 309- 312, 634

and fragile X syndrome, 634 and mating-type interconversion

in S. pombe, 457-464 and replication timing, 307-308,

310-311,634 Y chromosome and position-

effect variegation, 593- 594

INCENPs (inner centromere proteins)

as chromosome passenger proteins, 697-705

in mitosis, 680 Incision assay for excision repair,

606 Incision mechanism and DNA

repair, 626-628

SUBJECT INDEX 849

Initiation of transcription. See Preinitiation complex; RNA polymerase; Tran- scription

Initiator protein and initiation of replication. See Replica- tion of DNA

Insulator elements, 3-5, 22, 32, 46-47, 823. See also Fab- 7; Mcp; scs and scs t

Insulin gene and imprinted ex~ pression patterns, 307- 308

Insulin-like growth factor gene. See Ig['2 and receptor genes

Integration of DNA. See Retroviral DNA integration; Transposition

Interchromatin granule clusters and splicing, 785-786, 799-804, 813-814

Interchromosome domain (ICD) compartment, 778, 782, 786-788

Interfacial cavity, hydrated, 156 Interference

chiasma, 543-550 chromatid, 543

Interferon-~ gene (IFN-~), virus- induced enhancer complex and expression, 73- 80, 834

Interferon regulatory factor 1 (IRF-1), 77

Integration of DNA. See Retroviral DNA integration; Transposition

Interphase chromatin, 247-248 as random polymer, 771-772,

774 Interphase chromosome

functional organization of nucleus, 807-817

mapping and cytogenetic analysis with FISH, 771-774

territorial organization, 778 Inversions. See also Genomic se-

quencing FISH for cytogenetic analysis,

772-773 Gin inversion system of phage

Mu, 505-512 Invertebrates and DNA methyla-

tion, 281, 283 Inverted repeats. See Repeats Ionic strength

and processivity of telomerase, 713-716

and replication specificity, 391- 393, 400

IRF-1. See Interferon regulatory factor 1

I-Sce I sites, insertion of sites and physical mapping strategy, 358, 360

I silencers, 444. See also H M loci and repression

J

JB antigen, 699. See also IN- CENPs

J (joining) gene segment. See TCR Joining of DNA. See DNA ligases;

PARP. See also Repair of DNA

Joining (J) gene segment. See TCR

K

KEX2 ARS, 426-427. See also ARS Kinase activity

ofcdc2, 193, 638, 640 of CKII, 619, 621 of MPF, 193-195 of TFIIH, 187, 191-193, 195

Kinesins. See Mechanochemical motors

Kinetochore, 697. See also Centromere

CBF3 subunits in S. cerevisiae structure, 669-675

and chromosome passenger proteins, 699, 704

fibrous corona, 675 and FISH effect on nuclear to-

pography, 781-782 in S. pombe, 687

Kinetoplastida. See Trypanosomes "Kissing" interactions

in antisense RNA pairing, 554- 556

in pairing of homologous chromosomes, 554-557, 562

Klenow fragment of DNA polymerase I, crystal structure and mechanism, 495-503

K repeat in S. pombe centromere, 687-694

L

L1 fingerprinting for YAC contig map, 377-382

lac repressor, 824 retroviral DNA integration

targets, 533, 537-538 lacUV5 promoter and DNA bend-

ing in transcription initiation, 118-122

lacZ. See also ~-Galactosidase expression and enhancer trap-

ping, 590, 795-796 hsp26-lacZ fusion gene, 84

Lagging product site, 716-717 ~.. See Bacteriophage k Lamins A and C, 743-744

Lampbrush chromosomes, 45 loops and splicing, snRNPs,

747-749, 752 Large T antigen. See T antigen LBE. See Locus border element LCR (locus control region), globin,

97. See also Locus control function

developmental stages and com- petition among genes for interaction, 10-12

HS2, HS3, and HS4, 7-10 in thalassemias, 7 and transcription control, 1-3, 5,

7, 32-33, 822-823 LEF-1. See Lymphoid enhancer

factor-1 Leptotene chromosomes, pairing.

See Chromosome, pairing of homologous

Leucine repeat. See Zipper proteins

LexA -controlled proteins. See SOS

response and function of SNF/SWI

proteins, 257-258 LexA-GAL4 fusion protein, 258,

437 LFS. See Li-Fraumeni syndrome Li-Fraumeni syndrome (LFS), 650,

661-662 LIG1, 621-622 Ligand-modulated transcription

factors. See Estrogen receptor; Glucocorticoid receptor; Nuclear nonsteroidal receptors; Steroid receptor

Ligases. See DNA ligases; T4 ligase-mediated DNA cyclization

Li l ium and pairing of homologous chromosomes, 560, 563- 564

LIM15, 573-574 Linkage equilibrium at TCR locl,

342-343 Linkage map distance and

chiasma interference, 543-550

Linker histones. See H1; H5; Histones

Loci of genes, DNase sensitivity of chromatin, 37-39

Locus border element (LBE), 7 Locus control function, chicken

lysozyme gene, 37, 40- 42. See also LCR

Locus control region. See LCR Loops, DNA, 8, 45, 784, 786-787

and enhancer function, 823 in globin gene expression, 9-11 heterochromatin, 755-756, 758 HLH and b/HLH/Z transcription

factors, 123, 126-128

850 SUBJECT INDEX

Loops, DNA (continued) and HMG I(Y) role in IFN-~

gene expression, 79 lac repressor-induced, and

retroviral DNA integration targets, 537-538

loop base and SARs, 755, 758- 759

loop body, detection, 758-759 and loop/scaffold model of

chromosomes, 755-758 and RNA splicing/processing,

747-749, 752 Loops, RNA, interaction of

homologous, 555 LTR. See MMTV LTR promoter Lymphoid enhancer factor-1 (LEF-

1), 78 Lysozyme gene

A element as insulator, 3, 823 chromatin domains as

regulatory units for transcription, 37-43

M

Macromolecules in solution, NMR and X-ray diffraction studies, 149-156

Macronuclear division in Tetrahymena, 708-711, 715

Macrophages, lysozyme gene and transcription regulation, 37-41

Maintenance methylation, 323- 324, 328

Maize telomere-length regulation, 720

MAP 2C, 702 Mapping

genetic and chiasma interference,

543-550 of protein/protein interaction

domains during Gin/FIS- mediated recombination, 505-511

yeast chromosomes, 363-364 physical, 349, 354, 544

Alu-PCR hybridization, YAC to YAC, 378-382

C. elegans genome, 367-368 chromatin structure, 84-85 chromosomal origins

2-D gel analysis of replication intermediates, 415- 418, 425-426, 428-433, 436, 446-449, 467-472, 476-478, 490-491

