Correlative live and super-resolution imaging reveals the dynamic structure of replication domains

Xiang, Wanqing; Roberti, M. Julia; Hèriché, Jean-Karim; Huet, Sebastian; Alexander, Stephanie; Ellenberg, Jan

doi:10.1101/189373

Cited by 19 publications

(30 citation statements)

References 44 publications

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“…At large genomic distances, the chromosome structures of S-state cells are distinctly different from cancer cell lines. Forest domains in S-stage cells are seen to highly spatially segregate, consistent to a clustering of the early-replicating domain (52,53). On the other hand, the long-range P domain aggregation is much weaker in S stage cells than in cancer cells.…”

Section: Conclusion and Discussionmentioning

confidence: 64%

Domain segregated 3D chromatin structure and segmented DNA methylation in carcinogenesis

Xue

Yang

Tian

et al. 2020

Preprint

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The three-dimensional (3D) chromatin structure, together with DNA methylation and other epigenetic marks, profoundly affects gene expression and displays abnormal behaviors in cancer cells. We elucidated the chromatin architecture remodeling in carcinogenesis from the perspective of spatial interactions between CGI forest and prairie domains, which are two types of megabase-sized domains defined by different sequence features but show distinct epigenetic and transcriptional patterns. DNA sequence strongly affects chromosome spatial interaction, DNA methylation and gene expression. Globally, forests and prairies show enhanced spatial segregation in cancer cells and such structural changes are accordant with the alteration of CGI interactions and domain boundary insulation, which could affect vital cancer-related properties. As the cancer progresses, a gradual increase of the DNA methylation difference between the two types of DNA domains is also observed for many different types of cancers. These observations are consistent with the change of transcriptional level differences of genes in these two domains, suggesting a highly-connected global structural, epigenetic and transcriptional activity changes in carcinogenesis.3 development and its relationship with chromosomal structural changes remain largely unknown.In principle, both chromosomal structure and epigenetic modifications can influence gene expression. Based on Hi-C contact map, the chromatin is divided into compartments A and B (2).Genes are enriched in compartment A and their expression levels are higher than those in compartment B. But there are many questions remain unanswered, e.g. what factors determine the compartment formation, what are the driving forces of compartment switch, and what are the roles of compartmentalization in cancer? Our previous study (25) showed that the compartment formation is strongly related to the genome composition. Based on the uneven distribution of CGIs, the whole genome was divided into two types of megabase-sized domains, CGI-rich domains (named as CGI forest domains) and CGI-poor domains (named as CGI prairie domains).These two types of domains, differing in sequence features, show distinct epigenetic and transcriptional patterns and overlap strongly with the compartments A and B, respectively. Furthermore, the cell-specific spatial contact and separation between these two types of domains are strongly coupled with various biological processes, such as early embryonic development (26), cell differentiation, and senescence (27). The main goal of this study is to understand the sequence dependence of various carcinogenesis marks and we found that forest and prairie behave significantly differently, including their distribution in compartments, CGI interactions, TAD formation, gene expression and epigenetic marks, especially DNA methylation, which is closely associated with development stage of cancer. The property difference between forest and prairie enlarges in cancer, consistent with their increased spatial separati...

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Section: Conclusion and Discussionmentioning

confidence: 64%

Domain segregated 3D chromatin structure and segmented DNA methylation in carcinogenesis

Xue

Yang

Tian

et al. 2020

Preprint

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“…These replication sites persist as stable chromatin units (replication domains, RDs) throughout interphase and during subsequent cell cycles [40–43] and were chosen in our study as reference structures for CDs (see Discussion). Replicating DNA was visualized by pulse replication labeling (RL), using an approach where fluorophore-conjugated dUTPs are incorporated by a short scratch of S-phase cells [42, 44]. RDs could then be visualized through the remaining and the next cell cycle without further detection steps.…”

