Regulation of Gene Expression - PowerPoint Presentation

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Regulation of Gene Expression - PPT Presentation

13 February 2013 Ansuman Chattopadhyay PhD Head Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansumanpittedu Topics retrieve promoter sequences ID: 374362

pitt http www hsls http pitt hsls www genetics guides promoter media genome transcription molbio gene sequence biobase cgi

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Slide1

Regulation of Gene Expression13 February, 2013

Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of Pittsburghansuman@pitt.eduSlide2

Topicsretrieve promoter sequencesdetermine transcription factor occupancybrowse through the epigenetic biochemical markers Histone modifications,

DNA methylation etc., -predict the location of enhancers, silencers and promotersSlide3

Major Topicsidentify microRNA that have been reported or predicted to interact with a geneSlide4

Toolsidentify promoter sequence(s) present in your gene of interestBiobase TransproUCSC genome browser

predict transcription factor binding sitesTransfac (Biobase Match) Browse through the epigenomic markersENCODE Human Epigenome Atlas identify miRNA that have been reported or predicted to interact with a gene

MirtarbaseMirbase

http://www.hsls.pitt.edu/guides/geneticsSlide5

An excellent movie on transcription

http://www.hsls.pitt.edu/guides/geneticshttp://vcell.ndsu.edu/animations/transcription/index.htmSlide6

Promoter, Enhancer and SilencerSource: http://www.cbs.dtu.dk/dtucourse/cookbooks/dave/Lekt03bkg.html

http://www.hsls.pitt.edu/guides/geneticsSlide7

More Movies @ HSLS MolBio Videoshttp://www.hsls.pitt.edu/molbio/videosSlide8

Retrieve promoter sequence for a geneSlide9

Promoter SequenceGeneric Promoter SeqUCSC Genome BrowserHuman Curated Promoter SeqBiobase TransPromPROMDB

CSH TREDEukaryotic Promoter Database (EPD)http://www.hsls.pitt.edu/guides/geneticsSlide10

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

Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/sequence.swfhttp://media.hsls.pitt.edu/media/clres2705/sequence_2.swf ResourcesUCSC 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 Slide11

Fetching Promotershttp://www.hsls.pitt.edu/molbio/videos/play?v=37Slide12

Find Promoter SequenceRetrieve promoter sequence for :Human : BCL2, EGFRC. elegans : let-23Drosophila: son of sevenlessYeast: fus3Tips:Go to UCSC genome browserSearch by gene name

Click on UCSC genes/Wormbase genes/Flybase genesClick on Genomic sequencehttp://www.hsls.pitt.edu/guides/geneticsSlide13

http://goo.gl/un8UE

http://goo.gl/un8UESlide14

http://goo.gl/3JnmOSlide15

BIOBASE TransProhttp://www.hsls.pitt.edu/guides/geneticsSlide16

Transcription Start Site (TSS)http://www.hsls.pitt.edu/guides/geneticsSlide17

Epigenome andEncyclopedia of

DNA Elements ProjectSlide18

Spatiotemporal gene expressionTP53

EGFRSlide19

A movie on regulated transcriptionhttp://vcell.ndsu.edu/animations/regulatedtranscription/index.htmSlide20

Epigenetic mechanismsSource: NCBIhttp://www.ncbi.nlm.nih.gov/books/NBK45788/#epi_sci_bkgrd.About_EpigeneticsSlide21

Genome in 3Dhttp://www.nature.com/nature/journal/v470/n7333/pdf/470289a.pdfSlide22

Chromatin Immuno-Precititation-Seq(ChIP-Seq)Slide23

Epigenetic MarkersLandmark Paper:http://www.nature.com/ng/journal/v39/n3/full/ng1966.htmlSlide24

Histone Modificationshttp://goo.gl/GQ9V8

http://www.hsls.pitt.edu/guides/geneticsSlide25

Encode Projecthttp://www.genome.gov/10005107Slide26

ENCODE Projecthttp://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001046Slide27

Encode Cell Typeshttp://genome.ucsc.edu/ENCODE/cellTypes.htmlSlide28

Promoter Databasehttp://www.hsls.pitt.edu/guides/genetics

search.HSLS.MolBiohttp://search.hsls.pitt.edu/vivisimo/cgi-bin/query-meta?query=promoter+database&input-form=simple&v:sources=OBRCandBioMedCentral&v:project=BioInfoTools&submit=SearchSlide29