3-D gel analysis in DNA puffs, 491

using radiolabeled nascent DNA, 476-478

contigs and cosmid finger-

printing, 349-351, 359, 367-368

DNA sequence copy number in, 646

FISH, 377-379, 382, 767-774 human genome, 377-382 L1 and THE fingerprinting of

YACs, 377-382 lysozyme locus control func-

tion, 40-41 nested chromosomal frag-

mentation and I-Sce I, 358, 360

resolution -completeness criterion,

349-355 with FISH in metaphase and

interphase chromosomes, 768-774

restriction, 351-352 STS-content, 349, 352-354,

368, 378-382 YACs, YAC contigs, and

MegaYACs, 368, 377- 382

yeast genome, 358, 360, 363- 364, 416

Marker overlap and ordering. See Mapping

MARs (nuclear matrix attachment regions), 25-29, 31-32. See also Scaffold, -associated regions

in generation of DNase-I- hypersensitive sites, 97- 102

lysozyme locus, 38, 42 MATal protein, 159, 161, 165 MATa2 homeodomain, structure

and DNA-binding specificity, 159-165

Mating-type interconversion and imprinting in S. pombe,

457-464 S. cerewsme, 443, 462-463

Mating-type-specific gene expression. See a2 repressor; HM loci and repression

Max, X-ray crystal structure of b/HLH/Z form, 123, 126- 128

MCB (MulI cell-cycle box), 571, 638-639

MCBF. See DSC1 mcl (mitotic conditional lethals),

679 MCM1 protein, 159, 162, 165 Mcp, 51-52 m5C. See 5-Methylcytosine Mechanochemical motors, 683,

697. See also INCENPs; mukB and chromosome segregation

and NTP-binding motif, 681 MeCP1. See Methyl-CpG binding

protein

MegaYACs. See YACs Meiosis

-II-type separation in meiosis I in S. pombe, 690-692

and premeiosis, unstable interactions in pairing of homologous chromosomes, 553-564

Meiotic recombination. See Recom- bination

Metaphase to anaphase transition. See Chromosome, segregation

Metaphase chromosomes banding and SARs, 755-764 FISH and chromosome map

resolution, 768-774 Methotrexate (Mtx), 650, 657, 662,

664 Methylase. See dam methylase Methylation of deoxyadenosine.

See dam methylase Methylation of DNA, 281,319,

331,450, 539. See also Methyltransferases

ancestral protective function, 283

copy-number- and position- dependent in Neurospora, 325-328

de novo, 283, 324-325, 328 and embryonic development,

300, 303-304 and fragile X syndrome, 634 in imprinting, 282-283,288-

294, 297-304, 309-312, 634, 831

maintenance, 323-324, 328 non-CpG in Neurospora, 323 and replication control and

timing, 384-385, 634 and RIP mutation, 283,327-329 signal in Neurospora ~-~l region,

323-329 in transcription repression and

silencing, 281-284, 289, 293, 300-301,634

Methyl-CpG binding protein (MeCP1), 281-282

5-Methylcytosine (m5C), distribution in genome, 281,283. See also Methylation of DNA; Methyltrans- ferases

Methyl-directed mismatch repair. See Mismatch repair

Methyl green (MG) quenching, staining loop bodies with YOYO-1, 758-763

Methyl-methane sulfonate (MMS) damage to DNA, repair. See RAD proteins, Rad51

N-Methyl-N i -nitro-N- nitrosoguanidine. See MNNG

Methyltransferases (MTases), 288,

SUBJECT INDEX 851

297, 331. See also Methylation of DNA

HhaI crystal structure, 331-337 homologous recombination of

gene in study of methylation, imprinting, and mammalian development, 297-304

mfd gene product, 613, 630 MG. See Methyl green quenching MIC2 and X inactivation, 316-317 Microinjection

for studying pre-mRNA splicing, 8O2

of telomerase RNA gene, 708- 7O9

of YAC DNA in generating transgenic mice, 55-56, 58

Microsatellite STSs. See STS- content mapping, human genome

Microtubule, 669, 673-675, 677, 788-789, 794. See also Centromere; Kinetochore

assembly inhibitor. See Nocodazole

-associated proteins of nerve cells, 702

-binding activity of centromeres, 674, 681-683

and chromosome passenger proteins, 697-705

Mimosine, replication inhibitor, 468-473

rnin CDE system and cell division, 386

Minichromosomes BPV-1,408-409 Dp1187 and Dp400, genomic in-

stability in position- effect variegation, 585- 590

S. cerevisiae and centromere function, 682-

683 and chromatin-mediated tran-

scription repression, 237-244

and S. pombe centromere function, 687-688, 690-694

TRPIARS1 and SV40, retroviral DNA integration target, 534-536

Minicircle DNA DNA bending and retroviral

DNA integration, 538 topoisomers, RNA polymerase

binding and DNA bending, 117-122

Mismatch repair, 597-602 Mitomycin C, 612 Mitosis. See Centromere;

Chromosome, condensation; Chromosome, segregation; INCENPs;

Sister chromatids Mitosis promoting factor. See MPF Mitotic inhibitor. See Nocodazole Mitotic spindle and spindle pole

bodies, 677. See also Centromere; Kinetochore

association with CBF2p, 670, 675

centromeric repeat and spindle attachment, 690-692, 694

and chromosome passenger proteins, 697-705

spindle integrity and DSC1, 680 MLV (murine leukemia virus), in-

tegration target and integrase, 534-538

MMS (methyl-methane sulfonate) damage to DNA, repair. See RAD proteins, Radhl

MMTV LTR (mouse mammary tumor virus long terminal repeat) promoter

activation and nucleosome organization, 63-70, 825

and gene remodeling, 83, 88 MNNG (N-methyl-N ~ -nitro-N-

nitrosoguanidine), 600- 601

Motor proteins. See INCENPs; Mechanochemical motors; mukB and chromosome segregation

Mouse chromosome 7. See Chromosome

Mouse mammary tumor virus long terminal repeat. See MMTV LTR promoter

Mouse RAD51 gene, 573-575 MPF (mitosis promoting factor),

role in RNA polymerase II phosphorylation, 193- 195

mRNA transcription and processing. See Splicing; Tran- scription

mRNA-type promoter, VP16 and Oct-2 activation, 167- 169

MSA-36, 699. See also INCENPs MTases. See Methyltransferases Mtx. See Methotrexate Mu bacteriophage. See Phage Mu mukB and chromosome segrega-

tion, 385 MulI cell-cycle box. See MCB Murine leukemia virus. See MLV Mutations

in cis-regulatory units of bithorax complex, 51

-driven model of tumorigenesis, 655

missense, for DNA ligase I, 621- 622

point CpG to TpG transitions, 622

RIP, and DNA methylation, 283, 327-329

for recombination. See RAD proteins

suppressor, for FIS-independent Gin-mediated recombination, 507-511

temperature-sensitive. See also cdc mutations, genes, and proteins

and ARS function at HMR-E, 437, 449-450, 452

in study of macronuclear division and telomeric sequences, 709-711, 715

in study of ORC, 437-439 in study of sister chromatid

pairing and chromosome condensation in mitosis, 679-680

MutH and strand breaks, 597-598 c-myc, DNA domains containing

single-copy genes, 29-32 Myc oncoproteins, 126 Myelomonocytic lineage, ]ysozyme

gene and transcription regulation, 37, 39-40

MyoD, 821, 826, 833

N

NAT1/ARD1 genes, 733 NDCIO/CBF2, 669, 674 Nematode. See Caenorhabditis

elegans Neoplasia

and loss of genomic integrity. See Gene amplification

and telomere length, 721-722 Nested yeast chromosomal frag-

mentation. See Mapping Neurospora crassa, 544, 553,829

ancestral function of DNA methylation, 283

DNA methylation signal in ~-~1 region, 323-329

RIP mutation, 283, 327-329 Nevirapine cocrystallized with

reverse transcriptase, 495, 499-500

NF1/CTF, 64, 66-70 NF-E2 and globin gene expression,

8-9 NF-~B and virus induction of IFN-

gene, 74-79, 834 Nicked DNA. See DNA nifS gene, 359 NMR (nuclear magnetic

resonance) spectroscopy studies

DNA-binding domains of Tram- track and hormone receptor, 134, 141-146

protein hydration, 149-156 Nocodazole, 483, 678-680

852 SUBJECT INDEX

NOEs (nuclear Overhauser effects), measurements for protein hydration, 150- 154

Nonnucleoside inhibitor binding to reverse transcriptase, 499-500

NTP (nucleoside triphosphate) -binding motif of mechanochemi-

cal motors, 681 -binding sites and helicase motif,

259-262 Nuclear envelope (nuclear mem-

brane), 697, 788-789 and chromatin interaction, 248,

794 and gene-gating model of export,

794-796 and heterochromatin repression,

254 and licensing factor model of

coupling cell cycle to replication, 639

telomere attachment, 557 and telomere positioning by

SIR3 and SIR4, 735-737, 741-744, 830

Nuclear hormone receptors. See Estrogen receptor; Glucocorticoid receptor; Steroid receptor