Section: Resultsmentioning

confidence: 99%

Cohesin depleted cells rebuild functional nuclear compartments after endomitosis

Cremer

Brandstetter

Maiser

et al. 2019

Preprint

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43The human genome forms thousands of "contact domains", which are intervals of enhanced 44 contact frequency. Some, called "loop domains" are thought to form by cohesin-mediated loop 45 extrusion. Others, called "compartmental domains", form due to the segregation of active and 46 inactive chromatin into A and B compartments. Recently, Hi-C studies revealed that the 47 depletion of cohesin leads to the disappearance of all loop domains within a few hours, but 48 strengthens compartment structure. Here, we combine live cell microscopy, super-resolution 49 microscopy, Hi-C, and studies of replication timing to examine the longer-term consequences 50 of cohesin degradation in HCT-116 human colorectal carcinoma cells, tracking cells for up to 51 30 hours. Surprisingly, cohesin depleted cells proceed through an aberrant mitosis, yielding a 52 single postmitotic cell with a multilobulated nucleus. Hi-C reveals the continued disappearance 53 of loop domains, whereas A and B compartments are maintained. In line with Hi-C, microscopic 54 observations demonstrate the reconstitution of chromosome territories and chromatin 55 domains. An interchromatin channel system (IC) expands between chromatin domain clusters 56 and carries splicing speckles. The IC is lined by active chromatin enriched for RNA Pol II and 57 depleted in H3K27me3. Moreover, the cells exhibit typical early-, mid-, and late-DNA 58 replication timing patterns. Our observations indicate that the functional nuclear 59 compartmentalization can be maintained in cohesin depleted pre-and postmitotic cells.60 However, we find that replication foci -sites of active DNA synthesis -become physically 61 larger consistent with a model where cohesin dependent loop extrusion tends to compact 62 intervals of replicating chromatin, whereas their genomic boundaries are associated with 63 compartmentalization, and do not change.64 65 3 Abbreviations 66 3D FISH = 3D fluorescence in situ hybridization 67 3D SIM = 3D structured illumination microscopy 68 AID = auxin inducible degron 69 ANC / INC = active / inactive nuclear compartment 70 CT = chromosome territory 71 CD(C) = chromatin domain (cluster) 72 CTCF = CCCTC binding factor 73 DAPI = 4',6-diamidino-2-phenylindole 74 EdU = 5-Ethynyl-2'-deoxyuridine 75 Hi-C = chromosome conformation capturing combined with deep sequencing 76 IC = interchromatin compartment 77 MLN = multilobulated nucleus 78 NC = nucleosome cluster 79 PBS = phosphate buffered saline 80 PBST = phosphate buffered saline with 0.02% Tween 81 PR = perichromatin region 82 RD = replication domain 83 RL = replication labeling 84 TAD = topologically associating domain 85 86 109 strengthened, leading to the presence of compartment domains and even compartment loops110 (but no loop domains) in the treated cells [18]. Other studies, using different cell types and 111 approaches for cohesin elimination yielded similar results [19-21], (reviewed in [22]). 112Here, we study the longer-term consequences of cohesin depletion and its effects on 113 the higher order nuclear a...

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“…Notably, the nuclear landscape shown here must be viewed as a snapshot. Due to continuous local movements of chromatin domains, the shape of CDCs changes continuously. This scheme assumes that movements of TREs toward the CDC periphery allows in addition to the binding of transcription factors the binding of larger functional protein complexes for transcription and splicing formed and transported within the IC.…”

Section: Accessibility Of Tres By Tfs May Depend On the Active Or Silmentioning

confidence: 99%

Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences

Cremer

2019

Genes Chromosomes & Cancer

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Transcription regulatory elements (TREs) have been extensively studied on the biochemical level with respect to their interactions with transcription factors (TFs), other DNA segments, and larger protein complexes. In this review, we describe concepts and preliminary experimental evidence for positional changes of TREs within a dynamic, functional nuclear architecture. We suggest a multilayered shell‐like chromatin organization of chromatin domain clusters with increasing chromatin compaction levels from the periphery toward the interior with a decondensed transcriptionally active peripheral layer and compact repressed chromatin typically located in the interior. This model organization of nuclear architecture implies a differential accessibility of TFs to targets located in co‐aligned active and inactive nuclear compartments (ANC and INC). It is based on evidence that active, easily accessible chromatin (perichromatin region, PR) lines a network of channels (interchromatin compartment, IC) involved in nuclear import–export functions. The IC and PR constitute the ANC, whereas transcriptionally noncompetent chromatin with higher compactness is part of the likely less accessible INC. Preliminary experimental evidence shows an enrichment of active TREs in the ANC and of inactive TREs in the INC suggesting positional changes of TREs between the ANC and INC depending on changes in their functional state.

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Correlative live and super-resolution imaging reveals the dynamic structure of replication domains

Cited by 19 publications

References 44 publications

Domain segregated 3D chromatin structure and segmented DNA methylation in carcinogenesis

Domain segregated 3D chromatin structure and segmented DNA methylation in carcinogenesis

Cohesin depleted cells rebuild functional nuclear compartments after endomitosis

Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences

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