Bridging-mediated compaction of mitotic chromosomes

Nucleus, Journal Year: 2025, Volume and Issue: 16(1)

Published: May 9, 2025

Within living cells, chromosome shapes undergo a striking morphological transition, from loose and uncondensed fibers during interphase to compacted cylindrical structures mitosis. ATP driven loop extrusion performed by specialized protein complex, condensin, has recently emerged as key driver of this transition. However, while mechanism can successfully recapitulate the compaction chromatids early stages mitosis, it cannot capture observed after prophase. Here we hypothesize that condensin bridging activity plays an additional important role, review evidence - obtained largely through molecular dynamics simulations that, in combination with extrusion, generate compact metaphase cylinders. Additionally, resulting model qualitatively explains unusual elastic properties mitotic chromosomes micromanipulation experiments provides insights into role condensins formation abnormal associated common fragile sites.

Language: Английский

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Structure and dynamics of nuclear A/B compartments and subcompartments

Current Opinion in Cell Biology, Journal Year: 2024, Volume and Issue: 90, P. 102406 - 102406

Published: July 30, 2024

Mammalian chromosomes form a hierarchical structure within the cell nucleus, from chromatin loops, megabase (Mb)-sized topologically associating domains (TADs) to larger-scale A/B compartments. The molecular basis of structures loops and TADs has been actively studied. However, A B compartments, which correspond early-replicating euchromatin late-replicating heterochromatin, respectively, are still relatively unexplored. In this review, we focus on discuss their close relationship DNA replication timing (RT), introduce recent findings features subcompartments revealed by detailed classification doing so, speculate structure, potential function, developmental dynamics compartments in mammalian cells.

Language: Английский

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Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 16, 2024

Abstract Identity-specific interphase chromosome conformation must be re-established each time a cell divides. To understand how folding is inherited, we developed an experimental approach that physically segregates mediators of G1 are intrinsic to mitotic chromosomes from cytoplasmic factors. Proteins essential for nuclear transport, RanGAP1 and Nup93, were degraded in pro-metaphase arrested DLD-1 cells prevent the establishment nucleo-cytoplasmic transport during exit isolate decondensing chromatin daughter cytoplasm. Using this approach, discover transient intermediate entirely driven by chromosome-intrinsic In addition conventional compartmental segregation, program leads prominent genome-scale microcompartmentalization mitotically bookmarked type-specific cis-regulatory elements. This microcompartment formed telophase subsequently modulated second factors inherited through cytoplasm G1. import-dependent includes cohesin involved transcription RNA processing. The combined inter-dependent action programs determines as mitosis.

Language: Английский

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DNA replication and polymer chain duplication reshape the genome in space and time

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 12, 2024

In eukaryotes, DNA replication constitutes a complex process whereby multiple origins are stochastically fired, and from which the machinery proceeds along chromosomes to achieve faithful synthesis of two identical copies genome during S-phase cell cycle. Experimental evidence show functional correlation between dynamics spatial organization inside nuclei, suggesting that replicating may impact chromosome folding. However, theoretical mechanistic bases such an hypothesis remain elusive. To address question, we propose quantitative, minimal framework integrates polymer chain by accounting explicitly for progression resulting formation sister chromatids. By systematically characterizing 3D structural consequences replication, possible interactions active machineries, transient loops potentially across temporal scales, level individual global chain. Comparison with available microscopy conformation capture data in yeast suggests replication-dependent loop extrusion be acting vivo , shape as loose bottle-brushes S-phase. Lastly, explore post-replication relative chromatids demonstrate emergence catenations intertwined structures, regulated density fired origins.

Language: Английский

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Entangling and disentangling mitotic chromosomes

Molecular Cell, Journal Year: 2024, Volume and Issue: 84(8), P. 1398 - 1400

Published: April 1, 2024

Language: Английский

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Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis

The Journal of Cell Biology, Journal Year: 2024, Volume and Issue: 224(3)

Published: Dec. 3, 2024

How cells establish the interphase genome organization after mitosis is incompletely understood. Using quantitative and super-resolution microscopy, we show that transition from a Condensin to Cohesin-based occurs dynamically over 2 h. While significant fraction of Condensins remains chromatin-bound until early G1, Cohesin-STAG1 its boundary factor CTCF are rapidly imported into daughter nuclei in telophase, immediately bind chromosomes as individual complexes, sufficient build first TAD structures. By contrast, more abundant Cohesin-STAG2 accumulates on only gradually later responsible for compaction inside structures, forms paired complexes upon completed nuclear import. Our time-resolved mapping mitotic loop extruders single reveals nested architecture formed by sequential action two seamlessly replaced less compact but conceptually similar hierarchically driven Cohesins.