Nuclear magnetic resonance. See NMR spectroscopy studies

Nuclear matrix, 789, 815. See also MARs; Scaffold, -associated regions

Nuclear membrane. See Nuclear envelope

Nuclear nonsteroidal receptors, stereochemistry of interactions, 133-134, 136

Nuclear Overhauser effects. See NOEs

Nuclear RNA transcripts. See Nucleus; RNA, transcripts; snRNA and snRNPs

Nuclear scaffold. See Scaffold Nuclear skeleton. See Nuclear

matrix Nuclease~ regions.

See DNase I sensitivity of chromatin

Nucleolar bodies. See Prenucleolar bodies

Nucleolus, 807, 813, 816. See also snoRNPs

organizers, 591-592 and RNA synthesis, 747

Nucleoplasmin, 219, 221 Nucleoprotein filaments (helical)

formation by RecA and Radhl proteins, 567, 569

Nucleoside (modified) in silencing ofVSG gene, 108-109

Nucleoside triphosphate. See NTP Nucleosomal templates, 207-208 Nucleosomes, 273. See also

Chromatin; Histones A, 63, 70 array, 1, 45, 63, 83

discontinuities. See DNase I sensitivity of chromatin, hypersensitivity regions

effect of centromeric repeats, 692

in remodeled vs. preset genes, 83, 88

hsp26 as preset gene, 83-95 B of MMTV LTR, 63-70 construction and disruption of,

225-232 facilitated binding of GAL4 to

cores, 216-217, 221-222 footprinting cores, 65 helical repeats and discontinuity

of core DNA, 226, 228, 231-232

in higher-order chromatin structure, 15, 18-22, 45, 83- 84

and hormone receptors, 63-64, 66, 69, 94

and hsp26 gene insertion into heterochromatin, 92-95

-like structure. See O-some positioning and modification in

transcription, 1, 4-5, 32, 63, 222, 234, 253, 533- 534, 824

effect in regulating gene expression, 88, 92, 94-95, 237-244

and factor access. See Tram scription factors

mechanism, 65-66 "positioning" proteins, 94 in replication, 403, 408-409 and retroviral DNA integration

target, 533-540 role in transcription activa-

tion/repression, 83, 213 222, 824-825

structure comparison with histone oc-

tamer, rods of densities, 277-278

of core particle and histone location assignments, 265-271

in telomeres, 251 Nucleotide excision repair. See Ex-

cision and gap repair Nucleotide misincorporation,

reverse transcriptase vs. Klenew fragment, 495, 502-503

Nucleotide pool perturbation. See Antimetabolites

Nucleus. See also Nuclear envelope; Nucleolus;

Pronucleus; snoRNPs; snRNA and snRNPs

compacting chromosomal DNA within. See Chromatin

electric forces on chromosome territories, 787-789

functional compartmentaliza- tion, 807-817, 835

and chromosome territories, 777-789

localizing RNA transcripts and splicing/processing, 747- 753, 784-787, 793-797, 799-804, 807, 810-817

organization and site-specific replication initiation in metazoan chromosomes, 475-484

topography and FISH analysis, 781-782, 789, 808-810

O

OBR (origin of bidirectional replication), 475-484. See also Replication of DNA, origin

Oct-1 and Oct-2 homeodomain proteins, DNA-binding specificity and differential transcriptional regulation, 167-176, 826

Octamers. See Histones Oligonucleosomes in [3-globin

domain, solubility and structural stability, 15, 18-22

Oncogenic viruses in study of gene amplification, 648, 651- 652

Oocytes. See Xenopus Open complex of transcription in-

itiation and DNA bending, 116-118, 121 and TFIIH DNA helicase ac-

tivity, 193 Operators

a2, chromatin near, 237-244 MATa2, 162

O protein in k replication, 389, 391, 398, 4OO

ORC (origin recognition complex), yeast initiator protein, 437-441,830

Sciara equivalent, 492 orf-26, 526 ori. See Replication of DNA, origin Origin recognition complex. See

ORC Origin of replication. See Replica-

tion of DNA Orphan genes in yeast, 359, 361 O-some, 389, 398-399 Ovalbumin probe, DNase

sensitivity of ~-globin domain, 16-22

SUBJECT INDEX 853

P

p34 cdc2 kinase. See cdc mutations, genes, and proteins

p53 GAL4-p53(1-73) and DNA

replication, 410, 412 tumor suppressor gene, role in

gene amplification and cell cycle checkpoint control, 645, 649-651,658- 664, 832

Packaging chromatin. See Chromatin

Packaging chromosomes for mitosis. See Chromo- some, condensation

Paired ends of helices motif of histone octamer, 277

Pairing, 577. See also Recombina- tion; Repair of DNA

antisense RNA, 554-556 of homologous chromosomes, un-

stable interactions in, 553-564

of sister chromatids. See Sister chrematids

Pairing-sensitive elements and cis- regulatory units of bithorax complex, 48-53

Pairing-sensitive repression of white minigene, 52-53

Pair-rule transcript localization. See Drosophila

PALA (N-[phosphonoacetyl]-L- aspartate), CAD gene amplification and arrest of cell cycle, 647-652, 656-664

Papillomavirus. See BPV; HPV type 16 E6/E7 and gene amplification

Parallel 13 bridge of histone octamer, 277

Parental genotype and variegation, 593

Parental imprinting. See Imprint- ing

PARP (poly[ADP-ribose] polymerase), role in DNA joining, 619, 622- 623

PCNA (proliferating cell nuclear antigen), 606, 615, 628- 629, 631

PCR (polymerase chain reaction). See also Alu-PCR hybridization

-based assay for retroviral DNA integration, 533-536

P element and enhancer trapping, 586, 795 and position-effect variegation,

593

insertion in Dp1187 minichromosome, 586

and P-transposase-induced deletions, brown gene, 578-583

white gene insertion in heterochromatin, 84, 86, 93-95

Perichromatin fibrils and coordination of transcription and splicing, 785-786, 799-804, 813

PEV (position-effect variegation). See Heterochromatin

PGK1 and X inactivation, 316-317 Phage Mu

inversion system. See Gin/FIS- mediated site-specific recombination

transposition and target site preference at DNA strand transfer, 515-522

Phenotype, variegating. See Heterochromatin

P H 0 5 promoter, 83, 88 N-(Phosphonoacetyl)-L-aspartate.

See PALA Phosphorylation

in control of DNA replication and mitotic checkpoint, 638, 640

/dephosphorylation ofDNA ligases, 619-621 of DNA topoisomerase II, 621

of RNA polymerase II carboxy- terminal domain, 187, 190-197

Photoproduct repair, 613, 626 Physical mapping. See Mapping PIC. See Preinitiation complex Point mutations. See Mutations pol I, II, III. See RNA polymerase POLA and X inactivation, 316-318 Poly(ADP-ribose) polymerase. See

PARP Poly(A) RNA and pre-mRNA

metabolism, 799, 813-817

Polycomb group genes and proteins, 49-50, 52-53, 247,788, 823, 831

Polymerase chain reaction. See PCR

Polymerases. See DNA polymerases; PARP; RNA polymerase

Polymorphic STS mapping. See STS-content mapping, human genome

Polynucleosome array. See Nucleosomes

Polyomavirus large T antigen, 404-405, 482-483

Polytene chromosomes, 45, 487, 491, 544

Position-dependent methylation.

