Ultraconserved Elements in the Human Genome Bejerano, G., et.al. Katie Allen & Megan Mosher

Ultraconserved Elements  Segments longer than 200 base pairs that are absolutely conserved, showing 100% identity with no insertions or deletions, between orthologous regions of the human, mouse, and rat genomes  481 such segments

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

Location of U.C.E.s  Generally located in genes involving RNA processing or near genes involved in the regulation of transcription or development  Widely distributed  Often found in clusters

 ~ 5% of the human genome is more conserved than would be expected based on neutral evolution since the split with rodents  These highly conserved segments contain a large number of non-coding elements  They exhibit almost no natural variation within the human population  The probability of finding one such element in 2.9 billion bases is less than under a neutral evolution model

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

 Nearly all of these ultraconserved elements have been under extreme negative selection for more than 300 million years  The low level of variation suggests that these elements are changing at a rate roughly 20 times slower than the average for the genome

Of the 481 Ultra Conserved Elements:  111 are exonic – overlap the mRNA of a known human protein coding gene  256 are non-exonic – show no evidence of transcription  114 are possibly exonic

Exonic Non-Exonic Exonic Non-Exonic  Randomly distributed around the genome  Specifically associated with RNA processing  Congregate in clusters near transcription factors and developmental genes  Regulate transcription at the DNA level  Often found in “gene deserts”

Genes that overlap with U.C.E.s  Type 1 – overlap with exonic u.c.e.s - show enrichment for RNA binding and regulation of splicing - show enrichment for RNA binding and regulation of splicing - abundant in RNA recognition motif - abundant in RNA recognition motif

 Type 2 – near non-exonic u.c.e.s - enriched for regulation of transcription and DNA binding - enriched for regulation of transcription and DNA binding * Genes that flank intergenic ultraconserved elements are enriched for developmental genes, suggests that many u.c.e.s may be distal enhancers of early developmental genes

PTPB2 (Type 1 Gene)  Mostly intronic u.c.e.  May form an RNA structure that participates in the regulation of splicing through interactions with the splicesome  When this u.c.e. was folded into a secondary structure its energy was lower than all but 1 of 10,000 randomized versions of this sequence

“Flip” and “Flop” Exons  Exonic ultraconserved elements  Exhibit RNA editing and alternative splicing  Regulates the editing of adenosine to inosine

 The longest 3 ultraconserved elements are 779, 720, and 731bp long  All lie in the last three introns in the POLA gene – the DNA polymerase alpha-catalytic subunit on X  May be associated with the ARX gene  A similar u.c.e. lies near the ARX homeobox gene – involved in CNS development, associated with epilepsy, mental retardation, and cerebral malformations

Evolution of Ultraconserved Elements

Only 5% of the orthologs of u.c.e.s could be partially traced back to C. intestinalis, Drosiphilia, and C. elegans  All overlapped with coding exons  17 of 24 were alternatively spliced in humans  No case where an intronic element in humans was coding in any other species, showing intron has a function other than protein coding

 In cases where it could be traced beyond vertebrates, the orthologous introns in the more distant species were either very small or non-existent  It is possible that processes that produced ultra conserved elements in vertebrates also existed in other species  i.e. yeast

Paralogous Sets  12 paralogous sets of genes were found in the u.c.e.s  All paralogs have a highly conserved match in the chicken  Shows that significant divergence between paralogs in each cluster must have occurred in the early part of their evolution

“Near-freezing”  Most u.c.e.s represent chordate innovations that evolved rapidly but then slowed down considerably, becoming “near-frozen”  A significant number of shorter elements are different in birds but conserved in mammals – suggested that evolution followed by “near-freezing” is ongoing

 The conservation among u.c.e.s must result from a highly negative selection rate, a highly reduced mutation rate, or a combination of both  The problem with maintenance selection is that it does not result in total conservation unless multiple functions are overlaid on the same DNA

 Reduced mutation seems like a novel reason because it means the existence of regions of a few hundred bases with a 20-fold mutation rate reduction  There is no evidence however for hypomutable or hyper-repaired regions

Conclusion  Ultraconserved elements are important for organism development and gene regulation  Ultraconserved elements evolved quickly and have become “near-frozen”  This evolution seems to be ongoing  Conservation seems to have arisen from increased negative selection or decreased mutation rate