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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Increased substitution rates surrounding low-complexity regions within primate proteins.

Carolyn Lenz1, Wilfried Haerty, G Brian Golding

  • 1Department of Biology, McMaster University, Hamilton, Ontario, Canada.

Genome Biology and Evolution
|February 28, 2014
PubMed
Summary

DNA-flanking low-complexity regions (LCRs) increase DNA substitution rates in primates, including humans. This effect correlates with gene gaps and negative selection, diminishing with distance from LCRs.

Keywords:
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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Low-complexity regions (LCRs) are DNA sequences with repetitive patterns.
  • Previous research suggests LCRs are associated with elevated DNA substitution rates.
  • The impact of LCRs on genomic evolution requires further investigation across species.

Purpose of the Study:

  • To confirm and quantify the increased DNA substitution rate near LCRs in primate species.
  • To investigate the relationship between LCRs, gene alignment gaps, and substitution rates in human populations.
  • To analyze the selective pressures acting on sites near LCRs using dN/dS ratios.

Main Methods:

  • Comparative genomics analysis across multiple primate species.
  • Examination of human DNA sequences from the 1000 Genomes Project.
  • Calculation of average substitution rates and dN/dS ratios per site.
  • Correlation analysis between genomic features and distance from LCRs.

Main Results:

  • Confirmed increased substitution rates in the vicinity of LCRs in primates and humans.
  • Found a strong correlation between substitution rate, gene gaps, and distance from LCRs.
  • Demonstrated a negative relationship between distance from LCRs and the proportion of sites under negative selection.

Conclusions:

  • LCRs significantly influence DNA substitution rates and patterns of selection in primates.
  • The proximity to LCRs affects genomic stability and evolutionary dynamics.
  • Understanding LCRs is crucial for interpreting genetic variation and evolutionary history.