Publication Date
6-6-2023
Journal
37280210
DOI
10.1038/s41467-023-38429-1
PMID
37280210
PMCID
PMC10244318
PubMedCentral® Posted Date
6-6-2023
PubMedCentral® Full Text Version
Post-print
Published Open-Access
yes
Keywords
Chromatin, CCCTC-Binding Factor, Enhancer Elements, Genetic, Cell Nucleus, Promoter Regions, Genetic, Nuclear organization, Epigenomics, Genome informatics, Gene regulation
Abstract
Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.