Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.

ABSTRACT: Changes in cis-regulatory element composition that result in novel patterns of gene expression are thought to be a major contributor to the evolution of lineage-specific traits. Although transcription factor binding events show substantial variation across species, most computational approaches to study regulatory elements focus primarily upon highly conserved sites, and rely heavily upon multiple sequence alignments. However, sequence conservation based approaches have limited ability to detect lineage-specific elements that could contribute to species-specific traits. In this paper, we describe a novel framework that utilizes a birth-death model to trace the evolution of lineage-specific binding sites without relying on detailed base-by-base cross-species alignments. Our model was applie

SUBMITTER: Yokoyama KD 

PROVIDER: S-EPMC4140645 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature