1. http://cs273a.stanford.edu [Bejerano Fall10/11] 1 Any Project reflections?

2. http://cs273a.stanford.edu [Bejerano Fall10/11] 2 Lecture 16 Ultraconservation cont’d hCONDELs

3. http://cs273a.stanford.edu [Bejerano Fall10/11] 3 Ultraconservation as a Phenomenon Few species More and more species Hmmm…. We do not see a bump in the curve

4. Ultraconserved Elements: What we don’t What maintains so much conservation? http://cs273a.stanford.edu [Bejerano Fall10/11] 4 * * * * *

5. 5 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, chromatin and/or packed TFBS (Transcription factories?) TSS

6. http://cs273a.stanford.edu [Bejerano Fall10/11] 6 How special are the Ultras? election Ultraconservation

7. http://cs273a.stanford.edu [Bejerano Fall10/11] 7 Question “Average” conserved element (85%id to mouse) Ultraconserved element (100%id to mouse, rat) Both of these regions are clearly under purifying selection. Which one is more likely to be lost throughout evolution? [McLean & Bejerano, Genome Res., 2008] Is functional density (conservation %id) a good measure of dispensability (deletions)?

8. http://cs273a.stanford.edu [Bejerano Fall10/11] 88 Rodent-Dog Regions Lost in Primates Slope of best-fit line = 0.00006 Loss rate nearly constant regardless of conservation %id Similar loss rates for slowly-evolving non-exonic sequence and coding exons suggest functionality of non-exonic sequence Most all Non coding sequence under purifying selection clearly resists deletions.

9. http://cs273a.stanford.edu [Bejerano Fall10/11] 9 Deep orthology is a better predictor of persistence Rodent losses Primate losses If functional density doesn’t correlate with dispensability, what does?

10. http://cs273a.stanford.edu [Bejerano Fall10/11] 10 Genomic Distribution of Ultraconserved Elements exonic non possibly

11. http://cs273a.stanford.edu [Bejerano Fall10/11] 11 Outliers: Ultraconserved Element uc.338 uc.338 paralog family

12. http://cs273a.stanford.edu [Bejerano Fall10/11] 12 Coelacanth Homologs Closer than Human Ones [Bejerano et al., Nature, 2006]

13. http://cs273a.stanford.edu [Bejerano Fall10/11] 13 Uniquely Abundant in Coelacanth ? x Upto 80%id between Coelacanth instances and some human instances, inc uc.338. 100 diverged copies in a Gigabase 60 highly similar copies in a Megabase

14. http://cs273a.stanford.edu [Bejerano Fall10/11] 14 Cis-reg & Ultra elements from obile Elements [Yass is a small town in New South Wales, Australia.] Co-option event, probably due to favorable genomic context All other copies are destined to decay over time at a neutral rate [Bejerano et al., Nature 2006]

15. http://cs273a.stanford.edu [Bejerano Fall10/11] 15 The LF SINE (for Lobefin Fish / “Living Fossil”) Reconstruction out back target site duplications not similar to any known repeat [Bejerano et al., Nature 2006]

16. http://cs273a.stanford.edu [Bejerano Fall10/11] 16 Exapted Into Which Cellular Roles? ? x Human instances cluster together, found <1Mb from 35 TFs (P<3*10 -6 ). No evidence for Transcription (Tx) as small RNAs, no orientation preference in introns, not in antisense Tx.

17. http://cs273a.stanford.edu [Bejerano Fall10/11] 17 Repeat made Regulatory Region Reporter Gene Minimal Promoter Conserved Element in situ transgenic

18. http://cs273a.stanford.edu [Bejerano Fall10/11] 18 UC.338 comes from an ancient repeat novel coelacanth repeat ultraconserved exon enhancer [Bejerano et al, Nature,2006] LF-SINE

19. http://cs273a.stanford.edu [Bejerano Fall10/11] 19 A lot of conserved elements come from repeats conserved repetitive 50%5% 20%1.5% >100Mya highly conserved non-coding (think functional, regulatory) >100Mya mobile element instances [%age of H.G] 10,402 elements! 1Mb, avg len 100bp (But no other ultraconserved element to date) [Lowe, Bejerano &Haussler, PNAS,2007]

20. Ultraconserved Elements: What do we know? Excessive sequence conservation exists. Set is heterogeneous from a functional perspective. Four can be KO-ed with no clear phenotype. Yet, the set is under extreme selection in natural populations, both for mutations and deletions. Most ultras have deep orthology, and no paralogy. One ultra comes from a mobile element co-option events. Others may have come from similar events. Ultras appear the tip of a continuum, not a unique peak. http://cs273a.stanford.edu [Bejerano Fall10/11] 20

21. hCONDELs (pre-pub., slides omitted) http://cs273a.stanford.edu [Bejerano Fall10/11] 21