13S Condensin Actively Reconfigures DNA by Introducing Global Positive Writhe

Kimura, Kazuhiro; Rybenkov, Valentin V.; Crisona, Nancy J.; Hirano, Takeshi; Cozzarelli, Nicholas R.

doi:10.1016/s0092-8674(00)81018-1

Cited by 307 publications

(336 citation statements)

References 37 publications

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“…This presence of strong large-scale LRC might favour the formation of large solenoidal supercoils that would contribute to the supercoiling of chromatin. In eukaryotes, the LRC observed in the large-scale regime would favour the regular supercoiling of interphase chromatin by condensin [56,151,152,153]. We suggest that to some extent, this mechanism can be paralleled to the way small-scale LRC favour the supercoiling of nucleosomal DNA around the core histone.…”

Section: What Mechanisms Underly Lrc In Genome Sequences?mentioning

confidence: 78%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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Abstract. Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called 'wavelet transform microscope' reveals a characteristic scale of 100 − 200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called waveletbased multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1,2].

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Section: What Mechanisms Underly Lrc In Genome Sequences?mentioning

confidence: 78%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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“…The fivesubunit composition of the condensin complex is conserved in human cells (Kimura et al, 2001). The two SMC-type subunits are capable of binding DNA, and it has been proposed that by an ATP-dependent hinge-like action they promote the high-order compaction of chromatin at mitosis (Kimura et al, 1999). The specific functions in activating or regulating condensin activity of the remaining three non-SMC subunits are not known (Kimura and Hirano, 2001).…”

Section: Conservation Of the Condensin Complexmentioning

confidence: 99%

“…This suggests condensin regulatory mechanisms may have evolved to maintain established condensation of periodic macrodomains in the human genome. Thus, the mitotic activity of condensin could be regulated in at least three levels: mitosis-specific phosphorylation (Kimura et al, 1998(Kimura et al, , 1999Kimura and Hirano, 2000) mitosis-specific transcription, and mitosis-specific chromosome localization. Detection of the hCAP-H CЈ terminal epitope recognized by Ab2573 within nucleoli but not on mitotic chromatin suggests that the C terminus of hCAP-H may be unavailable for binding during chromosomal condensation.…”

Section: Cell Cycle-dependent Subcellular Localization Of Hcap-hmentioning

confidence: 99%

“…However, this activity does not require ATP, suggesting that the ATPdependent increase in condensation activity observed in Xenopus and human might be attributed to the other members of the 13S condensin complex. Mitosis-specific phosphorylation appears to play a key role in the chromosomal targeting of the condensin complexes Kimura and Hirano, 1997;Kimura et al, 1999Kimura et al, , 2001.…”

Section: Introductionmentioning

confidence: 99%

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Cell Cycle-dependent Expression and Nucleolar Localization of hCAP-H

Cabello¹,

Eliseeva

He³

et al. 2001

MBoC

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Condensin is a conserved 13S heteropentamer composed of two nonidentical structural maintenance of chromosome (SMC) family proteins, in Xenopus XCAP-C and XCAP-E, and three regulatory subunits, XCAP-D2, XCAP-G, and XCAP-H. Both biochemical and genetic analyses have demonstrated an essential role for the 13S condensin complex in mitotic chromosome condensation. Further, a potential requirement for condensin in completion of chromatid arm separation in early anaphase is demonstrated by the mutational phenotypes of the Drosophila homologues of XCAP-H, barren and XCAP-C, DmSMC4. In this study we have investigated the expression and subcellular distribution of hCAP-H, the human homolog of XCAP-H, in order to better understand its cellular functions. Transcription of hCAP-H was restricted to proliferating cells with highest expression during the G 2 phase of the cell cycle. In contrast, cellular hCAP-H protein levels were constant throughout the cell cycle. hCAP-H was found to be associated with mitotic chromosomes exhibiting a nonuniform but symmetric distribution along sister chromatids. The symmetry of hCAP-H association with sister chromatids suggests that there are sequence-dependent domains of condensin aggregation. During interphase hCAP-H, -C, and -E, have distinct punctate nucleolar localization, suggesting that condensin may associate with and modulate the conformation and function of rDNA. hCAP-H association with condensed chromatin was not observed in the early phase of chromosome condensation when histone H3 phosphorylation has already taken place. This finding is consistent with the hypothesis that histone H3 phosphorylation precedes condensin-mediated condensation.

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“…It consists of five subunits, which in addition to XCAP-C and XCAP-E include three unrelated proteins: XCAP-D2, XCAP-G, and XCAP-H . The 13S condensin complex is capable of binding DNA and using ATP to induce a global change in DNA configuration (Kimura and Hirano, 1997;Kimura et al, 1999). In mitosis, XCAP-H, and to a lesser extent XCAP-G and XCAP-D2, subunits are hyperphosphorylated, and the complex is targeted to the chromosomes .…”

Section: Introductionmentioning

confidence: 99%

Chromosome Condensation Factor Brn1p Is Required for Chromatid Separation in Mitosis

Ouspenski

Cabello

Brinkley

2000

MBoC

100

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This work describes BRN1, the budding yeast homologue of Drosophila Barren and Xenopus condensin subunit XCAP-H. The Drosophila protein is required for proper chromosome segregation in mitosis, and Xenopus protein functions in mitotic chromosome condensation. Mutant brn1 cells show a defect in mitotic chromosome condensation and sister chromatid separation and segregation in anaphase. Chromatid cohesion before anaphase is properly maintained in the mutants. Some brn1 mutant cells apparently arrest in S-phase, pointing to a possible function for Brn1p at this stage of the cell cycle. Brn1p is a nuclear protein with a nonuniform distribution pattern, and its level is up-regulated at mitosis. Temperature-sensitive mutations of BRN1 can be suppressed by overexpression of a novel gene YCG1, which is homologous to another Xenopus condensin subunit, XCAP-G. Overexpression of SMC2, a gene necessary for chromosome condensation, and a homologue of the XCAP-E condensin, does not suppress brn1, pointing to functional specialization of components of the condensin complex.

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13S Condensin Actively Reconfigures DNA by Introducing Global Positive Writhe

Cited by 307 publications

References 37 publications

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Cell Cycle-dependent Expression and Nucleolar Localization of hCAP-H

Chromosome Condensation Factor Brn1p Is Required for Chromatid Separation in Mitosis

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