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Related Experiment Videos

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

Shyam Prabhakar1, Francis Poulin, Malak Shoukry

  • 1Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. SPrabhakar@lbl.gov

Genome Research
|June 14, 2006
PubMed
Summary
This summary is machine-generated.

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Close species DNA comparisons are best for finding functional noncoding elements. More distant comparisons, like fish or birds, miss many important human regulatory elements.

Area of Science:

  • Comparative genomics
  • Evolutionary biology
  • Bioinformatics

Background:

  • Cross-species DNA sequence comparison is crucial for identifying functional noncoding elements in large genomes.
  • The impact of evolutionary distance on the effectiveness of these comparisons remains poorly understood.

Purpose of the Study:

  • To assess the relative merits of using evolutionarily close versus distant species comparisons for identifying functional noncoding elements.
  • To evaluate the predictive power of different evolutionary distances in identifying human regulatory elements.

Main Methods:

  • Utilized a uniform computational approach (Gumby) to identify evolutionarily conserved noncoding regions across various evolutionary distances (primate, mammalian, marsupial, avian, amphibian, fish).
  • Benchmarked predictions against known cis-regulatory elements and validated candidate enhancers using in vivo enhancer assays in transgenic mice.

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Main Results:

  • Comparisons with closely related species (eutherian mammals, simian primates) identified human regulatory elements with acceptable sensitivity (53%-80%) and true-positive rates (27%-67%).
  • More distant comparisons (marsupial, avian, amphibian, fish) significantly failed to detect many empirically validated functional noncoding elements.
  • Developed a model relating ancient and recent noncoding sequence conservation, explaining observed differences in predictive power.

Conclusions:

  • Close sequence comparisons offer practical utility and higher sensitivity for identifying functional noncoding elements.
  • Distant comparisons lead to a significant loss of sensitivity in detecting functional elements.
  • Genomic location and density of conserved elements are important factors, alongside conservation strength, for selecting candidate enhancers for in vivo testing.