Presentation on theme: "Regulation of Gene Expression 13 February, 2013"— Presentation transcript:
1Regulation of Gene Expression 13 February, 2013 Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of Pittsburgh
2retrieve promoter sequences determine transcription factor occupancy Topicsretrieve promoter sequencesdetermine transcription factor occupancybrowse through the epigenetic biochemical markersHistone modifications, DNA methylation etc.,-predict the location of enhancers, silencers and promoters
3Major Topicsidentify microRNA that have been reported or predicted to interact with a gene
4Tools identify promoter sequence(s) present in your gene of interest Biobase TransproUCSC genome browserpredict transcription factor binding sitesTransfac (Biobase Match)Browse through the epigenomic markersENCODE Human Epigenome Atlasidentify miRNA that have been reported or predicted to interact with a geneMirtarbaseMirbase
12Find Promoter Sequence Retrieve promoter sequence for :Human : BCL2, EGFRC. elegans : let-23Drosophila: son of sevenlessYeast: fus3Tips:Go to UCSC genome browserSearch by gene nameClick on UCSC genes/Wormbase genes/Flybase genesClick on Genomic sequence
31Link to the video tutorial: 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 ?ResourcesBiobase Transpro:Link to the video tutorial:
32What transcription factors bind to a promoter sequence?
39Information pertaining to a transcription factor
40Transcription Factors occupancy analysis Retrieve potential promoter sequence and predict transcription factors binding sites present in the promoter region:
41Link to the video tutorial: Retrieve potential promoter sequence of a yeast gene, fus3 and predict transcription factors binding sites present in the promoter region.ResourcesBiobase Match: https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgiLink to the video tutorial:
48Mol Biol Cell. 2007 Mar;18(3):1064-72. Epub 2007 Jan 10. EGFR and Sec61gRole of the Sec61 translocon in EGF receptor trafficking to the nucleus and gene expression.Liao HJ, Carpenter G.Mol Biol Cell Mar;18(3): Epub 2007 Jan 10.
49UCSC Genome Browser: http://genome.ucsc.edu/ Convert the human genomic region between genes sec61g and EGFR into mouse, rat and zebra fish genomesResourceUCSC Genome Browser:Link to the video tutorial:File: UCSC_convert.swf
50UCSC Genome Browser: Navigating a Genomic Region
51UCSC Genome Browser: Navigating a Genomic Region
52UCSC Genome Browser: Navigating a Genomic Region What transcription factors bind in this region?
54UCSC Genome Browser: http://genome.ucsc.edu/ Identify promoter, enhancer and silencer sequences by browsing the epigenomic markers generated by the ENCODE projectResourceUCSC Genome Browser:Link to the video tutorial:
64Link to the video tutorial: Identify miRNA(s) that have been reported or predicted to interact witha gene.Retrieve target genes of a miRNAResourcesMiRNA databaseMirbase:Target databaseMirtarbase:Targetscan:Miranda:Pictar:Link to the video tutorial:
65Result comparison of miRNA prediction algorithms ExprTarget: An Integrative Approach to Predicting Human MicroRNA TargetsPLOs One
66Thank you! Any questions? Carrie Iwema Ansuman Chattopadhyay