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

2019 ◽  
Author(s):  
Kristin Abramo ◽  
Anne-Laure Valton ◽  
Sergey V. Venev ◽  
Hakan Ozadam ◽  
A. Nicole Fox ◽  
...  
Keyword(s):  
Mitotic Chromosome ◽  
Chromatin Binding ◽  
Folding Intermediate ◽  
Binding Assays ◽  
Interphase Chromosome ◽  
Chromosome Conformation ◽  
Topologically Associating Domains ◽  
Late Telophase ◽  
Nested Loop ◽  
Inactive Chromatin

SummaryChromosome 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.

scholarly journals Topology, structures, and energy landscapes of human chromosomes

2015 ◽  
Vol 112 (19) ◽  
pp. 6062-6067 ◽  
Author(s):  
Bin Zhang ◽  
Peter G. Wolynes
Keyword(s):  
Liquid Crystalline ◽  
Spatial Organization ◽  
Human Chromosomes ◽  
Energy Landscapes ◽  
Interphase Chromosome ◽  
Chromosome Conformation ◽  
Information Theoretic ◽  
Knot Invariants ◽  
Topologically Associating Domains ◽  
And Topology

Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward “ideal” chromosome structures that represent hierarchical fibrils of fibrils.

scholarly journals A major role for Eco1 in regulating cohesin-mediated mitotic chromosome folding

2019 ◽  
Author(s):  
Lise Dauban ◽  
Rémi Montagne ◽  
Agnès Thierry ◽  
Luciana Lazar-Stefanita ◽  
Olivier Gadal ◽  
...  
Keyword(s):  
Mitotic Chromosome ◽  
Dna Looping ◽  
Loop Formation ◽  
Dna Loops ◽  
Sister Chromatids ◽  
Topologically Associating Domains ◽  
Dna Loop ◽  
Main Barrier ◽  
Structural Maintenance Of Chromosomes ◽  
Mitotic Chromatin

AbstractUnderstanding how chromatin organizes spatially into chromatid and how sister chromatids are maintained together during mitosis is of fundamental importance in chromosome biology. Cohesin, a member of the Structural Maintenance of Chromosomes (SMC) complex family, holds sister chromatids together 1–3 and promotes long-range intra-chromatid DNA looping 4,5. These cohesin-mediated DNA loops are important for both higher-order mitotic chromatin compaction6,7 and, in some organisms, compartmentalization of chromosomes during interphase into topologically associating domains (TADs) 8,9. Our understanding of the mechanism(s) by which cohesin generates large DNA loops remains incomplete. It involves a combination of molecular partners and active expansion/extrusion of DNA loops. Here we dissect the roles on loop formation of three partners of the cohesin complex: Pds5 10, Wpl1 11 and Eco1 acetylase 12, during yeast mitosis. We identify a new function for Eco1 in negatively regulating cohesin translocase activity, which powers loop extrusion. In the absence of negative regulation, the main barrier to DNA loop expansion appears to be the centromere. Those results provide new insights on the mechanisms regulating cohesin dependent DNA looping.

scholarly journals Large-scale chromatin structure of inducible genes: transcription on a condensed, linear template

2009 ◽  
Vol 185 (1) ◽  
pp. 87-100 ◽  
Author(s):  
Yan Hu ◽  
Igor Kireev ◽  
Matt Plutz ◽  
Nazanin Ashourian ◽  
Andrew S. Belmont
Keyword(s):  
Chromatin Structure ◽  
Transcriptional Activation ◽  
Large Scale ◽  
Nuclear Speckles ◽  
Interphase Chromosome ◽  
Chromosome Conformation ◽  
Dynamic Events ◽  
Classical Models ◽  
Chromatin Fibers

The structure of interphase chromosomes, and in particular the changes in large-scale chromatin structure accompanying transcriptional activation, remain poorly characterized. Here we use light microscopy and in vivo immunogold labeling to directly visualize the interphase chromosome conformation of 1–2 Mbp chromatin domains formed by multi-copy BAC transgenes containing 130–220 kb of genomic DNA surrounding the DHFR, Hsp70, or MT gene loci. We demonstrate near-endogenous transcription levels in the context of large-scale chromatin fibers compacted nonuniformly well above the 30-nm chromatin fiber. An approximately 1.5–3-fold extension of these large-scale chromatin fibers accompanies transcriptional induction and active genes remain mobile. Heat shock–induced Hsp70 transgenes associate with the exterior of nuclear speckles, with Hsp70 transcripts accumulating within the speckle. Live-cell imaging reveals distinct dynamic events, with Hsp70 transgenes associating with adjacent speckles, nucleating new speckles, or moving to preexisting speckles. Our results call for reexamination of classical models of interphase chromosome organization.

