The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus

Cremer, Marion; Hübner, Barbara; Silahtaroglu, Asli N.; Hendzel, Michael J.; Lanctôt, Christian; Strickfaden, Hilmar; Cremer, Christoph

doi:10.1002/bies.201900132

Cited by 78 publications

(99 citation statements)

References 170 publications

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“…In line with current views of chromatin organization based on the formation of chromatin droplets with distinct chromatin states [60], a recent Hi-C based genome-wide model depicts contact domains and TADs as separated chromatin balls [83]. We have postulated that the IC may provide preferred routes for imported transcription factors to their target sites, for the intranuclear passage of regulatory RNAs to remote functional sites, and for export routes of mRNPs towards nuclear pores [25]. In order to test this hypothesis, it is necessary to explore the space-time compaction and accessibility of CDs.…”

Section: Discussionmentioning

confidence: 59%

“…However, as a method based on 3D DNA-DNA contact frequencies Hi-C lacks the power to identify the system of IC-channels and the lining PR. These features have been demonstrated consistently in many cell types and species with super-resolved microscopy [24, 25]. The relationship of compartments A and B identified by Hi-C with the co-aligned compartments described by the ANC-INC model has not yet been clarified.…”

Section: Discussionmentioning

confidence: 99%

“…Hallmarks of the ANC-INC model (reviewed in [23–25], see Introduction) were retained in cohesin depleted pre- and postmitotic cell nuclei. These hallmarks include the preservation of chromosome territories (CTs), chromatin domain clusters (CDCs) structurally organized by different compaction levels, an interchromatin (IC) channel system and the maintenance of an active compartment (ANC), represented by markers for transcriptional competence (here active RNA Pol II and splicing speckles) and a co-aligned inactive compartment (INC) with repressed chromatin (H3K27me3).…”

Section: Discussionmentioning

confidence: 99%

“…Estimates of DNA densities based on super-resolved microscopy of CDs in various human and mouse cell nuclei indicate a range in the order of 5 - 200 Mb/µm 3 (C. Cremer, unpublished data). These estimates argue for an exclusion of macromolecular complexes from the interior of CDs with higher compaction levels and thus favor models proposing that macromolecular complexes involved in transcription and other important nuclear functions act at the periphery of CDs [24, 25, 80, 82]. The implications of this model for the mobility of CDs and functional DNA targets have remained elusive.…”

Section: Discussionmentioning

confidence: 99%

“…With Hi-C we confirm both the continued disappearance of loop domains and the maintenance of A and B compartments in MLN. With super-resolved microscopy we demonstrate that nuclei of pre- and postmitotic cohesin depleted cells maintain principal structural features of the ANC-INC model (reviewed in [23–25]). According to this model, which has been supported by electron microscopy and 3D super-resolution fluorescence microscopic studies from various species and cell types, the global nuclear landscape is shaped by chromosome territories (CTs) built up from chromatin domains (CDs) and chromatin domain clusters (CDCs).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 59%

Section: Discussionmentioning

confidence: 99%