See Methylation of DNA Position effects on gene expres-

sion. See Gene expression; Telomere

Position-effect variegation (PEV). See Heterochromatin

Positioning of nucleosomes. See Nucleosomes

Posttranslational regulation of DNA ligase I, 621

Potassium glutamate and replication specificity, 391-393, 400

POU homeodomain proteins Oct-1 and Oct-2, 167-176

P protein in ~ replication, 389, 391,398, 400

Prader-Willi/Angelman syndromes, 308, 311

PRDs. See Domains, positive regulatory

Preinitiation complex (PIC) assembly, 123, 125, 187-188

effect of transcriptional activators, 199-202

and nucleosome core/H1 inhibition, 222

and replication, 409, 638 BPV-1,404, 412 ~, 389, 393

and RNA polymerase phosphorylation, 187, 190-197

stable association with polymerase, GTF roles, 187-190

Premeiotic cells, unstable interactions in pairing of homologous chromosomes, 553-564

Pre-mRNA processing and splicing. See Splicing

Prenucleolar bodies, snoRNAs in, 750-753

Pre-rRNA processing and snurposomes, 747, 749-750, 752-753

Primase in ~ replication. See Bac-

teriophage :polymerase c~ and replication in-

itiation, 412, 637 Processing of transcripts. See Pre-

rRNA processing and snurposomes; Splicing

Processivity. See also RNA polymerase

ofE. coli RNA polymerase, 716 of telomerase, 711-717

Progesterone receptor, transcriptional activation and regulation, 68

Prokaryotic DNA invertases, 505. See also Inversions

Proliferating cell nuclear antigen. See PCNA

854 SUBJECT INDEX

Promoter. See also Gene expression; Transcription

activity and nucleosome-free regions, 83

~A-globin, 1, 17-18 -binding factors in antirepres-

sion, 205-212 core element in transcription

regulation, 123, 187. See also TATA box

cryptic and function of DNA methyla-

tion, 282, 284 and effect of LCR on chromatin

structure, 1-3, 5 enhancer core and genera-

tion of DNase-I- hypersensitivity sites, 97-102

GALl vs. CYC1 activation by SNF/SWI, 258

H19 gene and imprinting, 289- 291,293

hormone-receptor binding in activation, 63-64, 66, 68- 70

HSV IE, VP16 and Oct-1 activation, 167-169, 176

IFN-~, 73-80 Igf2 gene, 293 Kriippel. See GAGA factor lacUVh, DNA bending in tran-

scription initiation, 118- 122

MMTV LTR, 63-70, 825 mRNA-type, Oct-2 and VP16 ac-

tivation, 167-169 proximal elements in transcrip-

tion regulation, 123. See also Max

remodeling in activation, 83, 88 repression of. See Transcription,

repression and silencing -selective transcription factors,

179-184 o model of recognition, 179, 188 snRNA, Oct-1 activation, 167-

168 strength and DNA methylation,

281-282 SV40 early, 179 T7, ~ enhancer-mediated acces-

sibility and chromosomal position-independence, 97-102

TATA-containing, assembly of preinitiation complex on. See Preinitiation complex

TATA-deficient, role of TBP, 125, 181

and topological organization of domains, 33

Pronucleus microinjection ofYAC DNA into,

55-56, 58

snRNAs and snoRNAs in, 750- 753

Protein/DNA complexes and interactions, 515. See also cL2 repressor; Catabolite activator protein; DNA, bending; Domains; En- hancer; GAGA factor; GAL4; HhaI crystal structure; Histones; Homeodomain proteins; lac repressor; LexA; ORC; PARP; Rapl/RAP1; RecA; Recombination; RNA polymerase; RPA; RuvABC proteins; Tran- scription factors; Zinc fingers and zinc- stabilized motifs

involvement of hydration water in recognition, 155-156

relation between DNA bending and binding strength in, 115-122

structural studies. See X-ray crystal structure

Protein hydration in solution, NMR and X-ray diffraction studies, 149-156

Protein-protein interactions, mapping domains involved in. See Gin/FIS-mediated site-specific recombination

Protein structure, 826-827 determination of. See NMR spec-

troscopy studies; X-ray crystal structure

of hydrated molecules in physiological milieus, 149, 154-155

internal mobility, 149, 153 on surface, and molecular recog-

nition, 149, 156 Protein supercoil of histone oc-

tamer, 276-279 Provirus. See Retroviral DNA in-

tegration Pseudoautosomal region and

boundary, 316-317 Pseudogenes and genomic se-

quencing, 341-342 Puffs, DNA amplification and

transcription in, 487- 493

Pyridoxyl 5 ' phosphate cross- linking to reverse transcriptase and Klenow fragment, 497-498

Pyrimidine dimers and DNA repair. See Excision and gap repair

Pyrimidine precursor synthesis inhibition by PALA, 647- 651

Pyrophosphate inhibition of telomerase, 712-713

Q

Q-bands, 756-764 Quinacrine staining, 756

R

RAD proteins in excision repair, 611-613, 625,

627 RAD9, cell cycle checkpoint con-

trol, 651,657-658, 731, 832

Radhl, homology to RecA, domains, and DNA recombination/repair function, 567-575

rad52, 720 Rad52, strand-transfer activity

and DNA repair, 567- 569

Rad52- host strain for MegaYACS, 378

Radiation-sensitive mutants. See RAD proteins

Rapl/RAP1 (repressor activator protein 1)

and chromosome stability, 734, 744

immunolocalization, 735-737, 743-744

for replication origin function, 448, 452

in silencing, 250, 254, 444, 449, 733, 743-744

and telomere length, 720, 733- 734, 737, 739, 744

R-bands, 756-764 Rb-dependent cell cycle arrest, 664 RCC1 mutations, 642 rDNA, 591-592 rDNA ARS. See ARS RecA

-like recombination/repair proteins in eukaryotes, 567-575

-mediated recombination/repair, 525, 528, 567

Receptors. See also Estrogen receptor; Glucocorticoid receptor; Igf2 and receptor genes; Progesterone receptor; Retinoid receptors; Steroid receptor; TCR; Thyroid hormone receptor; Vitamin D 3 receptor

for uptake in trypanosomes, antigenic variation, 110- 111

RecG, 529-530

SUBJECT INDEX 855

Recombination. See also Homologous recombination; Mating-type interconversion

branch migration and Holliday junction resolution by Ruv proteins, 525-530

chiasma interference in Drosophila, 543-550

crossovers and homologous pairing of chromosomes, 556

fidelity. See Mismatch repair frequency

additivity, 543 following damage, 525

Gin/FIS-mediated site-specific inversion, 505-512

recA, function and homology. See RecA

retroviral DNA integration, 521, 533-534

nucleosomal DNA as target, 533-540

and SOS response, 525-526, 528 telomere-telomere in yeast

telomere replication, 725, 731

transposition of phage Mu, target-site pref-

erence at DNA strand transfer, 515-522

of Tyl and Ty3, integration target, 539-540

Recombination nodules and crossing-over, 548

Repair of DNA, 525, 529, 625. See also DNA ligases; Mating-type interconversion; PARP; RecA; Recombination

