Ultraconserved Elements in the Human Genome

Gill Bejerano, Michael Pheasant, Igor Makunin, Stuart Stephen, W. James Kent, John S.

Mattick, David HausslerScience Vol.304 28 May 2004

Presented By Victor Jensen

Overview

• Definition of an ultraconserved element

• Diversity of the elements

• Where are the elements

• Possible function

• Origins

• Summary

Definition of an Ultraconserved Element

• Segment of DNA with 100% sequence identity across species (mouse, rat & human)

• Orthologous location

• At least 200 bp

• Not rRNA

What they found

• Total of 481 sequences • Up to 779 bp• >5000 if you look at sequences >100bp

Diversity Across Species

Hum

an

Rat

Mouse

Chic

ken

Fugu

Dog

481 481 481

29

438

324

477

0

100

200

300

400

500

67%

95%

99.20%

100%

Diversity Within Species

• Ultraconserved elements have a total of 106,767 bases

• Only 6 bases have confirmed SNPs (dbSNP)

• Expect 119 based on neutral evolution

6 observed

119 expected SNPs

106,767 bases

Diversity Within Species

• With only 6 SNPs within these elements they show very low diversity

• This represents 20 times lower SNP density and rate of change compared to the rest of the genome

•Very similar in chimpanzees, 38 SNPs found where 716 are expected

There Must be Selection

• Random chance for one of these elements to occur is less than 10-22

• This is more conservation than most (if not all) proteins

• Evidence for very strong selection

So, why are these so important and where are they located??

Location of Elements

• Elements are everywhere!!

Location of Elements

Non-Exonic, 256

Exonic, 111

Possibly Exonic, 114

0

50

100

150

200

250

300

Elements

Non-Exonic elements

• Found in clusters

• 140 are >10 kb away from a gene (88 are >100kb away)

• Others lie in introns• Areas around elements are enriched for

developmental genes and transcription factors

Exonic

• Randomly distributed• Enriched for RNA processing proteins• Shows some correlation with RNA recognition

motif often associated with alternative splicing

Location of Elements

•Overview of GO term abundance vs. expected

Exonic, or Type 1

Non-exonic, or Type 2

Groups of Elements

• Some elements are paralogous• Significant divergence between paralogs• Surrounding genes are orthologous

Possible Function

• Conservation of important biological processes– Transcriptional element (cis-regulatory

elements)– RNA processing machinery (spliceosome)– Developmental regulation

Transcriptional Regulation

• cis-regulatory elements are often conserved between species

• Below is the 10kb upstream of PolA

RNA Processing

• Elements could represent RNA processing enzyme binding sites

• Alternative splicing

RNA Structure

• Hypothesized that RNA structure may play a role in function

• Many ultraconserved elements would have an RNA structure

• Splicing recognition?

Development

• Defects in developmental genes/gene regulation is often lethal

• Correlation of ultraconserved elements and developmental genes implies relationship

Elemental Origins

• Looked for elements in other sequenced genomes– C. elegans– D. melanogaster– C. intestinalis

Elemental Origins

• Found 24 of 481 elements

• All were exonic• 17 show alternative

spliced

Elemental Origins

• Elements have undergone a “freezing” of DNA code after chordate evolution

• Most are older than 300 million years

How are they conserved?

• Evolution of high negative selection

• Or

• Evolution of hypomutable regions

• Or a little of both

High Negative Selection

• Must have an important function

• Sensitive to minor changes

• RNA structure is very sensitive to changes

Hypomutable Regions

• Unlikely to be “hypomutable”

• Possibly “hyperrepaired”

Summary

• 481 ultraconserved elements >200bp• Exonic found with RNA processing genes• Non-exonic found with transcription factors

and developmental genes• 20x less change than expected• Connection to alternative splicing and

RNA structure• Low diversity

Questions

• Could some of these be RNA genes?

• Did they look for related elements not found in the same location in mice?

• What happens if there is a mutation in one of these elements?

• ???