1. http://cs273a.stanford.edu [Bejerano Fall09/10] 1 Milestones due today. Anything to report?

2. http://cs273a.stanford.edu [Bejerano Fall09/10] 2 Lecture 17 Ultraconservation evolutionary data Finish early – come hear the talk with us?

3. http://cs273a.stanford.edu [Bejerano Fall09/10] 3 Sequence Conservation implies Function which (but which function/s?...) human mouse mammalian ancestor...CTTTGCGA-TGAGTAGCATCTACTATTT......ACGTGGGACTGACTA-CATCGACTACGA... functional region! Comparative Genomics of Distantly related species:

4. http://cs273a.stanford.edu [Bejerano Fall09/10] 4 Human Genome: 3*10 9 letters Human Genome full of Conserved Non-Coding Elements 1.5% known function >50% junk 3x more functional DNA than known! compare to other species >5% human genome functional ~10 6 substrings do not code for protein What do they do then?

5. http://cs273a.stanford.edu [Bejerano Fall09/10] 5 Conserved elements in the Human Genome all human-mouse alignments human-mouse ancestral repeats alignment Difference: 5% of Human Genome [Mouse consortium, Nature 2002] election human-mouse ancestral repeats alignment 85%id on average

6. http://cs273a.stanford.edu [Bejerano Fall09/10] 6 Conserved elements in the Human Genome all human-mouse alignments human-mouse ancestral repeats alignment Difference: 5% of Human Genome [Mouse consortium, Nature 2002] election human-mouse ancestral repeats alignment 85%id on average Ultraconservation Simple but Unexpected (the lure of Bioinormtaics)

7. http://cs273a.stanford.edu [Bejerano Fall09/10] 7 Typical DNA Conservation levels Conserved elements between human and mouse are on average 85% identical. [mouse consortium, 2002] (dot = base identical to human)

8. http://cs273a.stanford.edu [Bejerano Fall09/10] 8 Ultraconserved Elements [Bejerano et al., Science 2004] fish 481 elements perfectly conserved (100%id) over 200bp or more between human, mouse and rat.

9. http://cs273a.stanford.edu [Bejerano Fall09/10] 9 Ultraconserved Elements: Why? Hundreds of long substrings identical between amniotes  they must have rejected many different changes. But... all functions we understand in our genome are encoded using redundant codes. * * * * * CDSncRNATFBS seq.

10. http://cs273a.stanford.edu [Bejerano Fall09/10] 10 Ultras are Functional Back in 2004 we hypothesized: 481 ultraconserved elements exonic subset – post transcriptional regulation [Ni et al., Genes Dev.; Lareau et al., Nature, 2007] “nonexonic” subset – transcriptional regulators [Pennacchio et al., Nature, 2006]

11. http://cs273a.stanford.edu [Bejerano Fall09/10] 11 Genomic Distribution of Ultraconserved Elements exonic non possibly

12. http://cs273a.stanford.edu [Bejerano Fall09/10] 12 UC.338 comes from an ancient repeat novel coelacanth repeat ultraconserved exon enhancer [Bejerano et al, Nature,2006] LF-SINE

13. http://cs273a.stanford.edu [Bejerano Fall09/10] 13 Ultras are Under Strong Human Selection Ultra DAF NonSyn DAF [Katzman et al, Science,2007] Mutational cold spots? NO. Rare (new) mutations are introduced to the population. Fierce purifying selection? YES. Very few of these get anywhere near fixation. chimp A humans A A G A

14. http://cs273a.stanford.edu [Bejerano Fall09/10] 14 Touch an Ultra And You - DIY [Ahituv et al., PLoS Biology, 2007]

15. http://cs273a.stanford.edu [Bejerano Fall09/10] 15 What can’t we measure in the lab? N e is population size, s selective dis/advantage. Both of which are VERY wrong in the lab.

16. http://cs273a.stanford.edu [Bejerano Fall09/10] 16 So it can happen – but does it FIX? t DNA element mouse

17. http://cs273a.stanford.edu [Bejerano Fall09/10] 17 Count Fraction Lost, Binned by %id t human macaque dog mouse rat 100bp sliding window count_all count_hole bin by %id human dog rat mouse macaque

18. http://cs273a.stanford.edu [Bejerano Fall09/10] 18 Quite Some Time Later

19. http://cs273a.stanford.edu [Bejerano Fall09/10] 19 Pragmatic Genomics define goal run sensible approach while (results full of artefacts*) { characterize artefact write handler into code rerun } bio cs * eg: sequencing errors, assembly errors contaminating sequence, ambiguous situations, etc.

20. http://cs273a.stanford.edu [Bejerano Fall09/10] 20 Ultras are Fiercely Retained through Evolution Ultras are >300 fold more persistent than neutral DNA (25% deleted) genomic deletion the genomic deletion is 100%id primates-dog: 1,691,090bp rodents deleted: 1,447bp (0.086%)

21. http://cs273a.stanford.edu [Bejerano Fall09/10] 21 How special are the Ultras? election Ultraconservation

22. http://cs273a.stanford.edu [Bejerano Fall09/10] 22 Adding More Species Aha!!

23. http://cs273a.stanford.edu [Bejerano Fall09/10] 23 Adding More Species Few species More and more species Hmmm….

24. http://cs273a.stanford.edu [Bejerano Fall09/10] 24 Most Non-Coding Elements likely work in cis… 9Mb “IRX1 is a member of the Iroquois homeobox gene family. Members of this family appear to play multiple roles during pattern formation of vertebrate embryos.” gene deserts regulatory jungles

25. http://cs273a.stanford.edu [Bejerano Fall09/10] 25 … and Ultras are the tip of a functional iceberg 9Mb This dense regulatory jungle contain a single ultra gene deserts regulatory jungles