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cis-regulatory element study in transcriptome

Jin ChenCSE891-001

Fall 2012

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What is Cis-element

Courey and Jia (2001)

A cis-regulatory element or cis-element is a region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA

Latin word “cis” means "on the same side as"

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Cis-element properties• Typically found in 5’ untranscribed region of the

gene (promoter region)

• Can be specific sites for binding of activators or repressors

• Position and orientation of cis-element relative to transcriptional start site is usually fixed

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Cis-element properties

• Short sequences• Recurring patterns • Sequence-specific binding sites

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Cis-element Representations

A G T A T AA G A T T AC G A C T CA G T G T AA G T G T G

Consensus sequence:

Prob(A) 0.8 0 0.4 0.2 0 0.6

Prob(C) 0.2 0 0 0.2 0 0.2Prob(G) 0 1 0 0.4 0 0.2Prob(T) 0 0 0.6 0.2 1 0

ProbabilityMatrix & sequence logo:

A G W N T A

Sequence 1:Sequence 2:Sequence 3:Sequence 4:Sequence 5:

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Cis-element Representation 1• Consensus based method

– Refer to a sequence that matches all examples of the binding site closely but not exactly

– Trade-off between ambiguity and sensitivity

code descriptionA AdenineC CytosineG GuanineT ThymineU UracilR Purine (A or G)Y Pyrimidine (C, T, or U)M C or AK T, U, or GW T, U, or AS C or GB C, T, U, or G (not A)D A, T, U, or G (not C)H A, T, U, or C (not G)

V A, C, or G (not T, not U)

N Any base (A, C, G, T, or U)

IUPAC codes

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Cis-element Representation 2

• Sequence logos

– A visual representation of the probability matrix

– The total height of each column is proportional to its information content

http://www-lmmb.ncifcrf.gov/~toms/sequencelogo.html

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Cis-element matching/discovery

• Pattern Matching– Discovery patterns in sequences from co-regulated

genes using JASPAR and TRANSFAC matrices– Pscan

• Pattern Discovery– Discovery patterns in sequences from co-regulated

genes without using known patterns – MEME, hmmbuild

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Pattern Matching

http://www.slideshare.net/Stewbacca/dna-motif-finding-2010

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Pattern Matching

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Pattern Matching

12http://159.149.109.9/pscan/

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Cis-element evolution

• Composition• Location• Modules

chiken aA

mouse aA

mouse d1

Gene control regions for eye lens chrystallins

Molecular Biology of the Cell, Alberts et al., 4th ed.

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Large Scale Analysis• Identify 264 co-regulated gene groups in S. serevisiae• Putative cis-regulatory elements– 80 known consensus binding sites– 597 elements by motif discovery with MEME

• Score enrichment of genes containing each putative element- 42 cis-elements in 35 unique groups

• Orthologous modules in other species• Enrichment of orthologous modules

A. P. Gasch et al., PLoS Biol., 2004

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Conservation of S. cerevisiae motifsG1 phase cell cycle ACGCG MCBAmino acid biosynthesis TGACTM Gcn4pNitrogen source GATAA GATA factors

Proteasome GGTGGCAAA Rpn4p

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Positions of binding sites

• Non random distribution• Similar across species• No correlations in locations

across species

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Spacing between binding sitesin Methionine Biosynthesis genes

• Small distance between Cbf1p and Met31/32p• Conserved across species• Independent of exact positions

20Control of iron metabolism in Mycobacterium tuberculosis. Rodriguez, Marcela. Trends in Microbiology, 2006.

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Poisson Method for module discovery

Look for matches to consensus sequences

Mcm1 : DCCYWWWNNRGSte12 : TGAAACA

Random DNA sequence:

“Pearson type III distribution”:

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( 2)!k axapdf x ax e

k

Exponential distribution:

axpdf x ae

Wagner A (1999) Bioinformatics 15(10): 776-784

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Cister & Comet

DNA sequence segment

Prob segment | cluster modelscore segment ln

Prob segment | random model

Cluster model:

Poisson-distributed cis-elements, embedded in random DNA

Frith MC, Hansen U, Weng Z (2001) Bioinformatics 17(10): 878-889. Frith MC, Spouge JL, Hansen U, Weng Z (2002) Nucleic Acids Research