scholarly journals Computational and experimental analyses of mitotic chromosome formation pathways in fission yeast

2020 ◽  
Author(s):  
Tereza Gerguri ◽  
Xiao Fu ◽  
Yasutaka Kakui ◽  
Bhavin S. Khatri ◽  
Christopher Barrington ◽  
...  
Keyword(s):  
Mitotic Chromosome ◽  
Probability Distributions ◽  
Mitotic Chromosomes ◽  
Stochastic Optical Reconstruction Microscopy ◽  
Chromosome Formation ◽  
Optical Reconstruction ◽  
Chromosome I ◽  
Chromatin Density ◽  
Chromosome Axis ◽  
Structural Maintenance Of Chromosomes

AbstractUnderlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (loop extrusion), or that they sequentially entrap two DNAs that come into proximity by Brownian motion (diffusion capture). To explore the implications of these two mechanisms, we perform biophysical simulations of a 3.76 Mb-long chromatin chain, the size of the long S. pombe chromosome I left arm. On it, the SMC complex condensin is modeled to perform loop extrusion or diffusion capture. We then compare computational to experimental observations of mitotic chromosome formation. Both loop extrusion and diffusion capture can result in native-like contact probability distributions. In addition, the diffusion capture model more readily recapitulates mitotic chromosome axis shortening and chromatin density enrichment. Diffusion capture can also explain why mitotic chromatin shows reduced, as well as more anisotropic, movements, features that lack support from loop extrusion. The condensin distribution within mitotic chromosomes, visualized by stochastic optical reconstruction microscopy (STORM), shows clustering predicted from diffusion capture. Our results inform the evaluation of current models of mitotic chromosome formation.

scholarly journals Molecular organization of mammalian meiotic chromosome axis revealed by expansion STORM microscopy

2019 ◽  
Vol 116 (37) ◽  
pp. 18423-18428 ◽  
Author(s):  
Huizhong Xu ◽  
Zhisong Tong ◽  
Qing Ye ◽  
Tengqian Sun ◽  
Zhenmin Hong ◽  
...  
Keyword(s):  
Meiotic Chromosome ◽  
Molecular Organization ◽  
Homologous Chromosomes ◽  
Meiotic Chromosomes ◽  
C Terminus ◽  
Stochastic Optical Reconstruction Microscopy ◽  
Optical Reconstruction ◽  
20 Nm ◽  
Chromosome Axis

During prophase I of meiosis, chromosomes become organized as loop arrays around the proteinaceous chromosome axis. As homologous chromosomes physically pair and recombine, the chromosome axis is integrated into the tripartite synaptonemal complex (SC) as this structure’s lateral elements (LEs). While the components of the mammalian chromosome axis/LE—including meiosis-specific cohesin complexes, the axial element proteins SYCP3 and SYCP2, and the HORMA domain proteins HORMAD1 and HORMAD2—are known, the molecular organization of these components within the axis is poorly understood. Here, using expansion microscopy coupled with 2-color stochastic optical reconstruction microscopy (STORM) imaging (ExSTORM), we address these issues in mouse spermatocytes at a resolution of 10 to 20 nm. Our data show that SYCP3 and the SYCP2 C terminus, which are known to form filaments in vitro, form a compact core around which cohesin complexes, HORMADs, and the N terminus of SYCP2 are arrayed. Overall, our study provides a detailed structural view of the meiotic chromosome axis, a key organizational and regulatory component of meiotic chromosomes.

scholarly journals Contribution of hCAP-D2, a Non-SMC Subunit of Condensin I, to Chromosome and Chromosomal Protein Dynamics during Mitosis

2005 ◽  
Vol 25 (2) ◽  
pp. 740-750 ◽  
Author(s):  
Erwan Watrin ◽  
Vincent Legagneux
Keyword(s):  
Rna Interference ◽  
Mitotic Spindle ◽  
Topoisomerase Ii ◽  
Mitotic Chromosome ◽  
Chromosomal Protein ◽  
Structural Components ◽  
Mitotic Chromosomes ◽  
Sister Chromatids ◽  
Chromosome Alignment ◽  
Structural Maintenance Of Chromosomes

