Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics
- 11 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Genetics
- Vol. 53 (3), 367-378
- https://doi.org/10.1038/s41588-021-00784-4
Abstract
Nuclear compartmentalization of active and inactive chromatin is thought to occur through microphase separation mediated by interactions between loci of similar type. The nature and dynamics of these interactions are not known. We developed liquid chromatin Hi-C to map the stability of associations between loci. Before fixation and Hi-C, chromosomes are fragmented, which removes strong polymeric constraint, enabling detection of intrinsic locus–locus interaction stabilities. Compartmentalization is stable when fragments are larger than 10–25 kb. Fragmentation of chromatin into pieces smaller than 6 kb leads to gradual loss of genome organization. Lamin-associated domains are most stable, whereas interactions for speckle- and polycomb-associated loci are more dynamic. Cohesin-mediated loops dissolve after fragmentation. Liquid chromatin Hi-C provides a genome-wide view of chromosome interaction dynamics.Keywords
Funding Information
- Foundation for the National Institutes of Health (HG003143, DK107980, HG009446, CA193419, GM105847, GM123195, GM123195, HG009446, CA193419, GM105847)
- Howard Hughes Medical Institute
This publication has 72 references indexed in Scilit:
- Self-organization of domain structures by DNA-loop-extruding enzymesNucleic Acids Research, 2012
- Cohesin Mediates Chromatin Interactions That Regulate Mammalian β-globin ExpressionOnline Journal of Public Health Informatics, 2011
- Recognition and Specificity Determinants of the Human Cbx ChromodomainsJournal of Biological Chemistry, 2011
- Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeresProceedings of the National Academy of Sciences of the United States of America, 2010
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human GenomeScience, 2009
- My5C: web tools for chromosome conformation capture studiesNature Methods, 2009
- Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)Nature Genetics, 2006
- Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elementsGenome Research, 2006
- CTCF mediates long-range chromatin looping and local histone modification in the β-globin locusGenes & Development, 2006
- Live Imaging of Telomeres: yKu and Sir Proteins Define Redundant Telomere-Anchoring Pathways in YeastCurrent Biology, 2002