scholarly journals Cohesin disrupts polycomb-dependent chromosome interactions

2019 ◽  
Author(s):  
JDP Rhodes ◽  
A Feldmann ◽  
B Hernández-Rodríguez ◽  
N Díaz ◽  
JM Brown ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Embryonic Stem ◽  
Cell Types ◽  
Gene Repression ◽  
Chromosome Conformation ◽  
Regulate Gene Expression ◽  
Topologically Associating Domains ◽  
Chromosome Organisation ◽  
Regulate Gene

AbstractHow chromosome organisation is related to genome function remains poorly understood. Cohesin, loop-extrusion, and CTCF have been proposed to create structures called topologically associating domains (TADs) to regulate gene expression. Here, we examine chromosome conformation in embryonic stem cells lacking cohesin and find as in other cell types that cohesin is required to create TADs and regulate A/B compartmentalisation. However, in the absence of cohesin we identify a series of long-range chromosomal interactions that persist. These correspond to regions of the genome occupied by the polycomb repressive system, depend on PRC1, and we discover that cohesin counteracts these interactions. This disruptive activity is independent of CTCF and TADs, and regulates gene repression by the polycomb system. Therefore, in contrast to the proposal that cohesin creates structure in chromosomes, we discover a new role for cohesin in disrupting polycomb-dependent chromosome interactions to regulate gene expression.

scholarly journals Nucleosome-constrained loop extrusion model for the origin of topologically associating domains

2020 ◽  
Author(s):  
Mary Lou P. Bailey ◽  
Ivan Surovtsev ◽  
Jessica F. Williams ◽  
Hao Yan ◽  
Simon G. J. Mochrie ◽  
...  
Keyword(s):  
Extrusion Direction ◽  
Boundary Elements ◽  
Experimental Measurements ◽  
Loop Formation ◽  
Chromosome Conformation ◽  
Nucleosome Remodeling ◽  
Naked Dna ◽  
Topologically Associating Domains

Chromosome conformation capture techniques (e.g Hi-C) reveal that intermediate-scale chromatin organization is comprised of “topologically associating domains” (TADs) on the tens to thousands of kb scale.1–5 The loop extrusion factor (LEF) model6–10 provides a framework for how TADs arise: cohesin or condensin extrude DNA loops, until they encounter boundary elements. Despite recent in vitro studies demonstrating that cohesin and condensin can drive loop formation on (largely) naked DNA11–13, evidence supporting the LEF model in living cells is lacking. Here, we combine experimental measurements of chromatin dynamics in vivo with simulations to further develop the LEF model. We show that the activity of the INO80 nucleosome remodeler enhances chromatin mobility, while cohesin and condensin restrain chromatin mobility. Motivated by these findings and the observations that cohesin is loaded preferentially at nucleosome-depleted transcriptional start sites14–18 and its efficient translocation requires nucleosome remodeling19–23 we propose a new LEF model in which LEF loading and loop extrusion direction depend on the underlying architecture of transcriptional units. Using solely genome annotation without imposing boundary elements, the model predicts TADs that reproduce experimental Hi-C data, including boundaries that are CTCF-poor. Furthermore, polymer simulations based on the model show that LEF-catalyzed loops reduce chromatin mobility, consistent with our experimental measurements. Overall, this work reveals new tenets for the origins of TADs in eukaryotes, driven by transcription-coupled nucleosome remodeling.

scholarly journals Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

2021 ◽  
Author(s):  
Abrar Aljahani ◽  
Peng Hua ◽  
Magdalena A. Karpinska ◽  
Kimberly Quililan ◽  
James O. J. Davies ◽  
...  
Keyword(s):  
Large Scale ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Interaction Data ◽  
Chromosome Conformation ◽  
Regulatory Interactions ◽  
Nano Scale ◽  
Topologically Associating Domains ◽  
Scale Structures ◽  
Local Insulation

Enhancers and promoters predominantly interact within large-scale topologically associating domains (TADs), which are formed by loop extrusion mediated by cohesin and CTCF. However, it is unclear whether complex chromatin structures exist at sub-kilobase-scale and to what extent fine-scale regulatory interactions depend on loop extrusion. To address these questions, we present an MNase-based chromosome conformation capture (3C) approach, which has enabled us to generate the most detailed local interaction data to date and precisely investigate the effects of cohesin and CTCF depletion on chromatin architecture. Our data reveal that cis-regulatory elements have distinct internal nano-scale structures, within which local insulation is dependent on CTCF, but which are independent of cohesin. In contrast, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.

scholarly journals Chromatin organization by an interplay of loop extrusion and compartmental segregation

2017 ◽  
Author(s):  
Johannes Nuebler ◽  
Geoffrey Fudenberg ◽  
Maxim Imakaev ◽  
Nezar Abdennur ◽  
Leonid Mirny
Keyword(s):  
Separation Process ◽  
Nuclear Volume ◽  
Chromatin Organization ◽  
Chromosome Organization ◽  
Topologically Associating Domains ◽  
Special Cases ◽  
Phase Separation Process ◽  
Chromosomal Territories ◽  
Active Mixing ◽  
Inactive Chromatin

