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Regulation of Gene Expression 13 February, 2013

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

2 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

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 Movies @ HSLS MolBio Videos

8 Retrieve promoter sequence for a gene

9 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)

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

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

13

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15 BIOBASE TransPro

16 Transcription Start Site (TSS)

17 Epigenome and Encyclopedia of DNA Elements Project

18 Spatiotemporal gene expression
EGFR TP53

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

28 Promoter Database search.HSLS.MolBio

29 Promoter Database

30 Biobase Knowledge Library Promoter report

31 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:

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 Properties Binding sites Matrix

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:
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:

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

49 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: Link to the video tutorial: File: UCSC_convert.swf

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 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: Link to the video tutorial:

55 Cell Lines K562 NHLF

56 Human Epigenome Atlas:

57

58 Regulome db Search rs rs

59 Regulome

60

61 Retrieve MicroRNA target genes

62 MicroRNA

63 MicroRNA Biology

64 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: Target database Mirtarbase: Targetscan: Miranda: Pictar: Link to the video tutorial:

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

66 Thank you! Any questions?
Carrie Iwema Ansuman Chattopadhyay


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