Language: Английский

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Heat Shock Alters the distribution and In Vivo Interaction of Major Nuclear Structural Proteins, Lamin and DNA Topoisomerase II, with Nucleic Acids

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 29, 2024

ABSTRACT Lamins and topoisomerases have been studied as major karyoskeletal proteins since early 80-ties. Today, lamins are thought to be responsible not only for maintenance structural support of cell nuclei but also involved, directly or indirectly, in regulation chromatin structure, distribution, gene expression, splicing, transcription transport. Topoisomerases involved chromosomal scaffold functions topology DNA, play an important role transcription. They necessary mitosis. For studying topoisomerase II, Drosophila melanogaster model has used many years flies genome contains single coding B-type (lamin Dm) A-type C). Flies II (Top2). We previously reported that lamin Dm (Lam (Top2) bind vivo both DNA RNA the properties modulated by specific phosphorylation on particular sites. Here we report first part results project focused demonstration Top2 expression organization upon heat shock (HS) induction recovery (R). demonstrated significantly induced at least S25, which affects distribution. Lam were relocated changed including solubility. Both interact with each other indirectly binding was increased under HS. The relocation associated detected polyploid third instar larvae nuclei. In photocrosslinking IP (immunoprecipitation) studies indicated a significant increase nucleic acids HS induction. highest affinity showed soluble fraction while lowest insoluble (“nuclear matrix” fraction). All changes location returned “normal” after from shock. Based thi s data our preliminary interactome believe essential roles proper response fly cells participation rearrangement protein complexes, RNA, remodelling regulation.

Language: Английский

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Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 2, 2024

Abstract Lamina-associated domains (LADs) are megabase-sized genomic regions anchored to the nuclear lamina (NL). Factors controlling interactions of genome with NL have largely remained elusive. Here, we identified DNA topoisomerase 2 beta (TOP2B) as a regulator these interactions. TOP2B binds predominantly inter-LAD (iLAD) chromatin and its depletion results in partial loss partitioning between LADs iLADs, suggesting that activity might protect specific iLADs from interacting NL. affects LAD lamin B receptor (LBR) more than lamins. LBR phenocopies effects depletion, despite different positioning two proteins genome. This suggests complementary mechanism for organising at Indeed, co-depletion causes LAD/iLAD inversion, reflecting changes typical oncogene-induced senescence. We propose coordinated axis controlled by maintains interior. Highlights differ supercoiling state controls interior preferentially Similar impact on genome-NL Co-depletion recapitulates reshaping

Language: Английский

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Polymer Model Integrates Super-Resolution Imaging and Epigenomic Sequencing to Elucidate the Role of Epigenetic Reactions in Shaping 4D Chromatin Organization

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 12, 2024

Abstract Chromatin, with its complex spatial and temporal organization, plays a crucial role in regulating gene expression. Recent advancements super-resolution microscopy have revealed that nanoscale domains of heterochromatin (repressed segments) embedded within euchromatin (active background are fundamental units 3D chromatin organization. In tissue-resident cells, the size these varies microenvironment, particularly stiffness, organization is also influenced by pharmacological epigenetic drugs. However, mechanisms governing domain under various conditions their impact on expression remain unclear. To address this knowledge gap, we developed dynamic, next-generation sequencing informed copolymer model. Our model simulates spatiotemporal evolution chromatin, driven passive diffusion active reactions, which interconvert heterochromatin. By integrating chromatin-chromatin interaction energetics diffusion-reaction dynamics, predict formation heterochromatin-rich establish scaling relationship between modulation reaction rates. Additionally, our predicts compaction changes response to global rates occur predominantly at boundaries. We validated predictions via Hi-C contact map analysis imaging hyperacetylated melanoma cells. Subsequent RNA-seq suggested pivotal shifts influencing metastatic potential further mesoscale findings against rearrangement hMSCs, exhibit sensitivity microenvironmental stiffness. Finally, evaluated effects cycling silico, mimicking cellular transition different extracellular conditions, back again. This finding reveals cell-type invariant mechanism boundaries, whereby guides memory formation. show reorganization resulting from alterations drug exposure disease progression impacts both immediate responses long-term memory.

Language: Английский

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Multi-omic analyses reveal a differential contribution of chromatin-associated PP1 holoenzymes to mitotic exit and G1 re-establishment

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 30, 2024

Summary Mitotic exit is an important part of the cell cycle that requires coordination many chromatin and cytoskeleton remodelling events to successfully complete division maintain identity. Protein de-phosphorylation a key step in directing mitotic phosphatase (PP1) essential this process, however specific contribution its numerous targeting subunits still unknown. Here we have investigated function three chromatin-associated PP1 exiting mitosis Repo-Man, Ki-67 PNUTS. We generated endogenously tagged, auxin-degradable alleles for each subunit used multi-omic approach address their towards transcription resumption, accessibility protein phosphorylation at transition from G1. This has identified distinct role exit, provided unique datasets community, highlighted novel functions Repo-Man genome stability organisation.

Language: Английский

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