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![Page 1: Regulation of Gene Expression 13 February, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.](https://reader036.fdocuments.net/reader036/viewer/2022070306/55168c3e5503469d698b624e/html5/thumbnails/1.jpg)
Regulation of Gene Expression
13 February, 2013
Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of [email protected]
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Topics
retrieve promoter sequences
determine transcription factor occupancy
browse through the epigenetic biochemical markers
Histone modifications, DNA methylation etc.,
-predict the location of enhancers, silencers and promoters
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Major Topics
identify microRNA that have been reported or predicted to interact with a gene
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Tools identify promoter sequence(s) present in your gene of interest
Biobase Transpro UCSC genome browser
predict transcription factor binding sites Transfac (Biobase Match)
Browse through the epigenomic markers ENCODE Human Epigenome Atlas
identify miRNA that have been reported or predicted to interact with a gene Mirtarbase Mirbase
http://www.hsls.pitt.edu/guides/genetics
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An excellent movie on transcription
http://www.hsls.pitt.edu/guides/genetics
http://vcell.ndsu.edu/animations/transcription/index.htm
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Promoter, Enhancer and Silencer
Source: http://www.cbs.dtu.dk/dtucourse/cookbooks/dave/Lekt03bkg.html
http://www.hsls.pitt.edu/guides/genetics
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More Movies @ HSLS MolBio Videoshttp://www.hsls.pitt.edu/molbio/videos
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Retrieve promoter sequence for a gene
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Promoter Sequence
Generic Promoter Seq UCSC Genome Browser
Human Curated Promoter Seq Biobase TransPro mPROMDB CSH TRED Eukaryotic Promoter Database (EPD)
http://www.hsls.pitt.edu/guides/genetics
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http://www.hsls.pitt.edu/molbio
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/sequence.swf
http://media.hsls.pitt.edu/media/clres2705/sequence_2.swf
Resources
UCSC Genome Browser: http://genome.ucsc.edu/NCBI Entrez Gene: http://www.ncbi.nlm.nih.gov/gene
Find sequence information for a gene
-genomic -promoter - intron-exon coordinates-mRNA -protein
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Fetching Promoters
http://www.hsls.pitt.edu/molbio/videos/play?v=37
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Find Promoter Sequence Retrieve promoter sequence for :
Human : BCL2, EGFR C. elegans : let-23 Drosophila: son of sevenless Yeast: fus3
Tips: Go to UCSC genome browser Search by gene name Click on UCSC genes/Wormbase genes/Flybase genes Click on Genomic sequence
http://www.hsls.pitt.edu/guides/genetics
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Transcription Start Site (TSS)
http://www.hsls.pitt.edu/guides/genetics
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Epigenome andEncyclopedia of DNA
Elements Project
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Spatiotemporal gene expression
TP53
EGFR
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A movie on regulated transcription
http://vcell.ndsu.edu/animations/regulatedtranscription/index.htm
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Epigenetic mechanisms
Source: NCBIhttp://www.ncbi.nlm.nih.gov/books/NBK45788/#epi_sci_bkgrd.About_Epigenetics
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Genome in 3D
http://www.nature.com/nature/journal/v470/n7333/pdf/470289a.pdf
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Chromatin Immuno-Precititation-Seq(ChIP-Seq)
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Epigenetic MarkersLandmark Paper:
http://www.nature.com/ng/journal/v39/n3/full/ng1966.html
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Histone Modifications
http://goo.gl/GQ9V8
http://www.hsls.pitt.edu/guides/genetics
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ENCODE Project
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001046
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Encode Cell Types
http://genome.ucsc.edu/ENCODE/cellTypes.html
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Promoter Database
http://www.hsls.pitt.edu/guides/genetics
search.HSLS.MolBio http://search.hsls.pitt.edu/vivisimo/cgi-bin/query-meta?query=promoter+database&input-form=si
mple&v:sources=OBRCandBioMedCentral&v:project=BioInfoTools&submit=Search
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Promoter Database
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Biobase Knowledge LibraryPromoter report
http://www.hsls.pitt.edu/guides/genetics
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http://www.hsls.pitt.edu/molbio
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/biobase.swf
Resources
Biobase Transpro:
Retrieve experimentally verified promoter sequence of a gene i.e. EGFR . What transcription factors binding sites are reported to be present in the gene regulatory region ?
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What transcription factors bind to a
promoter sequence?
