Nucleosome Positioning
description
Transcript of Nucleosome Positioning
![Page 1: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/1.jpg)
Nucleosome Positioning
Histones and DNA Bending
![Page 2: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/2.jpg)
DNA packaging
• 3 X 109 base pairs in human genome• ~1 m if unraveled• Compacted into nucleus
– 100 m in diamter
![Page 3: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/3.jpg)
Histones
![Page 4: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/4.jpg)
Histones
![Page 5: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/5.jpg)
PDBID = 1KX3
![Page 6: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/6.jpg)
Nucleosome Arrays
Dorigo B, et al. Science. 2004 306(5701):1571-3.
![Page 7: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/7.jpg)
Current Opinion in Structural Biology 2006, 16:336–343
![Page 8: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/8.jpg)
http://www2.kenyon.edu/Depts/BioEllipse/courses/biol114/Chap01/chrom1.gif
![Page 9: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/9.jpg)
Histones vs. DNA
• Histones fold DNA• DNA sequence determines histone
binding– Does histone bind sequence?
• Absence of direct sequence specific recognition
– Bending flexibility of DNA determines affinity for complementary protein surface
![Page 10: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/10.jpg)
DNA as a Rod
![Page 11: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/11.jpg)
Twist
Bend
![Page 12: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/12.jpg)
![Page 13: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/13.jpg)
Flexibility
• Torsional Flexibility– Angle between base pairs
• Bending Flexibility– Properties of individual base steps
• Flexibility of DNA is a Sequence-dependent property
![Page 14: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/14.jpg)
Flexibility determinants
• Hydrogen bonds• Electronic configuration of base pairs• Base Pair Stacking energy• Exocyclic groups in major and minor
grooves
![Page 15: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/15.jpg)
Base Pairing
http://en.wikipedia.org/wiki/Base_pair
![Page 16: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/16.jpg)
Base Pairing
![Page 17: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/17.jpg)
Base Stacking
http://researchnews.osu.edu/archive/dna_base_stacking.jpg
![Page 18: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/18.jpg)
Base Stacking
Richmond & Davey 2003
![Page 19: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/19.jpg)
Electrostatics
Philos. Transact. A Math Phys. Eng. Sci. 2004 Jul 15;362(1820):1423-38.
![Page 20: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/20.jpg)
![Page 21: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/21.jpg)
Sequence-directed positioning
Widlund et al. 1997• Mouse Genome• Micrococcal nuclease• 146 bp DNA fragments• DNA seq added to end• Amplify using PCR• 10 rounds cycles
– competitive nucleosome assembly
Chromatin: Structure and Function Alan P. Wolffe
![Page 22: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/22.jpg)
Intrinsically curved DNA sequences
• Oligo(dA).oligo(dT) tracts (4-6bp)– Phased with a periodicity similar to that
of DNA helix
• TATA boxes repeated every 10 bp• CA and CTG di/tri-nucleotide repeats
![Page 23: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/23.jpg)
Energy Landscape
![Page 24: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/24.jpg)
Matrix Method
• Nucleotide phasing of 10bp repeats influences bending of DNA
![Page 25: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/25.jpg)
Periodic occurrence of A/T & GC
• A/T & G/C out of phase
• A/T narrow minor groove
• G/C wide minor groove
Satchwell et al. J. Mol. Biol. 1986 191:659-75
![Page 26: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/26.jpg)
![Page 27: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/27.jpg)
![Page 28: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/28.jpg)
![Page 29: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/29.jpg)
![Page 30: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/30.jpg)
Minor Groove bending facilitated by Arg side chain into minor groove when it faces histone octamer
Major groove narrows to ~9Å
Minor groove narrows to ~3Å
![Page 31: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/31.jpg)
Structure of DNA in Nucleosome
• Discontinuous curvature
Richmond & Davey 2003
![Page 32: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/32.jpg)
Summary
Ong, Richmond & Davey 2007
• Major Gray• Minor White
![Page 33: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/33.jpg)
Unusual DNA conformation parameters induced by histone
binding• Implicates sequence-dependent
– protein recognition– nucleosome positioning– nucleosome mobility
• Can we predict DNA:Nucleosome binding based on sequence?
![Page 34: Nucleosome Positioning](https://reader036.fdocuments.net/reader036/viewer/2022062309/568150da550346895dbefbd4/html5/thumbnails/34.jpg)