ABSTRACT Condensins are heteropentameric complexes that were first identified as structural components of mitotic chromosomes. They are composed of two SMC (structural maintenance of chromosomes) and three non-SMC subunits. Condensins play a role in the resolution and segregation of sister chromatids during mitosis, as well as in some aspects of mitotic chromosome assembly. Two distinct condensin complexes, condensin I and condensin II, which differ only in their non-SMC subunits, exist. Here, we used an RNA interference approach to deplete hCAP-D2, a non-SMC subunit of condensin I, in HeLa cells. We found that the association of hCAP-H, another non-SMC subunit of condensin I, with mitotic chromosomes depends on the presence of hCAP-D2. Moreover, chromatid axes, as defined by topoisomerase II and hCAP-E localization, are disorganized in the absence of hCAP-D2, and the resolution and segregation of sister chromatids are impaired. In addition, hCAP-D2 depletion affects chromosome alignment in metaphase and delays entry into anaphase. This suggests that condensin I is involved in the correct attachment between chromosome kinetochores and microtubules of the mitotic spindle. These results are discussed relative to the effects of depleting both condensin complexes.

scholarly journals A pathway for mitotic chromosome formation

Science ◽  
2018 ◽  
Vol 359 (6376) ◽  
pp. eaao6135 ◽  
Author(s):  
Johan H. Gibcus ◽  
Kumiko Samejima ◽  
Anton Goloborodko ◽  
Itaru Samejima ◽  
Natalia Naumova ◽  
...  
Keyword(s):  
Cell Cultures ◽  
Mitotic Chromosome ◽  
Dependent Manner ◽  
Mitotic Chromosomes ◽  
Chromatin Loops ◽  
Nested Loops ◽  
Helical Winding ◽  
Combined Imaging ◽  
Chromosome Formation ◽  
Differential Action

Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis of synchronous DT40 cell cultures with polymer simulations. Here we show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner, and arrays of consecutive 60-kilobase (kb) loops are formed. During prometaphase, ~80-kb inner loops are nested within ~400-kb outer loops. The loop array acquires a helical arrangement with consecutive loops emanating from a central “spiral staircase” condensin scaffold. The size of helical turns progressively increases to ~12 megabases during prometaphase. Acute depletion of condensin I or II shows that nested loops form by differential action of the two condensins, whereas condensin II is required for helical winding.

scholarly journals A novel chromatin tether domain controls topoisomerase IIα dynamics and mitotic chromosome formation

2013 ◽  
Vol 203 (3) ◽  
pp. 471-486 ◽  
Author(s):  
Andrew B. Lane ◽  
Juan F. Giménez-Abián ◽  
Duncan J. Clarke
Keyword(s):  
Posttranslational Modifications ◽  
Mitotic Chromosome ◽  
Histone H3 ◽  
Important Class ◽  
Histone Tail ◽  
Mitotic Chromosomes ◽  
Topoisomerase Iiα ◽  
Dna Topoisomerase ◽  
Chromosome Formation ◽  
Dna Topoisomerase Iiα

DNA topoisomerase IIα (Topo IIα) is the target of an important class of anticancer drugs, but tumor cells can become resistant by reducing the association of the enzyme with chromosomes. Here we describe a critical mechanism of chromatin recruitment and exchange that relies on a novel chromatin tether (ChT) domain and mediates interaction with histone H3 and DNA. We show that the ChT domain controls the residence time of Topo IIα on chromatin in mitosis and is necessary for the formation of mitotic chromosomes. Our data suggest that the dynamics of Topo IIα on chromosomes are important for successful mitosis and implicate histone tail posttranslational modifications in regulating Topo IIα.

scholarly journals Identification of a Chromosome-Targeting Domain in the Human Condensin Subunit CNAP1/hCAP-D2/Eg7

