Considerations and caveats for analyzing chromatin compartments

Achyuth Kalluchi, Hannah L. Harris, Timothy E. Reznicek, M. Jordan Rowley

Research output: Contribution to journalReview articlepeer-review

3 Scopus citations


Genomes are organized into nuclear compartments, separating active from inactive chromatin. Chromatin compartments are readily visible in a large number of species by experiments that map chromatin conformation genome-wide. When analyzing these maps, a common step is the identification of genomic intervals that interact within A (active) and B (inactive) compartments. It has also become increasingly common to identify and analyze subcompartments. We review different strategies to identify A/B and subcompartment intervals, including a discussion of various machine-learning approaches to predict these features. We then discuss the strengths and limitations of current strategies and examine how these aspects of analysis may have impacted our understanding of chromatin compartments.

Original languageEnglish (US)
Article number1168562
JournalFrontiers in Molecular Biosciences
StatePublished - 2023


  • Hi-C
  • Micro-C
  • chromatin organization
  • compartments
  • eigenvector
  • subcompartment

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)


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