TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

Abstract

Background Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing lead to the discovery of cohesin-independent TAD-like structures, also known as single-cell domains, which are highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Recent computational modeling studies suggest that epigenetic interactions may underlie the formation of the single-cell domains. Results Here we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components and transcription mostly do not affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains. Conclusions In sum, this study suggests that single-cell domains are genome architecture building blocks independent of the tested major epigenetic components.

Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations

“…2, G to I). The radius of gyration is a metric that approximates the radial size of the chromosome territory ( 27 ), thereby allowing us to compare the approximate volume of individual chromosome copies. We found that the Xi-like chromosomes are significantly larger than the Xa-like chromosomes in IMR90 primed iPSCs (Fig.…”

“…The XIST RNA FISH probes that we used were the same as published before ( 27 ). Briefly, 50 probes were designed to target the XIST transcript.…”

“…To avoid these aforementioned complications in transcriptomically assessing the naïve female X chromosome, we leveraged recently developed orthogonal methods in three-dimensional (3D) genomics and spatial biology (24)(25)(26)(27)(28)(29)(30)(31)(32). We performed chromatin tracing (25) in naïve and primed cells, targeting the center 100 kb region of 40 selected topologically associated domains (TADs) across the whole X chromosome.…”

Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment

“…This suggests that the chromosome with a highly compact global structure has a more continuous structural landscape compared to the more specific and discrete states of the open and active chromosome. ( S8A , S8B and S8C Fig ) [ 63 ].…”

AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization

“…Such close proximity suggested that they may constitute a single Topologically Associating Domain (TAD) [ 62 ]; however, as investigated via TAD Knowledge Base (TADKB), they are a part of two adjacent TADs ( Figure 8 C and Figure S2 ). Although DNA sequences of single TAD interact more frequently than those from neighboring domains [ 63 ], adjacent TADs were also found to partially overlap [ 64 ], which provides a snippet of information on how AP-2δ targets might be organized in the genome.…”