Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not

Abstract

Megabase-scale intervals of active, gene-rich and inactive, gene-poor chromatin are known to segregate, forming the A and B compartments. Fine mapping of the contents of these A and B compartments has been hitherto impossible, owing to the extraordinary sequencing depths required to distinguish between the long-range contact patterns of individual loci, and to the computational complexity of the associated calculations. Here, we generate the largest published in situ Hi-C map to date, spanning 33 billion contacts. We also develop a computational method, dubbed PCA of Sparse, Super Massive Matrices (POSSUMM), that is capable of efficiently calculating eigenvectors for sparse matrices with millions of rows and columns. Applying POSSUMM to our Hi-C dataset makes it possible to assign loci to the A and B compartment at 500 bp resolution. We find that loci frequently alternate between compartments as one moves along the contour of the genome, such that the median compartment interval is only 12.5 kb long. Contrary to the findings in coarse-resolution compartment profiles, we find that individual genes are not uniformly positioned in either the A compartment or the B compartment. Instead, essentially all (95%) active gene promoters localize in the A compartment, but the likelihood of localizing in the A compartment declines along the body of active genes, such that the transcriptional termini of long genes (>60 kb) tend to localize in the B compartment. Similarly, essentially all active enhancers elements (95%) localize in the A compartment, even when the flanking sequences are comprised entirely of inactive chromatin and localize in the B compartment. These results are consistent with a model in which DNA-bound regulatory complexes give rise to phase separation at the scale of individual DNA elements.

Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

“…Another approach is to brute-force genome-wide Hi-C or Micro-C; by performing 150 separate Hi-C experiments and sequencing deeper than ever before, a recent preprint by Gu et al reached 33 billion contacts 14 . However, such efforts 14 are not accessible to most labs and poorly compatible with perturbation experiments vital to uncovering mechanisms of organization. Instead, with RCMC we reach the local equivalent of 200 billion contacts with relatively modest sequencing (Fig.…”

Control of Chromatin Organization and Chromosome Behavior during the Cell Cycle through Phase Separation

“…Fine-mapping of nuclear compartments using ultra-deep Hi-C showed that active promoter and enhancer elements are localized in the active A compartment, whereas the flanking sequences are comprised entirely of inactive chromatin and are localized in the B compartment. These results suggest that the DNA-binding regulatory complexes undergo phase separation at the scale of individual DNA elements [16]. Phase separation also drives aberrant chromatin looping and cancer development [17].…”

Predicting A/B compartments from histone modifications using deep learning

“…For example, a study (Sefer, 2021) found that H3K4me1, H3K9me3, and H3K27ac are some of the histone marks that are significantly predictive of most Hi–C interactions in human ES cells. Another study (Gu et al, 2021), using the ultra-resolution Hi-C contact map in lymphoblastoid cell lines (LCLs), observed the correlation of low H3K4me1 and H3K36me3 signals with the presence of discordant compartmentalization. Therefore, by modeling the relationship of histone modifications with the A/B compartments, CoRNN can capture the relevance of these marks in highlighting the properties of genomic compartmentalization.…”

“…This also means that it is difficult to predict the compartmental status of loci that have a mixture of both active and repressive chromatin marks, such as bivalent enhancers. Indeed, it is likely that these types of regulatory elements form unique chromatin interaction patterns (Gu et al, 2021).…”