Experimental and computational framework for a dynamic protein atlas of human cell division

Yin, Chen; Hossain, M. Julius; Hèriché, Jean-Karim; Politi, Antonio Z.; Walther, Nike; Koch, Birgit; Wachsmuth, Malte; Nijmeijer, Bianca; Kueblbeck, Moritz; Kavur, Marina Martinić; Ladurner, René; Alexander, Stephanie; Peters, Jan‐Michael; Ellenberg, Jan

doi:10.1101/227751

Cited by 18 publications

(53 citation statements)

References 51 publications

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“…5e-f). The timing of chromatin association of cohesin and CTCF is consistent with earlier studies 20,31,32 and with more recent chromatin immunoprecipitation experiments that showed CTCF re-binding at CTCF sites during anaphase-telophase, followed rapidly by cohesin accumulation at those sites 32,40 .…”

Section: Condensin Unloading and Cohesin Loading Occurs During The Ansupporting

confidence: 90%

“…Previous studies have shown that condensin I loading, already high in metaphase, further increases during anaphase and then rapidly decreases, while condensin II colocalizes with chromatin throughout the cell cycle 30 . Cohesin, mostly dissociated from chromatin during prophase and prometaphase 20,21 , reassociates with chromosomes during telophase and cytokinesis, as does CTCF 20,31,32 .). However, it is not known how these events relate to modulation of chromosome conformation and whether distinct chromosome folding intermediates exist in the pathway towards a fully formed interphase nucleus.…”

Section: Introductionmentioning

confidence: 99%

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A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

Abramo

Valton

Venev

et al. 2019

Preprint

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Chromosome folding is extensively modulated as cells progress through the cell cycle. During mitosis, condensin complexes fold chromosomes in helically arranged nested loop arrays. In interphase, the cohesin complex generates loops that can be stalled at CTCF sites leading to positioned loops and topologically associating domains (TADs), while a separate process of compartmentalization drives the spatial segregation of active and inactive chromatin domains. We used synchronized cell cultures to determine how the mitotic chromosome conformation is transformed into the interphase state. Using Hi-C, chromatin binding assays, and immunofluorescence we show that by telophase condensin-mediated loops are lost and a transient folding intermediate devoid of most loops forms. By late telophase, cohesin-mediated CTCF-CTCF loops and positions of TADs start to emerge rapidly. Compartment boundaries are also established in telophase, but long-range compartmentalization is a slow process and proceeds for several hours after cells enter G1. Our results reveal the kinetics and order of events by which the interphase chromosome state is formed and identify telophase as a critical transition between condensin and cohesin driven chromosome folding.

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Section: Condensin Unloading and Cohesin Loading Occurs During The Ansupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

Abramo

Valton

Venev

et al. 2019

Preprint

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“…In other words, introduction of more SA1 can lead to the establishment of new loops within Mbp-sized domains. This more dominant role for SA1 in loop formation is also supported by the reported lag between SA1 and SA2 association to chromatin after mitosis recorded in HeLa cells, which would suggest that loop extrusion by SA1 might commence earlier (Cai et al 2018).…”

Section: Discussionsupporting

confidence: 52%

Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control

Casa¹,

Gines²,

Gusmao

et al. 2019

Preprint

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Cohesin is a ring-shaped multiprotein complex that is crucial for 3D genome organization and transcriptional regulation during differentiation and development. It also confers sister chromatid cohesion and facilitates DNA damage repair. Besides its core subunits SMC3, SMC1A and RAD21, cohesin contains in somatic cells one of two orthologous STAG subunits, SA1 or SA2. How these variable subunits affect the function of the cohesin complex is still unclear. SA1-and SA2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of SA1 and SA2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron (AID) tag fused to either SA1 or SA2. Following rapid depletion of either subunit, we perform high resolution Hi-C, RNA-sequencing and sequential ChIP studies to show that SA1 and SA2 do not co-occupy individual binding sites and have distinct ways how they affect looping and gene expression. These findings are supported at the single cell level by single-molecule localizations via dSTORM super-resolution imaging. Since somatic and congenital mutations of the SA subunits are associated with cancer (SA2) and intellectual disability syndromes with congenital abnormalities (SA1 and SA2), we verified SA1-/SA2-dependencies using human neural stem cells, hence highlighting their importance for understanding particular disease contexts.

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“…Epigenetic marks, such as histone variant H2A.Z and H3K4 methylation marks, are maintained at both CTCF sites and TSSs in mitosis. Previous studies found evidence for CTCF binding to mitotic chromosomes using imaging and chromatin fractionation approaches (Cai et al 2018;Liu et al 2017;Burke et al 2005).…”

Section: Discussionmentioning

confidence: 99%

CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning

Oomen

Hansen

Liu

et al. 2018

Preprint

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CTCF plays a key role in formation of topologically associating domains (TADs) and loops in interphase. During mitosis TADs are absent, but how TAD formation is dynamically controlled during the cell cycle is not known. Several contradicting observations have been made regarding CTCF binding to mitotic chromatin using both genomics and microscopy-based techniques. Here we have used 4 different assays to address this debate. First, using 5C we confirmed that TADs and CTCF loops are readily detected in interphase, but absent during prometaphase. Second, ATAC-seq analysis showed that CTCF sites display greatly reduced accessibility and lose the CTCF footprint in prometaphase, suggesting loss of CTCF binding and rearrangement of the nucleosomal array around the binding motif. In contrast, transcription start sites remain accessible in prometaphase, although adjacent nucleosomes can also become repositioned and occupy at least a subset of start sites during mitosis. Third, loss of site-specific CTCF binding was directly demonstrated using CUT&RUN. Histone modifications and histone variants are maintained in mitosis, suggesting a role in bookmarking of active CTCF sites. Finally, live-cell imaging, fluorescence recovery after photobleaching and single molecule tracking showed that almost all CTCF chromatin binding is lost in prometaphase. Combined, our results demonstrate loss of CTCF binding to CTCF sites during prometaphase and rearrangement of the chromatin landscape around CTCF motifs. This contributes to loss of TADs and CTCF loops during mitosis, and reveals that CTCF sites, a key architectural ciselement of the genome, display cell cycle stage-dependent dynamics in factor binding and nucleosome positioning.

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Experimental and computational framework for a dynamic protein atlas of human cell division

Cited by 18 publications

References 51 publications

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control

CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning

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