AbstractMammalian chromatin is organized on length scales ranging from individual nucleosomes to chromosomal territories. At intermediate scales two dominant features emerge in interphase: (i) alternating regions (<5Mb) of active and inactive chromatin that spatially segregate into different compartments, and (ii) domains (<1Mb), i.e. regions that preferentially interact internally, which are also termed topologically associating domains (TADs) and are central to gene regulation. There is growing evidence that TADs are formed by active extrusion of chromatin loops by cohesin, whereas compartments are established by a phase separation process according to local chromatin states. Here we use polymer simulations to examine how the two processes, loop extrusion and compartmental segregation, work collectively and potentially interfere in shaping global chromosome organization. Our integrated model faithfully reproduces Hi-C data from previously puzzling experimental observations, where targeting of the TAD-forming machinery led to changes in compartmentalization. Specifically, depletion of chromatin-associated cohesin reduced TADs and revealed hidden, finer compartments, while increased processivity of cohesin led to stronger TADs and reduced compartmentalization, and depletion of the TAD boundary protein, CTCF, weakened TADs while leaving compartments unaffected. We reveal that these experimental perturbations are special cases of a general polymer phenomenon of active mixing by loop extrusion. This also predicts that interference with chromatin epigenetic states or nuclear volume would affect compartments but not TADs. Our results suggest that chromatin organization on the megabase scale emerges from competition of non-equilibrium active loop extrusion and epigenetically defined compartment structure.

scholarly journals CDK1-mediated phosphorylation at H2B serine 6 is required for mitotic chromosome segregation

2019 ◽  
Vol 218 (4) ◽  
pp. 1164-1181 ◽  
Author(s):  
Markus Seibert ◽  
Marcus Krüger ◽  
Nikolaus A. Watson ◽  
Onur Sen ◽  
John R. Daum ◽  
...  
Keyword(s):  
Chromosome Segregation ◽  
Chromosomal Instability ◽  
Mitotic Chromosome ◽  
Chromatin Modification ◽  
Genomic Stability ◽  
Cyclin B1 ◽  
Aurora B ◽  
Chromatin Binding ◽  
Histone H2b ◽  
Chromosome Separation

Faithful mitotic chromosome segregation is required for the maintenance of genomic stability. We discovered the phosphorylation of histone H2B at serine 6 (H2B S6ph) as a new chromatin modification site and found that this modification occurs during the early mitotic phases at inner centromeres and pericentromeric heterochromatin. This modification is directly mediated by cyclin B1–associated CDK1, and indirectly by Aurora B, and is antagonized by PP1-mediated dephosphorylation. H2B S6ph impairs chromatin binding of the histone chaperone SET (I2PP2A), which is important for mitotic fidelity. Injection of phosphorylation-specific H2B S6 antibodies in mitotic cells caused anaphase defects with impaired chromosome segregation and incomplete cytokinesis. As H2B S6ph is important for faithful chromosome separation, this modification may contribute to the prevention chromosomal instability and aneuploidy which frequently occur in cancer cells.

scholarly journals BHi-Cect: a top-down algorithm for identifying the multi-scale hierarchical structure of chromosomes

2020 ◽  
Vol 48 (5) ◽  
pp. e26-e26
Author(s):  
Vipin Kumar ◽  
Simon Leclerc ◽  
Yuichi Taniguchi
Keyword(s):  
Hierarchical Structure ◽  
Detection Methods ◽  
Interaction Patterns ◽  
Top Down ◽  
Chromosome Conformation ◽  
Multi Scale ◽  
Topologically Associating Domains ◽  
Genome Wide ◽  
The Hierarchical Structure ◽  
Respective Function

Abstract High-throughput chromosome conformation capture (Hi-C) technology enables the investigation of genome-wide interactions among chromosome loci. Current algorithms focus on topologically associating domains (TADs), that are contiguous clusters along the genome coordinate, to describe the hierarchical structure of chromosomes. However, high resolution Hi-C displays a variety of interaction patterns beyond what current TAD detection methods can capture. Here, we present BHi-Cect, a novel top-down algorithm that finds clusters by considering every locus with no assumption of genomic contiguity using spectral clustering. Our results reveal that the hierarchical structure of chromosome is organized as ‘enclaves’, which are complex interwoven clusters at both local and global scales. We show that the nesting of local clusters within global clusters characterizing enclaves, is associated with the epigenomic activity found on the underlying DNA. Furthermore, we show that the hierarchical nesting that links different enclaves integrates their respective function. BHi-Cect provides means to uncover the general principles guiding chromatin architecture.

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