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Find Transcription Factor Binding SitesBasic Search:
TESS (Transcription Element Search System) BIOBASE Match
Phylogenetic Footprinting: ConSite
http://asp.ii.uib.no:8090/cgi-bin/CONSITE/consite
Footer http://biodev.hgen.pitt.edu/footer_php/Footerv2_0.php
http://www.hsls.pitt.edu/guides/genetics
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Transcription Factors (TF)
Database: Transfac-BioBase https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi
Classification https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi
Properties Binding sites Matrix https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi
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Transcription Factors
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Transcription Factor
http://www.cisreg.ca/cgi-bin/tfe/home.pl
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Transcription Factor binding sites
Jonathan M. Keith (ed.), Bioinformatics, Volume II: Structure, Function and Applications, vol. 453, © 2008 Humana Press,
http://www.hsls.pitt.edu/guides/genetics
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Information pertaining to a transcription factor
http://www.hsls.pitt.edu/molbio/videos/play?v=74
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Transcription Factors occupancy analysis Retrieve potential promoter sequence and
predict transcription factors binding sites present in the promoter region:
http://media.hsls.pitt.edu/media/clres2705/match.swf
http://www.hsls.pitt.edu/guides/genetics
![Page 41: Regulation of Gene Expression 13 February, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.](https://reader036.fdocuments.net/reader036/viewer/2022070306/55168c3e5503469d698b624e/html5/thumbnails/41.jpg)
http://www.hsls.pitt.edu/molbio
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/match.swf
Resources
Biobase Match: https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi
Retrieve potential promoter sequence of a yeast gene, fus3 and predict transcription factors binding sites present in the promoter region.
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Use Biobase Match program
http://www.hsls.pitt.edu/molbio/videos/play?v=47
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Find conserved transcription factor binding sites• Footer
• http://biodev.hgen.pitt.edu/footer_php/Footerv2_0.php
• VISTA Tools• http://genome.lbl.gov/vista/index.shtml
• rVISTA• http://genome.lbl.gov/vista/rvista/submit.shtml
• Whole Genome rVISTA• http://genome-test.lbl.gov/cgi-bin/WGRVistaInputCommon.pl
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Footer Result Page
http://www.hsls.pitt.edu/guides/genetics
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Browsing the ENCODE Data
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Sec61g and EGFR
human chr7:54,801,956-55,305,954
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EGFR and Sec61g
Role of the Sec61 translocon in EGF receptor trafficking to the nucleus and gene expression.Liao HJ, Carpenter G.
Mol Biol Cell. 2007 Mar;18(3):1064-72. Epub 2007 Jan 10.
http://www.hsls.pitt.edu/guides/genetics
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http://www.hsls.pitt.edu/molbio
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/ucsc_convert.swfFile: UCSC_convert.swf
Resource
UCSC Genome Browser: http://genome.ucsc.edu/
Convert the human genomic region between genes sec61g and EGFR into mouse, rat and zebra fish genomes
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UCSC Genome Browser: Navigating a Genomic Region
http://www.hsls.pitt.edu/guides/genetics
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UCSC Genome Browser: Navigating a Genomic Region
http://www.hsls.pitt.edu/guides/genetics
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UCSC Genome Browser: Navigating a Genomic Region
What transcription factors bind in this region?
http://www.hsls.pitt.edu/guides/genetics
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Sec61g and EGFR
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http://www.hsls.pitt.edu/molbio
Link to the video tutorial:http://media.hsls.pitt.edu/media/molbiovideos/encode1-ac0212.swfhttp://media.hsls.pitt.edu/media/molbiovideos/encode2-ac0212.swfhttp://media.hsls.pitt.edu/media/molbiovideos/encode3-ac0212.swf
Resource
UCSC Genome Browser: http://genome.ucsc.edu/
Identify promoter, enhancer and silencer sequences by browsing the epigenomic markers generated by the ENCODE project
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Cell Lines
K562
NHLF
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Human Epigenome Atlas:
http://www.genboree.org/epigenomeatlas/edaccGridViewerPublic.rhtml
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Regulome
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Retrieve MicroRNA target genes
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MicroRNA Biology http://hstalks.com/main/search_bar.php?s=microRNA&l=252&k=TALK
http://www.hsls.pitt.edu/molbio
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http://www.hsls.pitt.edu/molbio
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/mirna.swf
Resources
MiRNA database• Mirbase: http://www.mirbase.org Target database• Mirtarbase: http://mirtarbase.mbc.nctu.edu.tw/• Targetscan: http://www.targetscan.org/• Miranda: http://www.microrna.org/• Pictar: http://pictar.mdc-berlin.de/
• Identify miRNA(s) that have been reported or predicted to interact with a gene.
• Retrieve target genes of a miRNA
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Result comparison of miRNA prediction algorithms
http://www.hsls.pitt.edu/molbio
ExprTarget: An Integrative Approach to Predicting Human MicroRNA Targets
PLOs One http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013534
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Thank you!Any questions?
Carrie Iwema Ansuman [email protected] [email protected] 412-383-6887 412-648-1297
http://www.hsls.pitt.edu/guides/genetics