MW 11:00-12:15 in Beckman B302 Profs: Serafim Batzoglou, Gill Bejerano

1. MW  11:00-12:15 in Beckman B302 Profs: Serafim Batzoglou, Gill Bejerano TAs: Cory McLean, Aaron Wenger http://cs273a.stanford.edu [Bejerano Aut08/09]

2. Lecture 18 • Guest Talks • Ultraconservation • The Projects http://cs273a.stanford.edu [Bejerano Aut08/09]

3. human chimp macaque mouse rat cow dog opossum platypus chicken zfish tetra fugu Comparative Genomics what made us human? * t http://cs273a.stanford.edu [Bejerano Aut08/09]

4. Genotype Phenotype 4 http://cs273a.stanford.edu [Bejerano Aut08/09]

5. human chimp macaque mouse rat cow dog opossum platypus chicken zfish tetra fugu Comparative Genomics How did some of our relatives go back? * t http://cs273a.stanford.edu [Bejerano Aut08/09]

6. human chimp macaque mouse rat cow dog opossum platypus chicken zfish tetra fugu Now at the Species Level How did we leave the ocean? * t http://cs273a.stanford.edu [Bejerano Aut08/09]

7. Conserved elements in the Human Genome all human-mouse alignments human-mouse ancestral repeats alignment human-mouse ancestral repeats alignment election Difference: 5% of Human Genome 85%id on average [Mouse consortium, Nature 2002] http://cs273a.stanford.edu [Bejerano Aut08/09]

8. Conserved elements in the Human Genome all human-mouse alignments human-mouse ancestral repeats alignment human-mouse ancestral repeats alignment election Difference: 5% of Human Genome Ultraconservation 85%id on average [Mouse consortium, Nature 2002] http://cs273a.stanford.edu [Bejerano Aut08/09]

9. Typical DNA Conservation levels Conserved elements between human and mouse are on average 85% identical. [mouse consortium, 2002] [Bejerano et al., Science 2004] http://cs273a.stanford.edu [Bejerano Aut08/09]

10. Ultraconserved Elements fish [Bejerano et al., Science 2004] http://cs273a.stanford.edu [Bejerano Aut08/09]

11. * * * * * No known function requires this much conservation ? CDS ncRNA TFBS seq. http://cs273a.stanford.edu [Bejerano Aut08/09]

12. Discovery can be fun (compared to 4 results day before our ScienceExpress paper) 31,800 http://cs273a.stanford.edu [Bejerano Aut08/09]

13. Predictions and Proofs I Based on public domain genome wide data: ultraconservedelements larger subset does not one subset codes protein generate testable hypotheses for function from existing knowledge (2004) [Pennacchio et al., Nature, 2006] http://cs273a.stanford.edu [Bejerano Aut08/09]

14. Predictions and Proofs II Based on public domain genome wide data: ultraconservedelements larger subset does not one subset codes protein generate testable hypotheses for function from existing knowledge (2004) post transcriptional modification [Pennacchio et al., Nature, 2006] http://cs273a.stanford.edu [Bejerano Aut08/09]

15. Of the 29 exonic ultraconserved elements in RNA-binding protein genes in human, 15 have human and/or mouse EST evidence suggesting the presence of AS-NMD in those regions. [Ni et al., Genes & Dev 2007 ] http://cs273a.stanford.edu [Bejerano Aut08/09]

16. Model for Homeostatic Auto/Cross-regulation [Ni et al., Genes & Dev 2007 ] http://cs273a.stanford.edu [Bejerano Aut08/09]

17. Ultras are Under Strong Human Selection Mutational cold spots? NO. Rare (new) mutations are introduced to the population. Fierce purifying selection? YES. Very few of these get anywhere near fixation. A A G A A humans chimp NonSyn DAF Ultra DAF [Katzman et al, Science ,2007] http://cs273a.stanford.edu [Bejerano Aut08/09]

18. Genomic Distribution of Ultraconserved Elements • exonic • non • possibly Origins? http://cs273a.stanford.edu [Bejerano Aut08/09]

19. UC.338 comes from an ancient repeat ultraconserved exon novel coelacanth repeat enhancer LF-SINE [Bejerano et al, Nature ,2006] http://cs273a.stanford.edu [Bejerano Aut08/09]

20. No Apparent Phenotype Touch an Ultra And You - DIY 4-8% of documented mouse KO genes display no phenotype (inc. Pbx2, Nkx6.2, Gli1) [Ahituv et al., PLoS Biology, 2007] http://cs273a.stanford.edu [Bejerano Aut08/09]

21. Hypothesis • Can ultraconserved element mutations • be under extreme purifying selection • but the whole element be expendable? http://cs273a.stanford.edu [Bejerano Aut08/09]

22. What did Mother Nature favor? DNA element t mouse http://cs273a.stanford.edu [Bejerano Aut08/09]

23. Quite Some Time Later The horror … The horror … http://cs273a.stanford.edu [Bejerano Aut08/09]

24. Ultras are Fiercely Retained No Apparent Phenotype rodents deleted 11/15157 = 0.072% Ultras are >300 fold more persistent than neutral DNA But Doomed ... (25% deleted) http://cs273a.stanford.edu [Bejerano Aut08/09]

25. Enough about us…. http://cs273a.stanford.edu [Bejerano Aut08/09]

26. What we do understand.. • Ultraconserved elements exist. • They are maintained via strong on-going selection. • It is a heterogeneous bunch: • Some mediate splicing • Some regulate gene expression • Some express ncRNAs • (categories are not necessarily mutually exclusive) • Knockouts of four regulatory ultras did not lead to severe phenotypes (similar protein cases: Pbx2, Nkx6.2, Gli1) http://cs273a.stanford.edu [Bejerano Aut08/09]

27. What we don’t understand • Their functional density: • How did they come to be? • What is the selective advantage that lets them persist? http://cs273a.stanford.edu [Bejerano Aut08/09]

28. Broad Guess • It’s about 3-D structure. • Observation: rDNA (18S, 28S) have ultraconserved stretches,multiple constraints in a complex 3-D structure, the Ribosome. • ncRNA ultras: structure confers function • Splicing related ultras: the Splicosome • Cis-reg ultras: TSS 3-D proximity, chromatinand/or packed TFBS (Transcription factories?) TSS http://cs273a.stanford.edu [Bejerano Aut08/09]