Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

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.

Unveiling Alterations of Epigenetic Modifications and Chromatin Architecture Leading to Lipid Metabolic Reprogramming during the Evolutionary Trastuzumab Adaptation of HER2‐Positive Breast Cancer

“…Specifically, more B-type compartments transitioned into A-type compartments, coinciding with the enrichment of activated epigenetic marks such as H3K4me3 and H3K27ac, and the loss of inhibitory epigenetic marks like H3K27me3. These observations are consistent across various cellular processes, [98][99][100][101] highlighting the strong connections between epigenetic modifications and chromatin states, and their pivotal role in transcriptional regulation during trastuzumab adaptation.…”

HiCrayon reveals distinct layers of multi-state 3D chromatin organization

“…Therefore, punctate loops in mammals are typically enriched for CTCF and RAD21, a member of the cohesin complex [7,[33][34][35][36]. We also recently showed that CTCF loops are often comprised of fairly diffuse interactions when viewed at high resolution [5] (Figure 2A, left panel).…”

“…Using this high-resolution Hi-C map in lymphoblastoid cell lines (LCLs) [5], we colored contacts by HiCrayon to visualize the overlap between chromatin interactions and published ChIP-seq for CTCF (red) and RAD21 (blue). We found that HiCrayon at high resolution can help visualize the center of loop foci where an intense Hi-C signal coincides with CTCF and cohesin together (purple) (Figure 2A).…”

“…We then examined near diagonal interactions in the recently published highresolution Hi-C map of human lymphoblastoid cell lines (LCL), which showed that compartment intervals can be smaller than CTCF loops [5]. HiCrayon visualization of the 1 kb resolved compartment eigenvector, alongside CTCF and RAD21 ChIPseq, effectively demonstrates that small compartment intervals can be smaller than CTCF loops and can segregate loci inside the loop (Figure 6B).…”

“…comparisons of the plaid-like Hi-C compartment pattern with histone modification ChIP-seq tracks reveal the propensity for chromatin with active histone modifications to locate in the A compartment [1]. When viewed at fine scale, we recently showed that localization to the A compartment is a precise, fundamental characteristic of active enhancers and promoters [5]. Another well-known example is the overlap between 2D punctate loops and 1D CTCF ChIP-seq data, revealing the overwhelming presence of CTCF at these loop anchors [7].…”