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MW  11:00-12:15 in Beckman B302Profs: Serafim Batzoglou, Gill BejeranoTAs: Cory McLean, Aaron Wenger

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Lecture 18

Guest TalksUltraconservation

The Projects

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human

mouserat

chimp

chicken

fugu

zfish

dog

tetra

opossum

cow

macaque

platypus

Comparative Genomics

t

*

what madeus human?

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PhenotypeGenotype

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human

mouserat

chimp

chicken

fugu

zfish

dog

tetra

opossum

cow

macaque

platypus

Comparative Genomics

t

How did some of ourrelatives go back?

*

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human

mouserat

chimp

chicken

fugu

zfish

dog

tetra

opossum

cow

macaque

platypus

Now at the Species Level

t

How did weleave the ocean?

*

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Conserved elements in the Human Genome

all human-mouse alignmentshuman-mouse ancestral repeats alignment

Difference: 5% of

Human Genome

[Mouse consortium, Nature 2002]

election

human-mouse ancestral repeats alignment

85%id on average

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Conserved elements in the Human Genome

all human-mouse alignmentshuman-mouse ancestral repeats alignment

Difference: 5% of

Human Genome

[Mouse consortium, Nature 2002]

election

human-mouse ancestral repeats alignment

85%id on average

UltraconservationUltraconservation

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Typical DNA Conservation levels

[Bejerano et al., Science 2004]

Conserved elements between human and mouse are on average 85% identical. [mouse consortium, 2002]

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Ultraconserved Elements

[Bejerano et al., Science 2004]

fish

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No known function requires this much conservation

CDS ncRNA TFBS

*****

seq.

?

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Discovery can be fun

(compared to 4 results day before our ScienceExpress paper)

31,800

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Predictions and Proofs I

Based on public domain genome wide data:

ultraconservedelements

one subsetcodes protein

larger subsetdoes not

generate testable hypotheses for function from existing knowledge (2004)

[Pennacchio et al., Nature, 2006]

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Predictions and Proofs II

Based on public domain genome wide data:

ultraconservedelements

one subsetcodes protein

larger subsetdoes not

generate testable hypotheses for function from existing knowledge (2004)

[Pennacchio et al., Nature, 2006]

post transcriptional modification

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[Ni et al., Genes & Dev 2007 ]

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.

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Model for Homeostatic Auto/Cross-regulation

[Ni et al., Genes & Dev 2007 ]

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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.

chimpA

humansA A G A

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Genomic Distribution of Ultraconserved Elements

•exonic•non•possibly

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UC.338 comes from an ancient repeat

novelcoelacanthrepeat

ultraconservedexon

enhancer

[Bejerano et al, Nature ,2006]

LF-SINE

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Touch an Ultra And You - DIY

[Ahituv et al., PLoS Biology, 2007]

4-8% of documented mouse KOgenes display no phenotype(inc. Pbx2, Nkx6.2, Gli1)

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Hypothesis

Can ultraconserved element mutationsbe under extreme purifying selectionbut the whole element be expendable?

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What did Mother Nature favor?

tDNA element

mouse

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Quite Some Time Later

The horror … The horror

…

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Ultras are Fiercely Retained

rodents deleted11/15157 = 0.072%

Ultras are>300 fold

more persistent

thanneutral DNA(25% deleted)

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Enough about us….

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What we do understand..Ultraconserved elements exist.They are maintained via strong on-going selection.It is a heterogeneous bunch:Some mediate splicingSome regulate gene expressionSome 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)

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What we don’t understand

Their functional density:How did they come to be?What is the selective advantage that lets them persist?

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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