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Related Experiment Videos

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.

David C King1, James Taylor, Ying Zhang

  • 1Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

Genome Research
|June 15, 2007
PubMed
Summary
This summary is machine-generated.

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Functional genomic regions, identified using comparative genomics, reveal diverse evolutionary histories. These findings highlight recent selection on specific regulatory elements, including a novel primate promoter.

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Identifying functional genomic regions is crucial for understanding gene regulation.
  • Interspecies comparisons are powerful tools for this identification, but require careful consideration of evolutionary constraints.

Purpose of the Study:

  • To investigate the evolutionary histories of putative transcriptional regulatory sequences.
  • To determine if comparative genomics tools can capture the diversity of these evolutionary patterns.
  • To identify potentially novel regulatory elements under recent selection.

Main Methods:

  • Utilized ENCODE experimental data to define sets of putative transcriptional regulatory sequences.
  • Applied comparative genomics tools across different phylogenetic depths.

Related Experiment Videos

  • Corrected for regional differences in neutral substitution rates.
  • Analyzed sequence alignability and associated gene functions across clades.

    • Main Results:

    • Putative transcriptional regulatory sequences exhibit a wide range of evolutionary histories, from deep conservation to lineage-specific elements.
    • Comparative genomics tools, with rate correction, can capture this diversity.
    • Associated genes are enriched for distinct functions.
    • Evidence for recent selection was found, including a primate-specific distal promoter.

    Conclusions:

    • The evolutionary span of regulatory sequences is diverse, necessitating comprehensive comparative genomics approaches.
    • Comparative genomics can reveal recent evolutionary events and novel regulatory elements.
    • A primate-specific distal promoter may indicate a novel regulatory mechanism.