ReviewFrontiers in molecular biosciences2023
Considerations and caveats for analyzing chromatin compartments.
Review in Frontiers in molecular biosciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed.
- Jointly-hic: joint decomposition of contact frequency maps captures salient features of genome architecture across tissues and development.Genome biology · 2026Article
- Kilobase-scale compartments enabled by CRUSH reveal regulatory programs across cell types, single-cells, and ancient mammoths.bioRxiv : the preprint server for biology · 2026Article
- esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.Genetics · 2026Article
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.bioRxiv : the preprint server for biology · 2025Article
- Unfolding neural diversity: how dynamic three-dimensional genome architecture regulates brain function and disease.Molecular psychiatry · 2025Review
- Rethinking chromatin accessibility: from compaction to dynamic interactions.Current opinion in genetics & development · 2025Review
- HiCrayon reveals distinct layers of multi-state 3D chromatin organization.NAR genomics and bioinformatics · 2024Article
- The chromatin tapestry as a framework for neurodevelopment.Genome research · 2024Review
- Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.Cell · 2024Article
- Mechanistic drivers of chromatin organization into compartments.Current opinion in genetics & development · 2024Review
- HiCrayon reveals distinct layers of multi-state 3D chromatin organization.bioRxiv : the preprint server for biology · 2024Article
- Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.Nature communications · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.