Promoter DatabaseSlide30

Biobase Knowledge LibraryPromoter reporthttp://www.hsls.pitt.edu/guides/geneticsSlide31

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

Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/biobase.swf ResourcesBiobase 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 ?Slide32

What transcription factors bind to a promoter sequence?Slide33

Find Transcription Factor Binding SitesBasic Search:TESS (Transcription Element Search System)BIOBASE MatchPhylogenetic Footprinting:ConSitehttp://asp.ii.uib.no:8090/cgi-bin/CONSITE/consiteFooterhttp://biodev.hgen.pitt.edu/footer_php/Footerv2_0.php

http://www.hsls.pitt.edu/guides/geneticsSlide34

Transcription Factors (TF)Database: Transfac-BioBasehttps://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgiClassificationhttps://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgiPropertiesBinding sitesMatrixhttps://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgiSlide35

Transcription FactorsSlide36

Transcription Factorhttp://www.cisreg.ca/cgi-bin/tfe/home.plSlide37

Transfac http://www.hsls.pitt.edu/guides/geneticsSlide38

http://www.hsls.pitt.edu/guides/geneticsSlide39

Information pertaining to a transcription factorhttp://www.hsls.pitt.edu/molbio/videos/play?v=74Slide40

Transcription Factors occupancy analysisRetrieve 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/geneticsSlide41

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

Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/match.swf ResourcesBiobase 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.Slide42

Use Biobase Match programhttp://www.hsls.pitt.edu/molbio/videos/play?v=47Slide43

Find conserved transcription factor binding sitesFooterhttp://biodev.hgen.pitt.edu/footer_php/Footerv2_0.php

VISTA Toolshttp://genome.lbl.gov/vista/index.shtmlrVISTAhttp://genome.lbl.gov/vista/rvista/submit.shtmlWhole Genome rVISTAhttp://genome-test.lbl.gov/cgi-bin/WGRVistaInputCommon.plSlide44

Footer Result Pagehttp://www.hsls.pitt.edu/guides/geneticsSlide45

Browsing the ENCODE DataSlide46

Sec61g and EGFR human chr7:54,801,956-55,305,954Slide47

EGFR and Sec61ghttp://www.hsls.pitt.edu/guides/geneticsSlide48

EGFR and Sec61gRole 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/geneticsSlide49

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

Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/ucsc_convert.swfFile: UCSC_convert.swf ResourceUCSC Genome Browser: http://genome.ucsc.edu/

Convert the human genomic region between genes sec61g and

EGFR into mouse, rat and zebra fish genomes

Slide50

UCSC Genome Browser: Navigating a Genomic Region

http://www.hsls.pitt.edu/guides/geneticsSlide51

UCSC Genome Browser: Navigating a Genomic Region

http://www.hsls.pitt.edu/guides/geneticsSlide52

UCSC Genome Browser: Navigating a Genomic Region

What transcription factors bind in this region?http://www.hsls.pitt.edu/guides/geneticsSlide53

Sec61g and EGFRSlide54

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 ResourceUCSC Genome Browser: http://genome.ucsc.edu/

Identify

promoter, enhancer

and

silencer

sequences by browsing the

epigenomic

markers

generated by the

ENCODE project

Slide55

Cell LinesK562NHLFSlide56

Human Epigenome Atlas: http://www.genboree.org/epigenomeatlas/edaccGridViewerPublic.rhtmlSlide57
Slide58

Regulome db Searchrs7216389 rs2853669 Slide59

RegulomeSlide60
Slide61

Retrieve MicroRNA target genesSlide62

MicroRNA

http://www.hsls.pitt.edu/molbio Slide63

MicroRNA Biologyhttp://hstalks.com/main/search_bar.php?s=microRNA&l=252&k=TALKhttp://www.hsls.pitt.edu/molbio Slide64

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

Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/mirna.swf ResourcesMiRNA databaseMirbase: http://www.mirbase.org

Target databaseMirtarbase:

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

miRNASlide65

Result comparison of miRNA prediction algorithmshttp://www.hsls.pitt.edu/molbio

ExprTarget: An Integrative Approach to Predicting Human MicroRNA TargetsPLOs One http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013534Slide66

Thank you!Any questions?Carrie Iwema Ansuman Chattopadhyayiwema@pitt.edu ansuman@pitt.edu

412-383-6887 412-648-1297http://www.hsls.pitt.edu/guides/genetics