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Published on: March 13, 2011
Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model
Sterling M Sawaya1, Dustin Lennon, Emmanuel Buschiazzo
1Centre for Reproduction and Genomics, Department of Anatomy and Structural Biology, University of Otago, Dunedin, New Zealand.
Genome Biology and Evolution
|May 18, 2012
Summary
Conserved microsatellites, repetitive DNA sequences, are often found near gene start sites. Their conservation depends on sequence, length, and genomic position, particularly for regulatory genes involved in growth and development.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Microsatellites constitute approximately 3% of the human genome.
- Emerging evidence suggests functional roles and selective conservation of certain microsatellites.
Purpose of the Study:
- To conduct a genome-wide analysis of human microsatellite conservation across mammalian evolution.
- To investigate factors influencing microsatellite gain and loss rates.
- To develop a conservation scoring system for microsatellites.
Main Methods:
- Genome-wide analysis of human microsatellites.
- Application of a binary character birth-death model on a mammalian phylogeny.
- Maximum likelihood estimation of birth and death rates.
- Utilized a mixture model to account for variable microsatellite death rates.
- Assigned probability-based conservation scores.
Main Results:
- Microsatellite gain and loss rates are influenced by sequence composition, length, and genomic location.
- Microsatellites located near transcription start sites (TSS) exhibit high conservation.
- Proximity to the nearest TSS is a strong predictor of microsatellite conservation scores.
- Genes with nearby conserved microsatellites are enriched for regulatory functions in growth and development.
Conclusions:
- Microsatellite evolution is shaped by sequence and genomic context.
- Genomic location, especially proximity to gene TSS, is critical for microsatellite conservation.
- Conserved microsatellites are frequently associated with key regulatory genes involved in development.
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