excision and gap repair, 578, 581,598, 625-631

excinuclease and Xeroderma pigmentosum, 605-615

mismatch repair, 597-602 postreplication gap repair, 528-

530 and SOS response, 525-526, 528 species-specificity of Rad51 and

Rad52 in, 574-575 transcription-dependent, 612-

613, 615, 629-630 Repair synthesis assay, 606 Repeat-induced point (RIP) muta-

tion and DNA methylation, 283, 327-329

Repeat, long terminal. See MMTV LTR promoter

Repeat polymorphisms in TCR loci, 342-343

Repeats, tandem and inverted att sites, 533-534 in C-bands, 756, 758 and function of DNA elimina-

tion, 591-592 gtx, 505-506

in S. pombe centromere, 687- 694

in telomeres, 707, 711, 719-720, 725

Replication bands, 311 Replication of DNA. See also

Abfl/ABF1; ARS; DNA polymerases; Preinitia- tion complex; Rapl/RAP1

antirepression and E2, 408-409, 411

BPV as model, problems, 482- 484

cell membrane in control, 384- 385

and chromatin assembly, 233, 408-409, 412, 453, 478- 482,484

chromosomal replication intermediates

analysis of origin and direction of fork movement. See Mapping

2-D gel analysis of direction of fork movement and timing of telomere replication, 727-728

and chromosome breakage, 656- 657

circle-to-circle in K, 389, 392, 399 of ColE1, antisense RNA pairing

in, 555-556 control. See also Replication of

DNA, timing coordinating with cell cycle,

384-386, 487, 637-642, 832

methylation of DNA in, 384- 385, 634

by protein phosphorylation, 638, 640

replicon model of regulation, 383-386, 435, 467

and dnaA protein, 384-385 ecdysone regulation and DNase-

I hypersensitivity in, 491-493

in heterochromatic regions, 250, 254

initiation, 384 and enhancer proteins in BPV-

1,404-412 in k in vitro, directionality and

effect of transcription, 389-400

selective inhibitor. See Mimosine

site-specific in Xenopus, role of nuclear organization, 478-484

in SV40, 637 initiator protein, 384, 467

in SV40. See T antigen in yeast, 436-441

nucleosomes and positioning in.

See Nucleosomes origin, 25, 32, 384, 405-406

of mammalian DHFR locus, 467-472

OBR in metazoan chromosomes, 475-484

oriC in E. coli, 384-386 orig., 389 in S. coprophila DNA puff,

488, 490-493 trans-acting factor in regula-

tion, 491 yeast, 386

activity of ARS elements, 415-422, 425-433, 435- 436

ORC as initiator protein at, 437-441,830

position effect, 421-422, 426-427

transcriptional silencer as, 443-454, 830

and pairing of sister chromatids, 677, 679

replication fork barriers/pause sites, 421,432

replication fork mechanism, 475

replication/repair proteins. See PCNA; RPA

role in establishing repressed state, 443-454

rolling-circle in K, 389, 392, 399 semiconservative, 458, 480, 627-

629 specificity in vitro and ionic

strength, 391-393, 400 T4, 398 of telomeres, 719, 725-731 termination in yeast, 431-433 timing

and allele-specific expression, 307-308, 310-311, 634, 831

ARS1, ARS305, ARS501, and KEX2 ARS, 426-427

and chromosome bands, 756 delayed, fragile X syndrome

and thalassemia, 633- 634

and telomeres, 427, 725-731 Replicative transposition of phage

Mu. See Phage Mu Replicon model of replication. See

Replication of DNA Repression of transcription. See

Insulator elements; Transcription, repression and silencing

Residence times of water molecules in hydration sites, 151-152, 155-156

Resolution of Holliday junctions. See Holliday junctions

Resolution of maps. See Mapping Resolvases, 506, 508, 529-530

856 SUBJECT INDEX

Restriction enzymes hormone-dependent access to

nucleosome B DNA of MMTV LTR, 66

in mapping. See also Mapping Alu-PCR hybridization, YAC

to YAC, 378-382 chromatin structure, 84-85 nested chromosomal frag-

mentation and I-Sce I, 358, 360

S. cerevisiae chromosomes, resolution-completeness profile, 351-352

methylation-sensitive, 289, 323 HhaI crystal structure, 331-

337 Retinoid receptors, 133-134, 136 Retrotransposons. See

Transposons and retrotransposons

Retroviral DNA integration, 521, 533-534

nucleosomal DNA as target, 533-540

Reverse transcriptase HIV, crystal structure and me-

chanism, 495-503 telomerase as specialized, 708

RFC, 629, 631 Ribonucleoproteins. See sneRNPs;

snRNA and snRNPs Rifl (RAPl-interacting factor 1),

720, 744 RIP. See Repeat-induced point

mutation and DNA methylation

RNA. See also Poly(A) RNA and pre-mRNA metabolism; rRNA; snRNA and snRNPs; tRNA genes

antisense, pairing, 554-556 processing. See pre-rRNA pro-

cessing and snurposomes; Splicing

synthesis inhibition and cell cycle arrest. See Antimetabolites

telomerase, 707-717, 719-720 transcripts

localization in nucleus, transcript domains, and export. See Nucleus

"track"- or "dot"-like accumula- tion, 784-785, 796, 810- 813, 815

RNA polymerase, 32. See also Transcription

c~-amanitin sensitivity, 800 I in transcription initiation, 123,

181-182 II

binding and DNA bending re- lationships, 115-122

at perichromatin fibrils, 785, 8O0-804

phosphorylation role in transcription initiation/elongation cycling, 187-197

promoter- and enhancer- binding factors in regulating, 205-212

o factors and promoter specificity, 188

and transcription initiation, 123, 199, 629

and nucleosomes, 83, 241- 242

TBP and TAF role, 179-184 III, 123, 181-182, 241,243 E. colt, 716

and directionality of ~. replication, 395-399

and T4 replication system, 398 T7, interaction with DNA, 97-

102 in transcription, effect of

chromatin structure, 4- 5, 63, 825. See also Chromatin; Transcrip- tion

RNase H, 802 and k replication, 396, 399-400 domain of reverse transcriptase,

495, 499-501 Rods of densities of nucleosome

and octamer structures, 278

Rolling-circle replication. See Replication of DNA

RPA, 405, 411,642,825 in BPV-1 replication, 410-412 in excision repair, 627-628, 631

rRNA genes and pseudogenes, 323, 813

domains and MARs, 26-29 factor access in nucleosome

containing, 225-234 processing, 807. See also pre-

rRNA processing and snurposomes

transcription and SL1, 181-182 RuvABC proteins, branch migra-

tion and Hollidayjunc- tion resolution, 525-530

S

Saccharomyces cerevisiae. See Yeast

SARs. See Scaffold, -associated regions

SC1,755 SC-35 splicing factor, 800-801,

813-816 Scaffold. See also Loops

-associated regions (SARs), 79. See also MARs

and chromosome banding, 755-764

daunomycin selective stain, 758-764

HMG I(Y) binding, 79, 755, 763

and topoisomerase II, 755, 763 /loop model of chromosomes,

755-758 protein SC1,755

Schizosaccharomyces pombe. See Yeast

Seiara coprophila, DNA puff amplification, 487-493

scs and scs t, 3, 32, 45-48, 823. See also Insulator elements

Segmentation genes, 48-53, 793- 794

Segregation of chromosomes. See Centromere; Chromosome; Kinetochore; Strand- segregation model

