Ultraconserved Elements in Ultraconserved Elements in the Human Genomethe Human Genome

Bejerano, G., et.al.Bejerano, G., et.al.

Katie Allen & Megan MosherKatie Allen & Megan Mosher

Ultraconserved ElementsUltraconserved Elements

Segments longer than 200 base pairs Segments longer than 200 base pairs that are absolutely conserved, showing that are absolutely conserved, showing 100% identity with no insertions or 100% identity with no insertions or deletions, between orthologous regions deletions, between orthologous regions of the human, mouse, and rat genomesof the human, mouse, and rat genomes

481 such segments481 such segments

PurposePurpose

To determine the longest segments of To determine the longest segments of the human genome that are maximally the human genome that are maximally conserved (considered ultraconserved conserved (considered ultraconserved based on the prior definition) with based on the prior definition) with orthologous segments in rodentsorthologous segments in rodents

Location of U.C.E.sLocation of U.C.E.s

Generally located in genes involving RNA Generally located in genes involving RNA processing or near genes involved in the processing or near genes involved in the regulation of transcription or developmentregulation of transcription or development

Widely distributedWidely distributed Often found in clustersOften found in clusters

~ 5% of the human genome is more conserved ~ 5% of the human genome is more conserved than would be expected based on neutral than would be expected based on neutral evolution since the split with rodentsevolution since the split with rodents

These highly conserved segments contain a These highly conserved segments contain a large number of non-coding elementslarge number of non-coding elements

They exhibit almost no natural variation within They exhibit almost no natural variation within the human populationthe human population

The probability of finding one such element in The probability of finding one such element in 2.9 billion bases is less than 102.9 billion bases is less than 10-22 -22 under a under a neutral evolution modelneutral evolution model

Location of U.C.E.s on the GenesLocation of U.C.E.s on the Genes

Nearly all of these ultraconserved Nearly all of these ultraconserved elements have been under extreme elements have been under extreme negative selection for more than 300 negative selection for more than 300 million yearsmillion years

The low level of variation suggests that The low level of variation suggests that these elements are changing at a rate these elements are changing at a rate roughly 20 times slower than the average roughly 20 times slower than the average for the genomefor the genome

Of the 481 Ultra Conserved Elements:Of the 481 Ultra Conserved Elements:

111 are 111 are exonic exonic – overlap the mRNA of a – overlap the mRNA of a known human protein coding geneknown human protein coding gene

256 are 256 are non-exonicnon-exonic – show no evidence – show no evidence of transcriptionof transcription

114 are possibly exonic114 are possibly exonic

Exonic Non-ExonicExonic Non-Exonic

Randomly distributed Randomly distributed around the genomearound the genome

Specifically Specifically associated with RNA associated with RNA processingprocessing

Congregate in Congregate in clusters near clusters near transcription factors transcription factors and developmental and developmental genesgenes

Regulate Regulate transcription at the transcription at the DNA levelDNA level

Often found in “gene Often found in “gene deserts”deserts”

Genes that overlap with U.C.E.sGenes that overlap with U.C.E.s

Type 1 – overlap with exonic u.c.e.sType 1 – overlap with exonic u.c.e.s

- show enrichment for RNA - show enrichment for RNA binding and regulation of binding and regulation of splicing splicing

- abundant in RNA recognition - abundant in RNA recognition motif motif

Type 2 – near non-exonic u.c.e.sType 2 – near non-exonic u.c.e.s - enriched for regulation of - enriched for regulation of

transcription and DNA binding transcription and DNA binding

* Genes that flank intergenic * Genes that flank intergenic ultraconserved elements are enriched for ultraconserved elements are enriched for developmental genes, suggests that developmental genes, suggests that many u.c.e.s may be distal enhancers of many u.c.e.s may be distal enhancers of early developmental genes early developmental genes

PTPB2 (Type 1 Gene)PTPB2 (Type 1 Gene)

Mostly intronic u.c.e. Mostly intronic u.c.e. May form an RNA structure that May form an RNA structure that

participates in the regulation of splicing participates in the regulation of splicing through interactions with the splicesomethrough interactions with the splicesome

When this u.c.e. was folded into a When this u.c.e. was folded into a secondary structure its energy was lower secondary structure its energy was lower than all but 1 of 10,000 randomized than all but 1 of 10,000 randomized versions of this sequenceversions of this sequence

