Abstract
ABSTRACTUltraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.
Highlights
Ultraconserved noncoding elements (UCNEs) are an especially unusual feature of vertebrate genomes
We find that UCNEs have less than 6% CpG density and retain methylation states that are clearly heritable by clade, apparently persisting for millions of years
UCNEs are currently used in phylogenetic studies to determine deep phylogenetic relationships as well as classifying museum specimens [45,46]
Summary
Ultraconserved noncoding elements (UCNEs) are an especially unusual feature of vertebrate genomes. In 2004, Bejerano et al compared genomes of human, mouse, and rat, finding 481 regions longer than 200 nt sharing 100% sequence identity [2] In 2013, Dimitriva and Bucher used slightly relaxed criteria to identify elements >200 nt long with >95% identity between human and chicken, and isolated their orthologues in 18 vertebrate species, within intergenic regions or noncoding regions of DNA. These were termed ‘ultraconserved noncoding elements’ [3]. Their database, UCNEbase, lists 4351 UCNEs and features a consistent naming scheme to identify elements across the 18 disparate genomes, along with descriptive statistics of element distribution and synteny maps
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