Selective pressures of histones, 278

Senescence and telemere length, 721

Sequence conservation. See Evolu- tion

Sequence-specific DNA recognition by transcription factors. See Transcription factors

Sequence-specificity of phage Mu transposition, 515-522

Sequence-tagged sites. See STS- content mapping

Sequencing. See Genomic sequencing

o factors, 179, 188, 821-822, 833 Silencing of genes. See Transcrip-

tion, repression and silencing

Single-copy genes, detecting domains containing, 29- 31

Single-stranded DNA-binding protein. See RPA

Sir/SIR proteins in positioning and length of

yeast telomeres, 733-745 and silencing of yeast mating-

type loci, 249-255, 443- 445, 450-452, 733-734, 737-740, 743-744, 824, 829-830

Sister chromatids attachment in meiosis I and

centromere-specific repeats, 690-692, 694

disjunction and movement. See Chromosome, segregation

pairing, 677-680 SL1, TBP and TAF role, 181-182 Small nuclear RNA and

riboproteins. See snRNA and snRNPs

SUBJECT INDEX 857

Small nucleolar riboproteins. See snoRNPs

Sm antigen, 785-786 SMC1 in mitotic chromosome

segregation, 680-681 SNF/SWI proteins in transcrip-

tional activation, 257- 262, 825

snoRNPs (small nucleolar riboproteins), 747, 749- 752

snRNA and snRNPs (small nuclear RNA and riboproteins)

imprinted gene, 287, 307-308, 311

snRNA promoter, Oct-1 activation, 167-168

in splicing and processing of nuclear transcripts, 747- 753, 785-787, 799, 802, 804, 813-817

Snurposomes, RNA processing, 747-753. See also snRNA and snRNPs

Solenoidal structure of DNA, 1, 45, 63, 69, 83, 248

Somatic cell hybrids in obtaining YAC contig map of

human genome, 378-379 in study of gene amplification,

649 in study of X-linked gene expres-

sion, 315-321 Somatic cells, unstable interac-

tions in pairing of homologous chromosomes, 553-564

Somatic DNA instability. See Genome, stability

Somatic pairing, role in trans- inactivation and dominant variegation, 577

Sordaria and pairing of homologous chromosomes, 553, 558- 560

SOS response, recombination/repair proteins in, 525-526, 528

Spl, 8, 74 in antirepression, 206-207, 209-

210 TBP and TAF role, 179-181, 183

Specialized chromatin structures in Drosophila. See scs and scs ~ in silencing yeast genes, 250-

254 S phase. See Cell cycle Sphere organelles, 749, 752 Spindle. See Mitotic spindle and

spindle pole bodies Splicing

nuclear recruiting mechanism and snRNPs in, 747-749, 752-753, 785-787, 799-

804, 813-815 nuclear RNA tracks as site, 810-

813 pattern alterations from dis-

rupted DNA methyltransferase gene, 299-300

and transcript domains, 799, 813-817

trans-splicing in trypanosome mRNA synthesis, 105- 106

Spodoptera HCF, 171-173 Sporulation, zygotic, 459 5S rRNA genes and pseudogenes.

See rRNA SSL2/RAD25, 611 STE6 gene, nucleosome position-

ing, 238-241 Steroid molting hormone. See Ec-

dysone Steroid receptor, transcriptional

activation and regulation, 63-64, 66, 69, 73, 133

stereochemistry of DNA interaction, 133-139

STH1 helicase-like domain, 259- 260

Strand breaks joining. SeeDNA ligases; PARP.

See also Repair of DNA MutH-introduced, 597-598

Strand exchange or transfer. See Recombination

Strand-segregation model, mating- type interconversion, 457-458, 460

Strand-specific mismatch repair. See Mismatch repair

Streptavidin/colloidal gold to visualize repair event, 626

STS (sequence-tagged site)- content mapping, 349, 354

human genome, 378-382 resolution-completeness profiles

in human Y chromosome, 352-353

for YAC-YAC linkage in C. elegans chromosome, 368

Supercoiled DNA. See DNA Supercoiled protein of histone oc-

tamer, 276-279 Suppressors

of FIS-independent phenotype for Gin-mediated recombination, 507-511

stage-specific for globin genes, 10

Surface elements of histone octamer, 277

Surface hydration of proteins, 149-156

SV40

early promoter, 179 minichromosome and retroviral

DNA integration target, 534, 536, 540

replication origin, 482-483 replication and T antigen, 411-

412, 637, 638 T antigen and CAD gene

amplification, 648 SWI/swi, 638-639

DNA cleavage and mating-type interconversion, 458- 462, 464

in transcriptional activation, 257-262, 825

Switching genes. See SWI/swi Syn aptic/syn aptonemal complex

(SC) of Gin/FIS-mediated recombina-

tion, 505-506, 508, 511- 512

and homologous pairing, 553, 556, 561

of phage Mu transposition, 515- 516

Synthesis of DNA. See Replication of DNA; Telomere, and telomerase

T

T antigen, 404-405, 411-412, 482- 483, 637-638, 648

T4 ligase-mediated DNA cyclization, 118-119

T4 replication system, 398 T7 promoter and RNA polymerase,

97-102 TAFs (TBP-associated factors),

123, 199, 202, 827-828 and coactivator activity of

TFIID, SL1, and TFIIIB, 181-184

Tandem repeats. See Repeats TATA box, 66, 87, 89, 93-94, 123,

222, 440, 824 -binding protein (TBP), 87-88,

123-124, 187-189, 199, 202. See also TAFs

phosphorylation-dependent interaction with RNA polymerase II, 190, 192, 195-197

in promoter-selective transcription initiation, 180- 184

X-ray crystallographic studies of TBP-2, 123-126

and positioned nucleosomes, 238, 240-241, 824

promoters containing, assembly of preinitiation complex on. See Preinitiation complex

promoters deficient in, TBP role, 125, 181

858 SUBJECT INDEX

z, 702 TBP. See TATA box, -binding

protein TBP-associated factors. See TAFs T-cell receptor. See TCR TCR (T-cell receptor)

-(z gene enhancer, 78 loci and genes, 622, 835

comparative large-scale DNA sequence analyses, 339- 347

evolution in mouse and human, 343-346

polypeptide regions and gene segments, 339

trypsinogen gene family in sequence, 346-347

TD-60, 699. See also INCENPs Telomere, 657, 683, 830. See also

Genomic sequencing "bouquet formation", 557, 741 and chromosome pairing via un-

stable interactions, 557- 558, 561

histone role in repression, 252 length, 720-722

RAP1 and sir3 and sir4 mutations effect, 733-734, 737-740, 744

and repression of VSG gene expression, 107-109

and macronuclear division, 708- 711, 715

mapping in C. elegans, 368 and replication origin activity

and timing of ARS elements, 421-422, 427

replication in yeast, 725-731 repression and position effects in

yeast, 249-255, 421-422, 427, 725, 733, 743-744

SIR3 and SIR4 in perinuclear positioning, 735-737, 741-744

sub-telomeric DNA modification in repressing expression, 108-109

and telomerase, 707-717, 719- 720, 722, 725, 832

and trypanosome VSG gene expression and silencing, 106-112

Temperature-sensitive mutants. See Mutations

Templates. See also Replication of DNA; Transcription

chromatin for BPV-1 replication, 408-409, 411-412

chromatin vs. histone-free for DNA transcription, 207- 209

function of telomerase RNA as, 707-711,716

nucleosomal, 207-208 specificity for ~. replication. See

Bacteriophage ~.

transcription factor interaction, 67-69

Tetrads and chiasma interference, 543-

550 frequency estimates, exchange

rates, and standard er- rors, 550-552

Tetrahymena telomeres length regulation, 720-721 and telomerase, 707-717, 719-

720, 725, 832 TF. See Transcription factors TFBP. See Transferrin-binding

protein and receptor Thalassemias, 7, 634 THE fingerprinting for YAC contig

map, 378-382 T-helper cells, 339 0-structure replication. See

Replication of DNA, circle-to-circle in ~.

