Regulation of Gene Expression 13 February, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu

retrieve promoter sequences determine transcription factor occupancy 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

Major Topics identify microRNA that have been reported or predicted to interact with a gene

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

An excellent movie on transcription http://vcell.ndsu.edu/animations/transcription/index.htm http://www.hsls.pitt.edu/guides/genetics

Promoter, Enhancer and Silencer Source: http://www.cbs.dtu.dk/dtucourse/cookbooks/dave/Lekt03bkg.html http://www.hsls.pitt.edu/guides/genetics

More Movies @ HSLS MolBio Videos http://www.hsls.pitt.edu/molbio/videos

Retrieve promoter sequence for a gene

Promoter Sequence Generic Promoter Seq Human Curated 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

Link to the video tutorial: Find sequence information for a gene -genomic -promoter - intron-exon coordinates -mRNA -protein Resources UCSC Genome Browser: http://genome.ucsc.edu/ NCBI Entrez Gene: http://www.ncbi.nlm.nih.gov/gene Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/sequence.swf http://media.hsls.pitt.edu/media/clres2705/sequence_2.swf http://www.hsls.pitt.edu/molbio

Fetching Promoters http://www.hsls.pitt.edu/molbio/videos/play?v=37

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

http://goo.gl/un8UE http://goo.gl/un8UE

http://goo.gl/3JnmO

BIOBASE TransPro http://www.hsls.pitt.edu/guides/genetics

Transcription Start Site (TSS) http://www.hsls.pitt.edu/guides/genetics

Epigenome and Encyclopedia of DNA Elements Project

Spatiotemporal gene expression EGFR TP53

A movie on regulated transcription http://vcell.ndsu.edu/animations/regulatedtranscription/index.htm

Epigenetic mechanisms Source: NCBI http://www.ncbi.nlm.nih.gov/books/NBK45788/#epi_sci_bkgrd.About_Epigenetics

Genome in 3D http://www.nature.com/nature/journal/v470/n7333/pdf/470289a.pdf

Chromatin Immuno-Precititation-Seq (ChIP-Seq)

Epigenetic Markers Landmark Paper: http://www.nature.com/ng/journal/v39/n3/full/ng1966.html

Histone Modifications http://goo.gl/GQ9V8 http://www.hsls.pitt.edu/guides/genetics

Encode Project http://www.genome.gov/10005107

ENCODE Project http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001046

Encode Cell Types http://genome.ucsc.edu/ENCODE/cellTypes.html

Promoter Database search.HSLS.MolBio http://search.hsls.pitt.edu/vivisimo/cgi-bin/query-meta?query=promoter+database&input-form=simple&v:sources=OBRCandBioMedCentral&v:project=BioInfoTools&submit=Search http://www.hsls.pitt.edu/guides/genetics

Promoter Database

Biobase Knowledge Library Promoter report http://www.hsls.pitt.edu/guides/genetics

Link 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 ? Resources Biobase Transpro: Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/biobase.swf http://www.hsls.pitt.edu/molbio

What transcription factors bind to a promoter sequence?

Find Transcription Factor Binding Sites Basic 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

Transcription Factors (TF) Database: Transfac-BioBase https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi Classification Properties Binding sites Matrix

Transcription Factors

Transcription Factor http://www.cisreg.ca/cgi-bin/tfe/home.pl

Transfac http://www.hsls.pitt.edu/guides/genetics

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

Information pertaining to a transcription factor http://www.hsls.pitt.edu/molbio/videos/play?v=74

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

Link to the video tutorial: Retrieve potential promoter sequence of a yeast gene, fus3 and predict transcription factors binding sites present in the promoter region. Resources Biobase Match: https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/match.swf http://www.hsls.pitt.edu/molbio

Use Biobase Match program http://www.hsls.pitt.edu/molbio/videos/play?v=47

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

Footer Result Page http://www.hsls.pitt.edu/guides/genetics

Browsing the ENCODE Data

Sec61g and EGFR human chr7:54,801,956-55,305,954

EGFR and Sec61g http://www.hsls.pitt.edu/guides/genetics

Mol Biol Cell. 2007 Mar;18(3):1064-72. Epub 2007 Jan 10. 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

UCSC Genome Browser: http://genome.ucsc.edu/ Convert the human genomic region between genes sec61g and EGFR into mouse, rat and zebra fish genomes Resource UCSC Genome Browser: http://genome.ucsc.edu/ Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/ucsc_convert.swf File: UCSC_convert.swf http://www.hsls.pitt.edu/molbio

UCSC Genome Browser: Navigating a Genomic Region http://www.hsls.pitt.edu/guides/genetics

UCSC Genome Browser: Navigating a Genomic Region http://www.hsls.pitt.edu/guides/genetics

UCSC Genome Browser: Navigating a Genomic Region What transcription factors bind in this region? http://www.hsls.pitt.edu/guides/genetics

Sec61g and EGFR

UCSC Genome Browser: http://genome.ucsc.edu/ Identify promoter, enhancer and silencer sequences by browsing the epigenomic markers generated by the ENCODE project Resource UCSC Genome Browser: http://genome.ucsc.edu/ Link to the video tutorial: http://media.hsls.pitt.edu/media/molbiovideos/encode1-ac0212.swf http://media.hsls.pitt.edu/media/molbiovideos/encode2-ac0212.swf http://media.hsls.pitt.edu/media/molbiovideos/encode3-ac0212.swf http://www.hsls.pitt.edu/molbio

Cell Lines K562 NHLF

Human Epigenome Atlas: http://www.genboree.org/epigenomeatlas/edaccGridViewerPublic.rhtml

Regulome db Search rs7216389 rs2853669

Regulome

Retrieve MicroRNA target genes

MicroRNA http://www.hsls.pitt.edu/molbio

MicroRNA Biology http://hstalks.com/main/search_bar.php?s=microRNA&l=252&k=TALK http://www.hsls.pitt.edu/molbio

Link to the video tutorial: Identify miRNA(s) that have been reported or predicted to interact with a gene. Retrieve target genes of a miRNA 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/ Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/mirna.swf http://www.hsls.pitt.edu/molbio

Result comparison of miRNA prediction algorithms ExprTarget: An Integrative Approach to Predicting Human MicroRNA Targets PLOs One http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013534 http://www.hsls.pitt.edu/molbio

Thank you! Any questions? Carrie Iwema Ansuman Chattopadhyay iwema@pitt.edu ansuman@pitt.edu 412-383-6887 412-648-1297 http://www.hsls.pitt.edu/guides/genetics