ArticleBMC genomics2020
Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 16 citations in OpenAlex.
- Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal.Briefings in bioinformatics · 2026Article
- Polymorphic 3D genome architecture mediated by transposable elements.bioRxiv : the preprint server for biology · 2026Article
- 3D Chromatin Architecture During Early Development: New Methods and New Findings.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Telomere interactions and structural variants in ALT cells revealed with TelSPRITE.bioRxiv : the preprint server for biology · 2024Article
- Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease.Epigenetics & chromatin · 2023Article
- Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.Nature methods · 2023Article
- Order and stochasticity in the folding of individual Drosophila genomes.Nature communications · 2021Article
- Evolving methodologies and concepts in 4D nucleome research.Current opinion in cell biology · 2020Review
- Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function.PeerJ · 2020Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundProximity ligation based techniques, like Hi-C, involve restriction digestion followed by ligation of formaldehyde cross-linked chromatin. Distinct chromatin states can impact the restriction digestion, and hence the visibility in the contact maps, of engaged loci. Yet, the extent and the potential impact of digestion bias remain obscure and under-appreciated in the literature.
resultsThrough analysis of 45 Hi-C datasets, lamina-associated domains (LADs), inactive X-chromosome in mammals, and polytene bands in fly, we first established that the DNA in condensed chromatin had lesser accessibility to restriction endonucleases used in Hi-C as compared to that in decondensed chromatin. The observed bias was independent of known systematic biases, was not appropriately corrected by existing computational methods, and needed an additional optimization step. We then repurposed this bias to identify novel condensed domains outside LADs, which were bordered by insulators and were dynamically associated with the polycomb mediated epigenetic and transcriptional states during development.
conclusionsOur observations suggest that the corrected one-dimensional read counts of existing Hi-C datasets can be reliably repurposed to study the gene-regulatory dynamics associated with chromatin condensation and decondensation, and that the existing Hi-C datasets should be interpreted with cautions.
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