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

Abramo, Kristin; Valton, Anne‐Laure; Venev, Sergey V.; Özadam, Hakan; Fox, A. Nicole; Dekker, Job

doi:10.1101/678474

Cited by 22 publications

(34 citation statements)

References 61 publications

(40 reference statements)

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“…This is in agreement with single-cell Hi-C analysis in mouse embryonic stem cells, which showed that the B compartment (largely overlapping with LADs [4]) gradually moves towards a more radial positioning in early G1 [37]. Similarly, Hi-C in synchronized cells showed that chromatin compartments appear in telophase and gradually gain in strength [38,39].…”

Section: Cell Cycle Dynamics Of Genome -Nl Interactionssupporting

confidence: 89%

Cell cycle dynamics of lamina associated DNA

Schaik

Vos

Peric-Hupkes

et al. 2019

Preprint

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words)In mammalian interphase nuclei more than one thousand large genomic regions are positioned at the nuclear lamina (NL). These lamina associated domains (LADs) are involved in gene regulation and may provide a backbone for the overall folding of interphase chromosomes. While LADs have been characterized in great detail, little is known about their dynamics during interphase, in particular at the onset of G1 phase and during DNA replication. To study these dynamics, we developed an antibody-based variant of the DamID technology (named pA-DamID) that allows us to map and visualize genome -NL interactions with high temporal resolution. Application of pA-DamID combined with synchronization and cell sorting experiments reveals that LAD -NL contacts are generally rapidly established early in G1 phase. However, LADs on the distal ~25 Mb of most chromosomes tend to contact the NL first and then gradually detach, while centromere-proximal LADs accumulate gradually at the NL. Furthermore, our data indicate that S-phase chromatin shows transiently increased lamin interactions. These findings highlight a dynamic choreography of LAD -NL contacts during interphase progression, and illustrate the usefulness of pA-DamID to study the dynamics of genome compartmentalization.genome-wide mapping of NL interactions, DamID has been the major method [1,22]. DamID is based on expression of a fusion protein of Dam and a NL protein (e.g. Lamin B1), which results in gradual accumulation of adenine methylation ( m6 A) on DNA that contacts the NL [23]. This m6 A labeled DNA is then amplified and sequenced. An added advantage of DamID is that the m6 A tags can be detected by a GFP-labeled m6 A-Tracer protein [8]. This enables visualization of LAD -NL contacts in situ, which greatly assists in the interpretation of genome-wide DamID mapping data.However, a major limitation of DamID is its poor temporal resolution. The activation of Dam and deposition of m6 A requires at least several hours [8,24], precluding detailed analysis of the NL interaction dynamics. To overcome these limitations, we developed pA-DamID -a hybrid of DamID and the CUT&RUN method [25]. This allows for both mapping and visualization of NL contacts with high temporal resolution. Using pA-DamID, we show that after mitosis NL contacts do not initiate at defined loci, but rather are widespread with an enrichment at LADs on distal regions of chromosomes. Furthermore, small LADs appear to be gradually displaced from the NL by larger LADs. Additionally, we found that replicating DNA shows transiently increasing lamin contacts. Results Principle of pA-DamID to map and visualize NL associated DNAThe pA-DamID method is a hybrid of the CUT&RUN and DamID technologies (Fig. 1A). In CUT&RUN, cells are permeabilized and incubated with an antibody against a nuclear protein of interest, followed by protein A (pA) fused to micrococcal nuclease (MNase). Subsequent activation of the tethered MNase by Ca ++ ions results in excision of DNA sequences that are in molecular proximity to the pro...

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Section: Cell Cycle Dynamics Of Genome -Nl Interactionssupporting

confidence: 89%

Cell cycle dynamics of lamina associated DNA

Schaik

Vos

Peric-Hupkes

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…This is in agreement with single‐cell Hi‐C analysis in mouse embryonic stem cells, which showed that the B compartment (largely overlapping with LADs; van Steensel & Belmont, 2017) gradually moves toward a more radial positioning in early G1 (Nagano et al , 2017). Similarly, Hi‐C in synchronized cells showed that chromatin compartments appear in telophase and gradually gain in strength (Abramo et al , 2019; Zhang et al , 2019). Noteworthy, the self‐aggregation of LADs occurs before NL positioning (preprint: Luperchio et al , 2018), suggesting that the formation of the B compartment and NL positioning are correlated but still separate processes.…”

Section: Discussionmentioning

confidence: 93%

Cell cycle dynamics of lamina‐associated DNA

et al. 2020

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In mammalian interphase nuclei, more than one thousand large genomic regions are positioned at the nuclear lamina (NL). These lamina‐associated domains (LADs) are involved in gene regulation and may provide a backbone for the folding of interphase chromosomes. Little is known about the dynamics of LADs during interphase, in particular at the onset of G1 phase and during DNA replication. We developed an antibody‐based variant of the DamID technology (named pA‐DamID) that allows us to map and visualize genome–NL interactions with high temporal resolution. Application of pA‐DamID combined with synchronization and cell sorting experiments reveals that LAD–NL contacts are generally rapidly established early in G1 phase. However, LADs on the distal ~25 Mb of most chromosomes tend to contact the NL first and then gradually detach, while centromere‐proximal LADs accumulate gradually at the NL. Furthermore, our data indicate that S‐phase chromatin shows transiently increased lamin interactions. These findings highlight a dynamic choreography of LAD–NL contacts during interphase progression and illustrate the usefulness of pA‐DamID to study the dynamics of genome compartmentalization.

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“…Indeed, LE activity of cohesin in vivo accounts for the peaks and strikes observed in Hi‐C matrices, which are commonly translated as topological associated regions (TADs) in G1 cells (Fudenberg et al, 2016, Sanborn et al, 2015). Recent studies confirmed that cohesin‐mediated loops and the positions of TADs emerge quickly after telophase by producing contact patterns consistent with a LE process (Abramo et al, 2019; Zhang et al, 2019).…”

Section: Discussionmentioning

confidence: 84%

Condensin minimizes topoisomerase II‐mediated entanglements of DNA in vivo

et al. 2020

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The juxtaposition of intracellular DNA segments, together with the DNA-passage activity of topoisomerase II, leads to the formation of DNA knots and interlinks, which jeopardize chromatin structure and gene expression. Recent studies in budding yeast have shown that some mechanism minimizes the knotting probability of intracellular DNA. Here, we tested whether this is achieved via the intrinsic capacity of topoisomerase II for simplifying the equilibrium topology of DNA; or whether it is mediated by SMC (structural maintenance of chromosomes) protein complexes like condensin or cohesin, whose capacity to extrude DNA loops could enforce dissolution of DNA knots by topoisomerase II. We show that the low knotting probability of DNA does not depend on the simplification capacity of topoisomerase II nor on the activities of cohesin or Smc5/6 complexes. However, inactivation of condensin increases the occurrence of DNA knots throughout the cell cycle. These results suggest an in vivo role for the DNA loop extrusion activity of condensin and may explain why condensin disruption produces a variety of alterations in interphase chromatin, in addition to persistent sister chromatid interlinks in mitotic chromatin.

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

Cited by 22 publications

References 61 publications

Cell cycle dynamics of lamina associated DNA

Cell cycle dynamics of lamina associated DNA

Cell cycle dynamics of lamina‐associated DNA

Condensin minimizes topoisomerase II‐mediated entanglements of DNA in vivo

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