Thymine dimer removal from DNA, 605, 626. See also Excinuclease in DNA repair

Thyroid hormone receptor, 133- 134, 136

T-killer cells, 339 Tn7 transposon, 515, 520-521 tolC, 385 Topoisomerase

I, 405,408-409, 827, 828 II, 475, 68O

cleavage sites in scs and scs ' , 46-47

in detection of DNA domains containing single-copy genes, 29-31

and DNase-I-hypersensitive sites, 26-28, 46

inhibitors. See Chromomycin; VM-26

and MARs/SARs, 25-29, 32, 755, 763

and pairing of homologous chromosomes, 561-563

phosphorylation by CKII, 621 stimulator. See Distamycin

IV, 385-386 Topoisomer distribution, ssn6 vs.

tupl mutants, 240 Topology and pairing of

homologous chromosomes, 553-564

Tramtrack, DNA-binding domain, 141-143, 146

trans-Acting factors and regulation, 5, 32-33, 225, 491, 593, 820-821,824-825

trans-Activator VP16. See VP16 Transcription. See also Enhancer;

Gene expression; Promoter; RNA polymerase; Suppressors; Tran- scription factors

activation. See also Domains; Enhancer; Transcription, antirepression

chromatin structure effect, 1- 4, 63-70, 824-826. See also Chromatin; Histones; Nucleosomes

hsp26 as preset gene, 83-95 preset genes vs. remodeling,

83, 88 role of (CT) n elements, 89,

94 coactivators and TAFs, 179-

184, 202 effect of activators on

preinitiation complex assembly, 199-202

by GAL4 derivatives. See GAL4

hormone receptors in. See Estrogen receptor; Glucocorticoid receptor; Progesterone receptor; Steroid receptor

MCB-directed. See MCB Oct-2 vs. Oct-1 in VP16-

induced complex, 167- 176

virus-inducible in IFN-fi, 73- 80

yeast SNF/SWI role, 257-262 allele-specific. See Imprinting antirepression, 205-213,825 attenuation in VSG gene, 109-

I10 and combinatorial control, 73-

80, 167-176, 832-834 "competence" and DNase

sensitivity. See DNase I sensitivity of chromatin

"concerted action model," 38, 42- 43

DNA methylation role. See Im- printing; Methylation of DNA

and DNA nicking, 32 and DNA repair, 612-613, 615,

629-630 ecdysone in regulation, 491-493 effect of chromatin assembly,

233 effect of DNA replication and

amplification, 490- 493

homeodomain proteins in regulation. See Homeodomain proteins

and inactivation in X chromosome. See Chromosome, X

inhibitors. See Actinomycin D; cr Amanitin

initiation. See also Preinitiation complex; RNA polymerase

DNA bending in, 115-122

S U B J E C T INDEX 859

to elongation cycling, role of RNA polymerase phosphorylation, 187- 197

and interchromosome domain compartment, 786-788

and ~. replication initiation, 389- 4OO

localization and export of transcripts. See Nucleus

long-range control, 210-211, 821-823. See also En- hancer; Insulator elements; LCR; Transcrip- tion, repression and silencing

in perichromatin fibrils, coordination with splicing, 785-786, 799-804

and processing. See pre-rRNA processing and snurposomes; Splicing

repression and silencing, 94, 159, 437, 441,822, 824. See also Heterochromatin; In- sulator elements

cell-stage specific inactivation of lysozyme gene, 39-40

chromatin compaction and electric forces role, 786- 788

chromatin- or Hi-mediated, counteracting. See Tran- scription, antirepression

chromatin structure and nucleosome positioning roles, 83,213-222,233, 237-244, 250-255, 743- 744, 823-826. See also Histones; Nucleosomes

g]obin genes, 11 mating-type genes in yeast,

248-255, 733, 737-740, 743-744, 824, 829-830

a-cell-specific and a2 repressor, 237-244

E and I silencers, 444 silencer as origin of DNA

replication, 443-454 methylation-mediated. See

Methylation of DNA pairing-sensitive repression of

white minigene, 52-53 pre- and postinduction of IFN-

[~, 73-74 silencers in TCR loci sequence,

346 sub-telomeric DNA modifica-

tion in attenuation, 108- 110

telomeric silencing, 107-109, 249-255, 421-422, 427, 725, 733, 743-744, 830

role in control of yeast S-phase- specific genes, 638-639

role of domain organization of DNA in control. See Domains

Transcription factors, 5, 167, 187, 199, 786, 821-822, 827- 828, 832-834. See also spectfic factors

access to DNA chromatin structure and

nucleosome/histone role, 5, 63-70, 217-218, 222, 225-234, 533

~t enhancer role, 97-102 and DNA methylation, 281-282 HLH and b/HLH/Z motifs, 123,

126-128 ligand-modulated. See Estrogen

receptor; Glucocorticoid receptor; Nuclear nonsteroidal receptors; Steroid receptor

and model for trans-inactivation. See trans-Inactivation of brown gene

promoter-selective, 179-184 role in DNA replication, 403-412 role of sequence-specific in

antirepression. See GAGA factor; Spl; VP16, GAL4-VP16

with same DNA-binding specificity, mechanisms for differential regulation of transcription, 167-176

sequence-specific DNA recognition, 141-146

stereochemistry of specific DNA mteractions, 133-139

synergistic interactions, 77-80, 822

TFIIA, 125, 187-189, 199, 827- 828

TFIIB, 192, 195, 199, 821-822 as target of acidic activators,

2O0-2O2 and TBP interaction, 188-189

TFIID, 64, 93-94, 123, 187-188, 195, 199, 202, 259, 821- 822,827-828. See also TAFs; TATA box, -binding protein

coactivator activity and TAFs, 180-184

TFIIE, 192, 195, 199, 821-822 TFIIF, 199, 821-822, 827-828

and polymerase association with preinitiation complex, 187-190, 192, 195

TFIIH, 199, 827 DNA helicase activity, 193,

197, 262 ERCC3 as subunit, 611,627,

629 kinase activity, 191-193, 195

TFIIJ, 195, 199

TFIIIA access to nucleosomal DNA,

225-234 zinc finger, 134, 141,225

TFIIIB TAFs, 182 X-ray crystallographic studies of

TBP, Max, and HNF- 3~fork head, 123-130, 826-827

Transcripts. See Nucleus; RNA, transcripts

Transferrin-binding protein (TFBP) and receptor, antigenic variation, 110- 111

Transformation P-element-mediated. See P ele-

ment of trypanosomes, 105

Transgenic mice and chromatin structure effect

on transcription, 1-3 generating with YACs covering

tyrosinase gene, 55-61 and globin gene switching, 7-12 and imprinting, 289, 291-294 and transcription regulatory

units for lysozyme gene, 37, 40-43

Transgenic yeast strains with I- Sce I sites for mapping, 358, 360

trans-Inactivation of brown gene, 577-583

Translational positioning of histone octamer core, 226-228, 231-232

Translocations. See also Genomic sequencing

FISH for cytogenetic analysis, 772-773

Transposases. See P element Transposition. See also P element

of phage Mu, target site preference at DNA strand transfer, 515-522

of Tyl and Ty3, integration target, 539-540

Transposons and retrotransposons, 52. See also bluetail transposon; P element; Tn7 transposon; Tyl and Ty3

copy number and regulation of position-effect variegation in heterochromatin, 592-594

enhancer trap. See Enhancer, trapping

trans-Splicing. See Splicing Transvection and communication

within and between domains, 33

Trithorax group genes, 49-50, 53 tRNA genes, 241, 243, 360, 370,

687

860 SUBJECT INDEX

TRPIARS1 minichromosomes and retroviral DNA integration target, 534

Trypanosomes control of antigenic variation,

105-112 and telomere length, 107-109,

720 Trypsin inhibitor. See BPTI Trypsinogen gene family in TCR

sequence, 346-347 TS, 664 Tumor initiation and progression.