““Flip” and “Flop” ExonsFlip” and “Flop” Exons

Exonic ultraconserved elementsExonic ultraconserved elements Exhibit RNA editing and alternative Exhibit RNA editing and alternative

splicingsplicing Regulates the editing of adenosine to Regulates the editing of adenosine to

inosineinosine

The longest 3 ultraconserved elements The longest 3 ultraconserved elements are 779, 720, and 731bp longare 779, 720, and 731bp long

All lie in the last three introns in the All lie in the last three introns in the POLA gene – the DNA polymerase POLA gene – the DNA polymerase alpha-catalytic subunit on Xalpha-catalytic subunit on X

May be associated with the ARX geneMay be associated with the ARX gene A similar u.c.e. lies near the ARX A similar u.c.e. lies near the ARX

homeobox gene – involved in CNS homeobox gene – involved in CNS development, associated with epilepsy, development, associated with epilepsy, mental retardation, and cerebral mental retardation, and cerebral malformationsmalformations

Evolution of Ultraconserved Evolution of Ultraconserved ElementsElements

Only 5% of the orthologs of u.c.e.s could be Only 5% of the orthologs of u.c.e.s could be partially traced back to partially traced back to C. intestinalisC. intestinalis, , DrosiphiliaDrosiphilia, ,

and and C. elegansC. elegans

All overlapped with coding exonsAll overlapped with coding exons 17 of 24 were alternatively spliced in 17 of 24 were alternatively spliced in

humanshumans No case where an intronic element in No case where an intronic element in

humans was coding in any other species, humans was coding in any other species, showing intron has a function other than showing intron has a function other than protein codingprotein coding

In cases where it could be traced beyond In cases where it could be traced beyond vertebrates, the orthologous introns in vertebrates, the orthologous introns in the more distant species were either very the more distant species were either very small or non-existentsmall or non-existent

It is possible that processes that It is possible that processes that produced ultra conserved elements in produced ultra conserved elements in vertebrates also existed in other speciesvertebrates also existed in other species i.e. yeasti.e. yeast

Paralogous SetsParalogous Sets

12 paralogous sets of genes were found 12 paralogous sets of genes were found in the u.c.e.sin the u.c.e.s

All paralogs have a highly conserved All paralogs have a highly conserved match in the chickenmatch in the chicken

Shows that significant divergence Shows that significant divergence between paralogs in each cluster must between paralogs in each cluster must have occurred in the early part of their have occurred in the early part of their evolutionevolution

““Near-freezing”Near-freezing”

Most u.c.e.s represent chordate Most u.c.e.s represent chordate innovations that evolved rapidly but then innovations that evolved rapidly but then slowed down considerably, becoming slowed down considerably, becoming “near-frozen”“near-frozen”

A significant number of shorter elements A significant number of shorter elements are different in birds but conserved in are different in birds but conserved in mammals – suggested that evolution mammals – suggested that evolution followed by “near-freezing” is ongoingfollowed by “near-freezing” is ongoing

The conservation among u.c.e.s must The conservation among u.c.e.s must result from a highly negative selection result from a highly negative selection rate, a highly reduced mutation rate, or a rate, a highly reduced mutation rate, or a combination of bothcombination of both

The problem with maintenance selection The problem with maintenance selection is that it does not result in total is that it does not result in total conservation unless multiple functions conservation unless multiple functions are overlaid on the same DNAare overlaid on the same DNA

Reduced mutation seems like a novel Reduced mutation seems like a novel reason because it means the existence reason because it means the existence of regions of a few hundred bases with a of regions of a few hundred bases with a 20-fold mutation rate reduction20-fold mutation rate reduction

There is no evidence however for There is no evidence however for hypomutable or hyper-repaired regionshypomutable or hyper-repaired regions

ConclusionConclusion

Ultraconserved elements are important for Ultraconserved elements are important for organism development and gene regulationorganism development and gene regulation

Ultraconserved elements evolved quickly and Ultraconserved elements evolved quickly and have become “near-frozen”have become “near-frozen”

This evolution seems to be ongoingThis evolution seems to be ongoing Conservation seems to have arisen from Conservation seems to have arisen from

increased negative selection or decreased increased negative selection or decreased mutation ratemutation rate