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Genome-wide analysis of E. coli MukB distribution using ChIP-sequencing

ABSTRACT: Paper abstract : The Escherichia coli SMC complex, MukBEF, interacts with the ParC subunit of topoisomerase IV (TopoIV), consistent with sequential roles in chromosome unlinking and segregation. Although clusters of MukBEF molecules are normally associated with the chromosome replication origin region (ori), we demonstrate their association with the replication termination region (ter), which is enhanced when ATP hydrolysis by MukB is impaired. We show that MukBEF interacts in vivo and in vitro with MatP, which binds matS sites in ter. The MatP-MukBEF interaction limits the stable association of MukBEF complexes with ter and the availability of functional TopoIV during decatenation of sister ters. The MukBEF-TopoIV interaction is influenced by the nucleotide state of MukBEF. The combined action of MukBEF and MatP helps position MukBEF clusters in relation to the chromosome, thereby, influencing chromosome organization and segregation. Finally, we demonstrate that the regulated sequential action of TopoIV and MukBEF promotes chromosome decatenation and segregation.

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE67221 | GEO | 2016/01/28

SECONDARY ACCESSION(S): PRJNA279886

REPOSITORIES: GEO

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Replication termination is mediated by Top2 and occurs at genomic loci containing pausing elements

Project description:[original title] Chromosome replication initiates at multiple replicons and terminates when forks converge. In Escherichia coli, the Tus-TER complex mediates polar fork converging at the terminator region and aberrant termination events challenge chromosome integrity and segregation. Since in eukaryotes termination is less characterized, we used budding yeast to identify the factors assisting fork fusion at replicating chromosomes. Using genomic and mechanistic studies we have identified and characterized 71 chromosomal termination regions (TERs). TERs contain fork pausing elements that influence fork progression and merging. The Rrm3 DNA helicase assists fork progression across TERs counteracting the accumulation of X-shaped structures. The Top2 DNA topoisomerase associates at TERs in S-phase and G2/M facilitates fork fusion and prevents DNA breaks and genome rearrangements at TERs. We propose that in eukaryotes replication fork barriers, Rrm3 and Top2 coordinate replication fork progression and fusion at termination regions thus counteracting abnormal genomic transitions. Signal tracks in BED format suitable for visualization on the UCSC genome browser can be found at http://bio.ifom-ieo-campus.it/supplementary/Fachinetti_et_al_MOLCELL_2010

2010-08-28 | GSE19061 | GEO

Comparison of genome wide binding of S. cerevisiae condensin, topo II and cohesin by ChIP

Project description:The chromosomal condensin complex gives metaphase chromosomes structural stability. In addition, condensin is required for sister chromatid resolution during their segregation in anaphase. How condensin promotes chromosome resolution is poorly understood. Chromosome segregation during anaphase also fails after inactivation of topoisomerase II (topo II), the enzyme that removes catenation between sister chromatids left behind after completion of DNA replication. This has led to the proposal that condensin promotes DNA decatenation, but direct evidence for this is missing and alternative roles for condensin in chromosome resolution have been suggested. Using the budding yeast rDNA as a model, we now show that anaphase bridges in a condensin mutant are resolved by ectopic expression of a foreign (Chlorella virus) but not endogenous topo II. This suggests that catenation prevents sister rDNA segregation, and that yeast topo II is ineffective in decatenating the locus without condensin. Condensin and topo II colocalize along both rDNA and euchromatin, consistent with coordination of their activities. We investigate the physiological consequences of condensin-dependent rDNA decatenation and find that late decatenation determines the late segregation timing of this locus during anaphase. Regulation of decatenation therefore provides a means to finetune segregation timing of chromosomes in mitosis. Keywords: ChIP-chip, Cell Cycle

2008-07-18 | GSE11988 | GEO

Condensin association with chromosomes depends on a DNA binding domain formed by its HEAT-repeat subunits

