http://cs273a.stanford.edu [Bejerano Fall09/10] 1

Milestones due today.

Anything to report?

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Lecture 17

Ultraconservation evolutionary data

Finish early – come hear the talk with us?

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Sequence Conservation implies Function

(but whichwhich function/s?...)

human

mouse

mammalianancestor

...CTTTGCGA-TGAGTAGCATCTACTATTT...

...ACGTGGGACTGACTA-CATCGACTACGA...

functional region!

Comparative Genomics of Distantly related species:

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HumanGenome:

3*109 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

~106 substrings do not code for protein

What do they do then?

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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

http://cs273a.stanford.edu [Bejerano Fall09/10] 6

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

Simple

but

Unexpected

(the lure of Bioinormtaics)

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Typical DNA Conservation levels

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

(dot = base identical to human)

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Ultraconserved Elements

[Bejerano et al., Science 2004]

fish

481 elements perfectly conserved (100%id) over

200bp or more between human, mouse and rat.

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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.

**

*

**

CDS ncRNA TFBS

seq.

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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]

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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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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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Touch an Ultra And You - DIY

[Ahituv et al., PLoS Biology, 2007]

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What can’t we measure in the lab?

sN

s

e ee

esN 21

1),|fixationPr(

Ne is population size, s selective dis/advantage.Both of which are VERY wrong in the lab.

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So it can happen – but does it FIX?

tDNA element

mouse

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Count Fraction Lost, Binned by %id

t human

macaque

dog

mouse

rat

100bp

sliding

window

count_all

count_hole

bin

by

%id

humandog rat mouse

macaque

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Quite Some Time Later

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Pragmatic Genomics

define goalrun sensible approachwhile (results full of artefacts*){ characterize artefact write handler into code rerun}

bio

bio

cs

cs

* eg: sequencing errors, assembly errors

contaminating sequence, ambiguous situations, etc.

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Ultras are Fiercely Retained through Evolution

Ultras are

>300 fold

more

persistent

than

neutral DNA(25% deleted)

the genomic deletiongenomic deletion is

100%id primates-dog: 1,691,090bp

rodents deleted: 1,447bp (0.086%)

sN

s

e ee

esN 21

1),|fixationPr(

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How special are the Ultras?

election

UltraconservationUltraconservation

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Adding More Species

Aha!!

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Adding More Species

Few species More and more species

Hmmm….

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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

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… and Ultras are the tip of a functional iceberg

9Mb

This dense regulatory jungle contain a single ultra

gene deserts

regulatory jungles