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Transcription factor binding sites are frequently under accelerated evolution in primates
Xinru Zhang1,2,3, Bohao Fang4, Yi-Fei Huang5,6
1Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. xmz5176@psu.edu.
Nature Communications
|February 11, 2023
Summary
More than 6000 transcription factor binding sites (TFBSs) show accelerated evolution in primates, exceeding human accelerated elements (HARs). This accelerated evolution in TFBSs near developmental genes may drive primate developmental divergence.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Comparative genomic studies have identified human accelerated elements (HARs) with high substitution rates in the human lineage.
- The extent of accelerated evolution in transcription factor binding sites (TFBSs) across primates remains largely unexplored.
Purpose of the Study:
- To investigate the accelerated evolution of TFBSs in humans and other primates.
- To develop sensitive phylogenetic methods for detecting accelerated evolution in TFBSs.
Main Methods:
- Introduction of two novel pooling-based phylogenetic methods with enhanced sensitivity.
- Application of these methods to analyze TFBSs across primate lineages (Hominini, apes, Old World monkeys).
Main Results:
- Over 6000 annotated human TFBSs exhibit accelerated evolution in Hominini, apes, and Old World monkeys.
- Collectively, accelerated TFBSs are more abundant than HARs, despite weaker individual signals.
- Accelerated evolution in Pol III binding sites may result from positive selection, while other TFBSs might be influenced by nonadaptive forces.
- Accelerated TFBSs are frequently located near developmental genes.
Conclusions:
- Accelerated evolution in TFBSs is a significant feature of primate evolution.
- Accelerated TFBSs near developmental genes suggest a role in primate developmental divergence.
- Distinct evolutionary forces may shape the evolution of different TFBS classes.
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