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Sequence-level mechanisms of human epigenome evolution.

James G D Prendergast1, Emily V Chambers2, Colin A M Semple3

  • 1The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom prenderj@gmail.com james.prendergast@roslin.ed.ac.uk.

Genome Biology and Evolution
|June 27, 2014
PubMed
Summary
This summary is machine-generated.

Human epigenome evolution is largely conserved after gene duplication, but regulatory regions diverge due to sequence changes. Alu elements significantly shaped this divergence, impacting DNA methylation and gene expression.

Keywords:
chromatinduplicationepigenomeevolutionmethylationparalogous

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Area of Science:

  • Genomics
  • Epigenetics
  • Evolutionary Biology

Background:

  • DNA methylation and chromatin states are crucial for development and disease.
  • Understanding human epigenome evolution and its drivers remains limited.

Purpose of the Study:

  • To investigate the relationship between genome sequence and human epigenome evolution.
  • To examine DNA methylation and chromatin state divergence after segmental duplication events.

Main Methods:

  • Comparative analysis of DNA methylation and chromatin states in paralogous regions within human samples.
  • Identification of sequence differences and their association with epigenome divergence.
  • Assessment of the role of Alu elements in shaping epigenome evolution.

Main Results:

  • Epigenome states were generally conserved post-duplication, largely independent of surrounding DNA sequence changes.
  • Tissue-specific regulatory regions showed higher divergence rates.
  • Sequence motif alterations, particularly from Alu elements, correlated with DNA methylation and chromatin state changes.
  • Human-specific AluY insertions linked to DNA methylation landscape and gene expression evolution, notably in neurological genes.

Conclusions:

  • Epigenome evolution is not strictly coupled with genome sequence evolution.
  • Alu elements are key drivers of human epigenome evolution, influencing methylation and gene expression.
  • Divergence in regulatory regions and specific motifs, especially Alu elements, significantly shapes the human epigenome.