2002 ◽  
Vol 22 (16) ◽  
pp. 5769-5781 ◽  
Author(s):  
Alexander R. Ball, ◽  
John A. Schmiesing ◽  
Changcheng Zhou ◽  
Heather C. Gregson ◽  
Yoshiaki Okada ◽  
...  
Keyword(s):  
Mitotic Chromosome ◽  
Mitotic Chromosomes ◽  
Family Protein ◽  
Localization Signal ◽  
The Individual ◽  
Mitotic Chromosome Condensation ◽  
Structural Maintenance Of Chromosomes

ABSTRACT CNAP1 (hCAP-D2/Eg7) is an essential component of the human condensin complex required for mitotic chromosome condensation. This conserved complex contains a structural maintenance of chromosomes (SMC) family protein heterodimer and three non-SMC subunits. The mechanism underlying condensin targeting to mitotic chromosomes and the role played by the individual condensin components, particularly the non-SMC subunits, are not well understood. We report here characterization of the non-SMC condensin component CNAP1. CNAP1 contains two separate domains required for its stable incorporation into the complex. We found that the carboxyl terminus of CNAP1 possesses a mitotic chromosome-targeting domain that does not require the other condensin components. The same region also contains a functional bipartite nuclear localization signal. A mutant CNAP1 missing this domain, although still incorporated into condensin, was unable to associate with mitotic chromosomes. Successful chromosome targeting of deletion mutants correlated with their ability to directly bind to histones H1 and H3 in vitro. The H3 interaction appears to be mediated through the H3 histone tail, and a subfragment containing the targeting domain was found to interact with histone H3 in vivo. Thus, the CNAP1 C-terminal region defines a novel histone-binding domain that is responsible for targeting CNAP1, and possibly condensin, to mitotic chromosomes.

scholarly journals SMC complexes organize the bacterial chromosome by lengthwise compaction

2020 ◽  
Vol 66 (5) ◽  
pp. 895-899 ◽  
Author(s):  
Jarno Mäkelä ◽  
David Sherratt
Keyword(s):  
Mitotic Chromosome ◽  
Molecular Machines ◽  
Bacterial Chromosome ◽  
Chromosome Organization ◽  
Partner Protein ◽  
Domains Of Life ◽  
A Cell ◽  
Chromosome Formation ◽  
Structural Maintenance Of Chromosomes ◽  
Accessible Form

Abstract Structural maintenance of chromosomes (SMC) complexes are ancient and conserved molecular machines that organize chromosomes in all domains of life. We propose that the principles of chromosome folding needed to accommodate DNA inside a cell in an accessible form will follow similar principles in prokaryotes and eukaryotes. However, the exact contributions of SMC complexes to bacterial chromosome organization have been elusive. Recently, it was shown that the SMC homolog, MukBEF, organizes and individualizes the Escherichia coli chromosome by forming a filamentous axial core from which DNA loops emanate, similar to the action of condensin in mitotic chromosome formation. MukBEF action, along with its interaction with the partner protein, MatP, also facilitates chromosome individualization by directing opposite chromosome arms (replichores) to different cell halves. This contrasts with the situation in many other bacteria, where SMC complexes organise chromosomes in a way that the opposite replichores are aligned along the long axis of the cell. We highlight the similarities and differences of SMC complex contributions to chromosome organization in bacteria and eukaryotes, and summarize the current mechanistic understanding of the processes.

scholarly journals Mitotic chromosomes are compacted laterally by KIF4 and condensin and axially by topoisomerase IIα

2012 ◽  
Vol 199 (5) ◽  
pp. 755-770 ◽  
Author(s):  
Kumiko Samejima ◽  
Itaru Samejima ◽  
Paola Vagnarelli ◽  
Hiromi Ogawa ◽  
Giulia Vargiu ◽  
...  
Keyword(s):  
Mitotic Chromosome ◽  
Chromosome Morphology ◽  
Mitotic Chromosomes ◽  
Topoisomerase Iiα ◽  
Intrinsic Structure ◽  
Vitro Assay ◽  
Sister Chromatids ◽  
Parallel Pathway ◽  
Chromosome Formation

