Regulation of Gene Expression 13 February, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.

Regulation of Gene Expression

13 February, 2013

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

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

http://vcell.ndsu.edu/animations/transcription/index.htm

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 Videoshttp://www.hsls.pitt.edu/molbio/videos

Retrieve promoter sequence for a gene

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

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

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 andEncyclopedia of DNA

Elements Project

Spatiotemporal gene expression

TP53

EGFR

A movie on regulated transcription

http://vcell.ndsu.edu/animations/regulatedtranscription/index.htm

Epigenetic mechanisms

Source: NCBIhttp://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 MarkersLandmark 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

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

Promoter Database

Biobase Knowledge LibraryPromoter report

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

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 ?

What transcription factors bind to a

promoter sequence?

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

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

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

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.

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

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

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

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

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

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

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

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

Thank you!Any questions?

Carrie Iwema Ansuman Chattopadhyayiwema@pitt.edu ansuman@pitt.edu 412-383-6887 412-648-1297

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