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

TITLE=Considerations and caveats for analyzing chromatin compartments

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=10

YEAR=2023

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2023.1168562

DOI=10.3389/fmolb.2023.1168562

ISSN=2296-889X

ABSTRACT=<p>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.</p>