See Gene amplification Tumor suppressor genes. See p53;

Rb-dependent cell cycle arrest

Tyl and Ty3, integration targets, 539-540

Tyl-17, 421 Tyrosinase gene, YACs covering,

55-61 Tyrosine hydroxylase gene and im-

printing, 307-308

U

Ubx gene. See Bithorax complex Unidirectional and bidirectional

replication in )~, 389-400 URA3 gene and telomeric repres-

sion, 249, 733 UV-irradiated DNA, recombina-

tion and repair, 525, 529, 625. See also Recombina- tion; Repair of DNA; Xeroderma pigmentosum

UV-mediated cross-linking. See Cross-linking

UvrABC excision repair enzymes, 528, 605, 630. See also (A)BC excinuclease

V

V (variable) gene segment. See TCR

Variable (V) gene segment. See TCR

Variant surface glycoprotein (VSG) gene, antigenic variation, 106-112

Variegating phenotype. See Heterochromatin

VCAF. See HCF Vertebrates

development and DNA methylation. See Imprinting

function of DNA methylation in, 281-284

Viral machinery as probe of chromatin structure. See Retroviral DNA integration

Viral oncogenes and gene amplification, 648, 651- 652

Viral sequence proliferation, DNA methylation role, 283

Virus-inducible enhancer complex for IFN-~ gene and HMG I(Y), 73-80, 834

Vitamin D 3 receptor, 133-134, 136 Vitellogenin

B1 gene and nucleosomes, 94 probe, oligonucleosome

solubility, 16, 19-22 VM-26, 26-31 Vmw65. See VP16 VP16

acidic activator region interaction with TFIIB, 200- 201

GAL4-VP16 in antirepression/activation of

transcription, 206-207, 209-211,213-214, 219- 222

and DNA replication, 409-412 -induced complex of HSV, com-

binatorial control of transcription, 167-176

VSG. See Variant surface glycoprotein gene

W

Water molecules in hydration sites, residence times, 151-152, 155-156

white gene. See Drosophila Writhe, 117, 121-122

X

Xce (X chromosome controlling element) locus, 319-320

X chromosome. See Chromosome Xenopus, 488

GV of oocytes and pronuclei, snurposomes and coiled bodies in, 747-753

and licensing factor model for coupling cell cycle to replication, 639

recombinant nucleosome core particles and globular domain of H1, 266, 270- 271

rRNA gene-containing nucleosome and transcription factor access, 225-234

site-specific replication initiation, role of nuclear organization, 478-484

TFIIIA, 134, 141, 225-234 vitellogenin B 1 gene. See Vitel-

logenin

Xeroderma pigmentosum (XP), complementation groups and excision repair, 605- 615,625-631

X inactivation and X/C (X inactivation center). See Chromosome, X

X I S T / X i s t gene, 813, 816 noncoding RNA transcript, 320 and X inactivation, 294, 303,

317-321,831 X-linked genes. See Chromosome,

X XP and XPAC protein. See

Xeroderma pigmentosum X-ray crystal structure, 826-827

FIS, 505 HhaI, 331-337 MATa2 homeodomain/DNA,

159-165 nucleosomes and histone oc-

tamers, 265-271,275- 276

receptor DNA-binding domains, 133-139, 141, 143-146

reverse transcriptase and Klenow fragment, 495- 501

in study of protein hydration, 149, 151, 153-155

TBP, Max, and HNF-3/fork head, 123-130, 826- 827

Tramtrack DNA-binding domains, 141-143, 146

X-ray-induced DNA nicking and transcription sensitivity, 32

X-ray-induced recombination and repair, 567. See also Recombination; Repair of DNA

Y

YACs (yeast artificial chromosomes), 31-32, 642, 767

amplifiable, 55, 57-58 covering tyrosinase gene for gen-

erating transgenic mice, 55-61

DNA introduction into cells, 55 in mapping, 349,353

C. elegans, 368 human genome, MegaYACs

and YAC to YAC Alu- PCR hybridization, 377- 382

Y chromosome. See Chromosome Yeast, 66, 829-830. See also

Abfl/ABF1; ARS; cdc mutations, genes, and proteins; GAL4; Mini- chromosomes

SUBJECT INDEX 861

a-cell-specific gene and a2 repressor. See a2 repres- s o r

artificial chromosomes. See YACs

CDC9 and cdc17 + gene product homology with DNA ligases, 619

checkpoint control of cell cycle. See RAD proteins, RAD9

chromatin structure, dam methylase in study of, 251

excision repair genes and proteins, 611-613, 627

HM loci. See HM loci and repression

MATal protein, 159, 161,165 MATch2 homeodomain, structure

and DNA-hinding specificity, 159-165

MCM1 protein, 159, 162, 165 Saccharomyces cerevisiae

centromere/kinetochore, 669- 675, 681-683

chromosome structure and function in mitosis, 677- 684

heterochromatin, 679 position effects and silencing

of genes, 248-255 mapping

genetic, 363-364 physical, 358, 360, 363-364 restriction, resolution-

completeness profile, 351-352

mating-type interconversion, 443,462-463

pairing of homologous chromosomes, 553-554

RAD51 and RAD52 genes for recombination/repair, 567-575

replication, 386 and A R S element function,

409, 415-422, 425-433, 435-436

initiator protein ORC, 436- 441

position effects on origin, 421-422, 426-427

transcriptional silencer as origin, 443-454

sequencing genome, 357-365 GC periodicity, 363,365

SNF/SWI proteins in transcriptional activation, 257-262

Schizosaccharom yces pombe centromere structure and

function, 687-694 DNA replication and coordina-

tion with mitosis, 639- 642

mating-type interconversion and imprinting, 457-464

position effects at centromere, 249

RAD51 gene for recombination/repair, 569-575

telomere length, 720, 733-734, 737-740, 744

telomere replication, 725-731 telomeric repression and posi-

tion effects, 249-255, 421-422,427, 725, 733, 743-744

transcriptional control of S- phase-specific genes, 638-639

Tyl and Ty3, integration targets, 539-540

yellow gene. See Drosophila YOYO-1 and YOYO/MG staining

of loop bodies, 758-763 yp-1 enhancer blocking, 47-48

Z

zeste protein and topological organization of domains, 33

~-~ region of Neurospora and DNA methylation, 323-329

Zinc fingers and zinc-stabilized motifs

of ATF-2, 76 of DNA-binding domains of

hormone receptors, 134, 141, 143-146

of DNA-binding domain of Tram- track, 141-143, 146

of TFIIB, 188 of TFIIIA, 134, 141,225

Zipper proteins, 123, 126-128 Z X D A / B genes and X inactivation,

316-317 Zygotic meiosis and pairing of

homologous chromosomes, 553, 558- 560, 562

Zygotic sporulation, 459

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