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

2. Lecture 18 Guest Talks Ultraconservation The Projects
[Bejerano Aut08/09]

3. Comparative Genomics what made us human? * t
mouse
rat
chimp
chicken
fugu
zfish
dog
tetra
opossum
cow
macaque
platypus *
While we may not agree about everything…
Incomplete list: also cat, armadillo, elephant, rabbit, shrew, tenrec, wallaby (2x)
Some not mammals, obviously, but useful outgroups in phylogenetic analysis of mammals t
[Bejerano Aut08/09]

4. Genotype Phenotype http://cs273a.stanford.edu [Bejerano Aut08/09]
With the vast genomic resources available nowadays, we can isolate both genotypic and phenotypic differences between species. However, a gap still exists in our ability to associate genotype with phenotype, and an overarching goal in biology today is to start bridging that gap, to be able to say:
This inversion causes foot shape alterations
This duplication and that substitution both play a role in brain size
Or going from phenotype to genotype,
This sweat-related gene has some change in chimpanzee relative to human
The study I am talking about today tries to link genotype to phenotype for a single type of genomic rearrangement, human-specific deletions.
Genotype
Phenotype 4
[Bejerano Aut08/09] 4

5. Comparative Genomics How did some of our relatives go back? * t
human
mouse
rat
chimp
chicken
fugu
zfish
dog
tetra
opossum
cow
macaque
platypus *
While we may not agree about everything…
Incomplete list: also cat, armadillo, elephant, rabbit, shrew, tenrec, wallaby (2x)
Some not mammals, obviously, but useful outgroups in phylogenetic analysis of mammals t
[Bejerano Aut08/09]

6. Now at the Species Level
How did we
leave the ocean?
human
mouse
rat
chimp
chicken
fugu
zfish
dog
tetra
opossum
cow
macaque
platypus *
While we may not agree about everything…
Incomplete list: also cat, armadillo, elephant, rabbit, shrew, tenrec, wallaby (2x)
Some not mammals, obviously, but useful outgroups in phylogenetic analysis of mammals t
[Bejerano Aut08/09]

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

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

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

10. Ultraconserved Elements
fish
[Bejerano Aut08/09]
[Bejerano et al., Science 2004]

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

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

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

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

16. Model for Homeostatic Auto/Cross-regulation
[Ni et al., Genes & Dev 2007 ]
[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
Ultra DAF
NonSyn DAF
[Katzman et al, Science ,2007]
[Bejerano Aut08/09]

18. Genomic Distribution of Ultraconserved Elements
exonic
non
possibly
Origins?
[Bejerano Aut08/09]

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

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

21. Hypothesis Can ultraconserved element mutations
be under extreme purifying selection
but the whole element be expendable?
[Bejerano Aut08/09]

22. What did Mother Nature favor?
DNA element t
mouse
[Bejerano Aut08/09]

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

25. Enough about us….
[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)
[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?
[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, chromatin and/or packed TFBS (Transcription factories?)
TSS
[Bejerano Aut08/09]