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Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution.

Noboru Jo Sakabe1, Marcelo A Nobrega

  • 1Department of Human Genetics, University of Chicago, , Chicago, IL 60637, USA.

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|November 13, 2013
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Summary

Evolutionary changes in gene expression are driven by alterations in transcription enhancers. Genome-wide chromatin immunoprecipitation (ChIP) reveals high divergence in these regulatory elements across species, impacting gene regulation.

Keywords:
enhancerevolutiongenomicstranscription

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Molecular biology

Background:

  • Complex gene expression patterns are frequently regulated by distal transcription enhancers.
  • Sequence changes in enhancers can alter gene expression, serving as a key evolutionary mechanism.
  • Genome-wide chromatin immunoprecipitation (ChIP) enables identification of protein-DNA interactions, pinpointing putative cis-regulatory elements.

Purpose of the Study:

  • To review studies utilizing genome-wide ChIP to investigate the evolution of transcription enhancers.
  • To compare protein-DNA binding maps for identifying regulatory differences and inferring gene expression changes across species.

Main Methods:

  • Review of existing studies employing genome-wide chromatin immunoprecipitation (ChIP).
  • Comparative analysis of protein-DNA binding maps across different species.
  • Identification of transcription factor binding events as potential cis-regulatory elements.

Main Results:

  • High divergence of cis-regulatory elements (enhancers) is observed between species.
  • Extensive creation and loss of regulatory elements, alongside rewiring of target genes, may compensate for this divergence.
  • Genome-wide ChIP facilitates the identification of regulatory differences and patterns of evolutionary change.

Conclusions:

  • Comparative genomics using ChIP reveals significant evolutionary divergence in enhancers.
  • The functional impact of identified binding event divergence on species-specific gene expression requires further investigation.
  • Future studies are needed to link biochemical protein-DNA interactions to biological function and evolutionary outcomes.