Nichols, M. H. | Search bioRxiv

bioRxiv2021

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

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, nearly 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.

genomics↗

bioRxiv2020

Principles of 3D Compartmentalization of the Human Genome

Chromatin is organized in the nucleus by CTCF loops and compartmental domains, the latter of which contain sequences bound by proteins capable of mediating interactions among themselves. While compartmental domains are one of the most prominent features of genome 3D organization at the chromosome scale, we lack a nuanced understanding of the different types of compartmental domains present in chromosomes and a mechanistic knowledge of the forces responsible for their formation. In this study, we compared different cell types to identify distinct paradigms of compartmental domain formation in human tissues. We identified and quantified compartmental forces correlated with histone modifications characteristic of transcriptional activity as well as previously underappreciated roles for compartmental domains correlated with the presence of H3K9me3, H3K27me3, or none of these histone modifications. We present a simple computer simulation model capable of predicting compartmental organization based on the biochemical characteristics of independent chromatin features. Using this computational model, we show that the underlying forces responsible for compartmental domain formation in human cells are conserved and that the diverse compartmentalization patterns seen across cells are due to differences in chromatin features. We extend these findings to Drosophila to suggest that the same fundamental forces are at work beyond humans. These results offer mechanistic insights into the fundamental forces driving the 3D organization of the genome.

bioinformatics↗