Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases.

ABSTRACT: The first microRNAs (miRNAs) were identified as essential, conserved regulators of gene expression, targeting the same genes across nearly all bilaterians. However, there are also prominent examples of conserved miRNAs whose functions appear to have shifted dramatically, sometimes over very brief periods of evolutionary time. To determine whether the functions of conserved miRNAs are stable or dynamic over evolutionary time scales, we have here defined the neutral turnover rates of short sequence motifs in predicted primate 3'-UTRs. We find that commonly used approaches to quantify motif turnover rates, which use a presence/absence scoring in extant lineages to infer ancestral states, are inherently biased to infer the accumulation of new motifs, leading to the false inference of continual

SUBMITTER: Simkin AT 

PROVIDER: S-EPMC4069616 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature