Short tandem repeats delineate gene bodies across eukaryotes

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Short tandem repeats (STRs) are hypermutable DNA regions influencing gene expression.
• Transcription factors (TFs) can be affected by STRs near their binding sites.
• The genome-wide distribution of STR motif repetitiveness in eukaryotes remains largely unexplored.

Purpose of the Study:

• To investigate the distribution and characteristics of monomer and dimer STR motif repetitiveness in eukaryotic genomes.
• To explore the correlation between STR repetitiveness landscapes and gene function.
• To understand the relationship between STRs, TF binding sites, and gene evolution.

Main Methods:

• Analysis of 5.1 billion 10-bp windows upstream of translation starts and downstream of translation stops.
• Examination of 25 million genes across 1270 eukaryotic species.
• Identification of monomer and dimer STR motif repetitiveness.

Main Results:

• All surveyed eukaryotic genomes exhibit gene-proximal shifts in STR motif repetitiveness.
• Gene-proximal repetitiveness landscapes correlate with gene function; housekeeping genes are depleted in repetitiveness.
• Repetitiveness landscapes are linked to TF binding sites, suggesting co-evolution.

Conclusions:

• STR repetitiveness is not random but is canalized along eukaryotic genomes.
• STRs play a significant role in cis-regulatory evolution and contribute to regulatory and eco-evolutionary dynamics.
• The interplay between STRs and TFs shapes gene function and evolutionary trajectories across eukaryotes.