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

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Presentation on theme: "Regulation of Gene Expression 13 February, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System."— Presentation transcript:

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

2 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

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

4 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

5 An excellent movie on transcription

6 Promoter, Enhancer and Silencer Source:

7 More HSLS MolBio Videos

8 Retrieve promoter sequence for a gene

9 Promoter Sequence Generic Promoter Seq UCSC Genome Browser Human Curated Promoter Seq Biobase TransPro mPROMDB CSH TRED Eukaryotic Promoter Database (EPD)

10 Link to the video tutorial: Resources UCSC Genome Browser: NCBI Entrez Gene: Find sequence information for a gene -genomic- promoter - intron-exon coordinates -mRNA-protein

11 Fetching Promoters

12 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

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15 BIOBASE TransPro

16 Transcription Start Site (TSS)

17 Epigenome and Encyclopedia of DNA Elements Project

18 Spatiotemporal gene expression TP53 EGFR

19 A movie on regulated transcription

20 Epigenetic mechanisms Source: NCBI

21 Genome in 3D

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

23 Epigenetic Markers Landmark Paper :

24 Histone Modifications

25 Encode Project

26 ENCODE Project

27 Encode Cell Types html html

28 Promoter Database search.HSLS.MolBio form=simple&v:sources=OBRCandBioMedCentral&v:project=BioInfoTools&submit=Search form=simple&v:sources=OBRCandBioMedCentral&v:project=BioInfoTools&submit=Search

29 Promoter Database

30 Biobase Knowledge Library Promoter report

31 Link to the video tutorial: 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 ?

32 What transcription factors bind to a promoter sequence?

33 Find Transcription Factor Binding Sites Basic Search: TESS (Transcription Element Search System) BIOBASE Match Phylogenetic Footprinting: ConSite Footer

34 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

35 Transcription Factors

36 Transcription Factor

37 Transfac

38 Transcription Factor binding sites Jonathan M. Keith (ed.), Bioinformatics, Volume II: Structure, Function and Applications, vol. 453, © 2008 Humana Press,

39 Information pertaining to a transcription factor

40 Transcription Factors occupancy analysis Retrieve potential promoter sequence and predict transcription factors binding sites present in the promoter region:

41 Link to the video tutorial: Resources Biobase Match: https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi 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.

42 Use Biobase Match program

43 Find conserved transcription factor binding sites Footer VISTA Tools rVISTA Whole Genome rVISTA

44 Footer Result Page

45 Browsing the ENCODE Data

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

47 EGFR and Sec61g

48 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 Mar;18(3): Epub 2007 Jan 10.

49 Link to the video tutorial: File: UCSC_convert.swf Resource UCSC Genome Browser: Convert the human genomic region between genes sec61g and EGFR into mouse, rat and zebra fish genomes

50 UCSC Genome Browser: Navigating a Genomic Region

51 UCSC Genome Browser: Navigating a Genomic Region

52 UCSC Genome Browser: Navigating a Genomic Region What transcription factors bind in this region?

53 Sec61g and EGFR

54 Link to the video tutorial: Resource UCSC Genome Browser: Identify promoter, enhancer and silencer sequences by browsing the epigenomic markers generated by the ENCODE project

55 Cell Lines K562 NHLF

56 Human Epigenome Atlas:

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58 Regulome db Search rs rs

59 Regulome

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61 Retrieve MicroRNA target genes

62 MicroRNA

63 MicroRNA Biology

64 Link to the video tutorial: Resources MiRNA database Mirbase: Target database Mirtarbase: Targetscan: Miranda: Pictar: Identify miRNA(s) that have been reported or predicted to interact with a gene. Retrieve target genes of a miRNA

65 Result comparison of miRNA prediction algorithms ExprTarget: An Integrative Approach to Predicting Human MicroRNA Targets PLOs One

66 Thank you! Any questions? Carrie IwemaAnsuman Chattopadhyay


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