ArticlePLoS computational biology2014
Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 28 citations in OpenAlex.
- Acute IL-6 exposure triggers canonical IL6Ra signaling in hiPSC microglia, but not neural progenitor cells.Brain, behavior, and immunity · 2023Article
- Transcription factor binding sites are frequently under accelerated evolution in primates.Nature communications · 2023Article
- Maternal immune activation primes deficiencies in adult hippocampal neurogenesis.Brain, behavior, and immunity · 2021Review
- Functional signatures of evolutionarily young CTCF binding sites.BMC biology · 2020Article
- The Role of Chromatin Accessibility in cis-Regulatory Evolution.Genome biology and evolution · 2019Article
- Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.Genome research · 2019Article
- Predicting CTCF-mediated chromatin loops using CTCF-MP.Bioinformatics (Oxford, England) · 2018Article
- Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus.Nature communications · 2017Article
- Evolution of Epigenetic Regulation in Vertebrate Genomes.Trends in genetics : TIG · 2016Review
- Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression.Molecular biology and evolution · 2016Article
- Article
- Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution.Nucleic acids research · 2015Article
- Populational landscape of INDELs affecting transcription factor-binding sites in humans.BMC genomics · 2015Article
- Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development.Nucleic acids research · 2015Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
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 applied to analyze the evolution of binding sites based on the ChIP-seq data for six transcription factors (GATA1, SOX2, CTCF, MYC, MAX, ETS1) along the lineage toward human after human-mouse common ancestor. We estimate that a substantial fraction of binding sites (∼58-79% for each factor) in humans have origins since the divergence with mouse. Over 15% of all binding sites are unique to hominids. Such elements are often enriched near genes associated with specific pathways, and harbor more common SNPs than older binding sites in the human genome. These results support the ability of our method to identify lineage-specific regulatory elements and help understand their roles in shaping variation in gene regulation across species.
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