Mitotic chromosome formation involves a relatively minor condensation of the chromatin volume coupled with a dramatic reorganization into the characteristic “X” shape. Here we report results of a detailed morphological analysis, which revealed that chromokinesin KIF4 cooperated in a parallel pathway with condensin complexes to promote the lateral compaction of chromatid arms. In this analysis, KIF4 and condensin were mutually dependent for their dynamic localization on the chromatid axes. Depletion of either caused sister chromatids to expand and compromised the “intrinsic structure” of the chromosomes (defined in an in vitro assay), with loss of condensin showing stronger effects. Simultaneous depletion of KIF4 and condensin caused complete loss of chromosome morphology. In these experiments, topoisomerase IIα contributed to shaping mitotic chromosomes by promoting the shortening of the chromatid axes and apparently acting in opposition to the actions of KIF4 and condensins. These three proteins are major determinants in shaping the characteristic mitotic chromosome morphology.

scholarly journals Ki-67 and condensins support the integrity of mitotic chromosomes through distinct mechanisms

2017 ◽  
Author(s):  
Masatoshi Takagi ◽  
Takao Ono ◽  
Toyoaki Natsume ◽  
Chiyomi Sakamoto ◽  
Mitsuyoshi Nakao ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Fluorescence Recovery After Photobleaching ◽  
Mitotic Chromosome ◽  
Structural Integrity ◽  
External Surface ◽  
Mitotic Chromosomes ◽  
Topoisomerase Iiα ◽  
Ki 67 ◽  
Nuclear Envelope Breakdown ◽  
Structural Maintenance Of Chromosomes

AbstractAlthough condensins play essential roles in mitotic chromosome assembly, Ki-67, a protein localizing to the periphery of mitotic chromosomes, had also been shown to make a contribution to the process. To examine their respective roles, we generated a set of HCT116-based cell lines expressing Ki-67 and/or condensin subunits that were fused with an auxin-inducible degron for their conditional degradation. Both the localization and the dynamic behavior of Ki-67 on mitotic chromosomes were not largely affected upon depletion of condensin subunits, and vice versa. When both Ki-67 and SMC2 (a core subunit of condensins) were depleted, ball-like chromosome clusters with no sign of discernible thread-like structures were observed. This severe defective phenotype was distinct from that observed in cells depleted of either Ki-67 or SMC2 alone. Our results show that Ki-67 and condensins, which localize to the external surface and the central axis of mitotic chromosomes, respectively, have independent yet cooperative functions in supporting the structural integrity of mitotic chromosomes.List of Abbreviations usedAIDauxin-inducible degronDOXdoxycyclineFRAPfluorescence recovery after photobleachingIAAindol-3-acetic acidmAClmAID-mClovermAChmAID-mCherryNEBDnuclear envelope breakdownSMCstructural maintenance of chromosomesSTLCS-Trityl-L-cysteinetopo IIαtopoisomerase IIα

Cohesin dependent compaction of mitotic chromosomes

2016 ◽  
Author(s):  
Stephanie A Schalbetter ◽  
Anton Goloborodko ◽  
Geoffrey Fudenberg ◽  
Jon M Belton ◽  
Catrina Miles ◽  
...  
Keyword(s):  
Sister Chromatid ◽  
Mitotic Chromosome ◽  
Protein Complexes ◽  
Budding Yeast ◽  
Mitotic Chromosomes ◽  
Chromosome Conformation ◽  
Sister Chromatids ◽  
Chromatid Cohesion ◽  
Structural Maintenance Of Chromosomes

Structural Maintenance of Chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply-conserved SMC complexes, organize chromosomes in budding yeast. The canonical role of cohesins is to co-align sister chromatids whilst condensins generally compact mitotic chromosomes. We find strikingly different roles in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosomes arms, independent of and in addition to its role in sister-chromatid cohesion. Cohesin dependent mitotic chromosome compaction can be fully accounted for through cis-looping of chromatin by loop extrusion. Second, condensin is dispensable for compaction along chromosomal arms and instead plays a specialized role, structuring rDNA and peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that SMC-dependent looping is readily deployed in a range of contexts to functionally organize chromosomes.

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