1. cis-regulatory element study in transcriptome Jin Chen CSE891-001 Fall 2012 1

2. What is Cis-element Courey and Jia (2001) 2 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"

3. 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 3

4. Cis-element properties Short sequences Recurring patterns Sequence-specific binding sites 4

5. Cis-element Representations A G T A T A A G A T T A C G A C T C A G T G T A A G T G T G Consensus sequence: Prob(A)0.800.40.200.6 Prob(C)0.200 0 Prob(G)0100.400.2 Prob(T)000.60.210 Probability Matrix & sequence logo: A G W N T A Sequence 1: Sequence 2: Sequence 3: Sequence 4: Sequence 5: 5

6. 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 6 codedescription AAdenine CCytosine GGuanine TThymine UUracil RPurine (A or G) YPyrimidine (C, T, or U) MC or A KT, U, or G WT, U, or A SC or G BC, T, U, or G (not A) DA, T, U, or G (not C) HA, 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

7. 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 7 http://www-lmmb.ncifcrf.gov/~toms/sequencelogo.html

8. 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 8

9. Pattern Matching 9 http://www.slideshare.net/Stewbacca/dna-motif-finding-2010

10. Pattern Matching 10

11. Pattern Matching 11

12. 12 http://159.149.109.9/pscan/

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15. Cis-element evolution Composition Location Modules chiken  A mouse  A mouse  1 Gene control regions for eye lens chrystallins Molecular Biology of the Cell, Alberts et al., 4 th ed. 15

16. 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 16 A. P. Gasch et al., PLoS Biol., 2004

17. Conservation of S. cerevisiae motifs G1 phase cell cycle ACGCGMCB Amino acid biosynthesis TGACTMGcn4p Nitrogen source GATAA GATA factors Proteasome GGTGGCAAARpn4p 17

18. Positions of binding sites Non random distribution Similar across species No correlations in locations across species 18

19. Spacing between binding sites in Methionine Biosynthesis genes Small distance between Cbf1p and Met31/32p Conserved across species Independent of exact positions 19

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

21. Poisson Method for module discovery Look for matches to consensus sequences Mcm1 : DCCYWWWNNRG Ste12 : TGAAACA Random DNA sequence: “Pearson type III distribution”:Exponential distribution: 21 Wagner A (1999) Bioinformatics 15(10): 776-784

22. Cister & Comet DNA sequencesegment Cluster model: Poisson-distributed cis-elements, embedded in random DNA 22 Frith MC, Hansen U, Weng Z (2001) Bioinformatics 17(10): 878-889. Frith MC, Spouge JL, Hansen U, Weng Z (2002) Nucleic Acids Research