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  5. Biological Sciences
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  9. Epigenetics (incl. Genome Methylation And Epigenomics)
  11. Interspecies Regulatory Landscapes And Elements Revealed By Novel Joint Systematic Integration Of Human And Mouse Blood Cell Epigenomes

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Guanjue Xiang1,2,3, Xi He1, Belinda M Giardine4

  • 1Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

Genome Research
|July 1, 2024

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View abstract on PubMed

Summary
This summary is machine-generated.

This study created comparable regulatory maps of cis-regulatory elements (CREs) in human and mouse blood cells. These maps reveal conserved and species-specific gene regulation patterns, aiding complex trait research.

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Area of Science:

  • Genomics
  • Epigenetics
  • Comparative Biology

Background:

  • Understanding cis-regulatory elements (CREs) is crucial for gene regulation and complex trait genetics.
  • Previous species-specific studies limited cross-species comparisons of CREs.
  • Epigenetic features are key indicators for identifying functional regulatory elements.

Purpose of the Study:

  • To develop interspecies-comparable regulatory maps of CREs in blood cells.
  • To identify conserved and divergent patterns of CREs between human and mouse.
  • To provide a resource for studying gene regulation and genetic variant impact.

Main Methods:

  • Integrative modeling of eight epigenetic features in human and mouse blood cells.
  • Identification and cataloging of candidate CREs (cCREs) using the Validated Systematic Integration (VISION) Project.
  • Estimation of epigenetic state regulatory potential (esRP) scores and joint clustering of cCREs.

Main Results:

  • Generated comparable catalogs of cCREs across human and mouse blood cell types.
  • Discovered conserved and species-specific transcription factor binding motifs in cCREs.
  • Demonstrated that epigenetic landscape comparisons can identify functionally similar regulatory elements without sequence alignment.

Conclusions:

  • The VISION Project provides valuable resources for interspecies gene regulation studies.
  • Epigenetic comparisons reveal evolutionary patterns of CREs.
  • This approach facilitates the identification of regulatory elements with conserved functions across species.