Conservation and Evolution of Cis -Regulatory Systems

1. Conservation and Evolution of Cis-Regulatory Systems Tal El-Hay Computational Biology Seminar חנוכה תשס"וDecember 2005

2. Evolution in Action "Nothing in biology makes sense except in the light of evolution." - Theodosius Dobzhansky Science, 23 December 2005

3. Molecular Evolution Wikipedia

4. How Genomes Evolve • Random mutations • Transposable DNA • Gene duplication • Divergence • Whole genome duplication (+divergence) • Recombination of exons • Purifying selection Molecular Biology of the Cell, Alberts et al., 4th ed.

5. Evolution of Regulation • “Relative dearth of species specific genes” • “Seeming abundance of functionally homologous proteins”(A. P. Gasch et al., PLoS Biol., 2004) • Additional mechanisms for diversification Such as timing, location and level of proteins • Our focus – Gene Expression

6. Outline of Questions • Conserved and evolved properties • Mechanisms of conservation and evolution • Bridging Genotype and Phenotype

7. Cis-Regulatory Factors • 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.

8. Goal • Explore evolution of gene expression regulation • Mainly through examination of cis-elements

9. The Fungul Family A. P. Gasch et al., PLoS Biol., 2004

10. 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 search 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

11. Proteasome GGTGGCAAA Rpn4p Conservation of S. cerevisiae motifs G1 phase cell cycle ACGCG MCB Amino acid biosynthesis TGACTM Gcn4p Nitrogen source GATAA GATA factors

12. Novel Sequences Ribosomal proteins AGCCCTAA Ribosomal proteins GTGACTGT tRNA synthetases TGACTCAN

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

14. Spacing between binding sitesin Methionine Biosynthesis genes • Small distance between Cbf1p and Met31/32p • Conserved across species • Independent of exact positions

15. Zooming In – The Proteasome • The proteasome is regulated by Rpn4p • Consensus sequence enriched across all hemiascomycete • Slight differences between C. Albicans and S. Serevisiae • Exploring evolution of the sequence

16. Proteazome Cis-Element Evolution Procedure: • Generate ‘meta matrix’ • Species specific matrix • Hierarchical clustering GGTGGCAAAW AGTGGCAAAN GGTGGCAAYA GRAGGCAAAA

17. Binding specificities of Rpn4p Sc element Common element CA element

18. Validation of specificities? • GGTGGCAAAA • GAAGGCAAAA • AGTGGCAACA • GGTGGCAAAA • AGTGGCAAAA • GGTGGCAACA • CTGCATTTGG Sc_Rpn4p Ca_Rpn4p hybrid

19. Intermediate Summary - Conservation • Conserved cis-elements in ‘un-align-able’ non coding regions • Correspondence of conservation and evolutionary distance • Did not observe position conservation • Similar position distributions • Found an example of conserved spacing • Interaction constraint between TF?

20. Intermediate Summary - Evolution • Novel sequences in coregulated orthologous modules • Conserved expression patterns with evolved regulation (e.g. Proteasome, Ribosome) • Individual example for: • Addition of gene targets to a regulatory network (S1 phase cell cycle) • Coevolution in a regulatory network • Cooption of a regulatory system

21. Goals • Learn mechanisms of evolution of regulation systems • Integrating comparative expression and sequence analysis

22. Computational framework Identify conserved modules Derive orthologous modules Identify cis-elements profiles Reconstruction of evolution

23. Orthologous Modules in Yeast • S-phase module • Respiration • Amino acid metabolism • Ribosomal proteins synthesis • Stress • Ribosome biogenesis

24. Conserved and Diverged Regulatory Mechanisms • Conserved cis-elements – Respiration module • Mlu cell cycle element (ACGCGT) • Bound by MBF complexes in both species • Diverged - Ribosomal protein synthesis • RAP1 and IFHL in S. cerevisae (TACATCCGTACAT &TCCGCCTAG resp.) • Homol-D box and Homol-E site in S. pombe (TGTGACTG & ACCCTACCCTA) • Conserved and diverged – Ribosome biogenesis module

25. Apparent redundancy ofbinding sites Switching from Homol-D to RAP1 The evolution of the Ribosomal Regulatory Program Gradual Evolution in the IFHL Box

26. Evidence for Regulator Switching • Evolution of Transcription factor • RAP1 is a submotif of telomeric repeat • Rap1p regulates telomer length • Association of events:Rap1p Gained of Trans activation domain, RAP1 joined RP module • Interacation of RAP1 & Homol-D? • usually 2-6 base pairs apart • Conserved order

27. Convergent domain duplication or Acquired dimerization domain? Gradual Evolution of IFHL Box TCTGCCTA AGGGCTATAGCCCT GCCCTA CCCTACCCTA

28. Spatial Configuration • HomolD-RAP1Sites are tightly coupled • Rap1-IFHLVariable probably to modified role of IFHL • RAP1-RAP1Sites are tightly coupled • IFHL-IFHLCoupling mainly inA. gossypii and K. Waltii

29. Intermediate Summary -Modes of Evolution • Conserved modules with diverged regulatory mechanisms • Some changes via redundant intermediate programs

30. Goals • Genotype and Phenotype

31. Background – Yeast Growth • Some Yeast species are fermentative • Others can employ only respiration • Connection to whole genome duplication

32. Analysis of Genetic Basis of Phenotypic Diversity • Examine gene expression program • S. Cerevisiae with 1000 expression profiles • C. Albicans with198 profiles • Motif search in related modules • Validation of motif role • Comparison of motif and phenotype evolution

33. Transcriptional Wiring Differences RP Cytoplasmic ribosomal proteins rRNA rRNA processing genes MRP Mitochondrial RP STR Environmental Stress response

34. Cis or Trans? Cis element search: • PAC in rRNA of bothspecies • None for MRP inS. Serevisiae • AATTTT in MRP, putative rRNA regulator Validation of cis-regulatory Role of AATTTT in MRP

35. Spatial Configuration of AATTTT Both species: • Position is confined in RP and rRNA • Not represented in STR C. Albicans: • AATTTT Regulates also MRP • Rapid growth element

36. Loss or Gain of Binding Site? • Loss of binding site in MRP associated with whole genome duplication

37. Evolution of Genome and Phenotype • “Gene duplication can facilitate the evolution of new function” • by specialization of new coding sequences • Also by facilitating the evolution of gene expression

38. Summary of methodologies • Integration of sequence and gene-expression • Finding orthologous modules • Finding orthologous binding motifs • Exploiting phylogenetic trees • Find genotype change rules • Associate phenotype and genotype changes • Exploit gene expression data of extremes

39. Summary of principles • Conservation of regulatory programs • Binding site conservation • Position and spacing • Conservation of module with evolution of control • Loss and gain • Drift • Switching, could be explained via redundancy • Evolution of regulatory programs -> Evolution of phenotype • Addition of gene targets • Cooption or loss of TF • Also facilitated by whole genome duplication

40. Points for thought • How can simultaneous change of cis-elements happen? • Evolution of elaborate wiring • Evolution of other modes of regulation • Is there gene expression data for more species? • Look for conserved patterns?