Project description:Condensin protein complexes play central roles in the three-dimensional organization of chromosomes during mitotic and meiotic cell divisions. How condensin interacts with its chromatin substrates to promote sister chromatid decatenation and segregation is largely unknown. Previous work suggested that condensin, in addition to encircling chromatin fibers topologically within the large ring-shaped structure formed by its structural maintenance of chromosomes (SMC) and kleisin subunits, contacts DNA directly. Here we describe the discovery of a binding domain for double-stranded DNA helices formed by condensinM-bM-^@M-^Ys HEAT-repeat subunits. Using detailed mapping data of the interfaces between the HEAT-repeat and the kleisin subunits, we generated mutant complexes that lack the Ycg1/CAP-G HEAT-repeat subunit. These tetrameric condensin complexes fail to associate stably with chromosomes in yeast and human cells. We suggest that condensin controls chromosome architecture by stabilizing chromatin loops of chromatin fibers through interaction with its unconventional HEAT-repeat DNA binding domain. Analysis of condensin binding genomewide in a wild type and a condensin mutant

2014-05-16 | E-GEOD-55948 | biostudies-arrayexpress

Genome-wide distribution of Tus-GFP in KRX E. coli

Project description:We examined the chromosomal distribution of GFP-tagged Tus (Tus-GFP) in exponentially growing E. coli (KRX) using chromosome immunoprecipitation (ChIP)-Seq. Our ChIP-seq allowed delineation of a refined minimal replication fork trap within E. coli comprising two clusters of three Ter sites

2021-12-01 | GSE163680 | GEO

Spindle-localized mRNA translation mediated by CPEB1 and CPEB4 controls mitotic progression

Project description:Here we show sequential functions of CPEB1 and CPEB4 in the localization of repressed mRNAs to the mitotic spindle and their subsequent phase -specific activation to promote cell phase transitions and correct chromosome segregation.

2021-06-29 | GSE99810 | GEO

Identification of MukBHN conformational changes upon AcpP binding using cross-linking mass spectrometry

Project description:Structural Maintenance of Chromosomes (SMC) complexes contribute ubiquitously to chromosome organization-segregation. SMC proteins have a conserved architecture, with a dimerization hinge and an ATPase head domain separated by a long antiparallel intramolecular coiled-coil. Dimeric SMC proteins interact with essential accessory proteins, kleisins that bridge the two subunits of an SMC dimer, and HAWK/KITE accessory proteins that interact with kleisins. The ATPase activity of the Escherichia coli SMC protein, MukB, is essential for in vivo function and is regulated by interactions with its dimeric kleisin, MukF, and KITE, MukE. Here we demonstrate that, in addition, MukB interacts with Acyl Carrier Protein (AcpP) that has essential functions in fatty acid synthesis. We characterize the AcpP interaction site at the joint of the MukB coiled-coil and show that the interaction is essential for MukB ATPase and for MukBEF function in vivo. Therefore, AcpP is an essential co-factor for MukBEF action in chromosome organization-segregation.

2021-11-25 | PXD026017 | Pride

Identification of AcpP-MukB binding sites using cross-linking mass spectrometry

2021-11-25 | PXD026062 | Pride

Condensin association with chromosomes depends on a DNA binding domain formed by its HEAT-repeat subunits

Project description:Condensin protein complexes play central roles in the three-dimensional organization of chromosomes during mitotic and meiotic cell divisions. How condensin interacts with its chromatin substrates to promote sister chromatid decatenation and segregation is largely unknown. Previous work suggested that condensin, in addition to encircling chromatin fibers topologically within the large ring-shaped structure formed by its structural maintenance of chromosomes (SMC) and kleisin subunits, contacts DNA directly. Here we describe the discovery of a binding domain for double-stranded DNA helices formed by condensin’s HEAT-repeat subunits. Using detailed mapping data of the interfaces between the HEAT-repeat and the kleisin subunits, we generated mutant complexes that lack the Ycg1/CAP-G HEAT-repeat subunit. These tetrameric condensin complexes fail to associate stably with chromosomes in yeast and human cells. We suggest that condensin controls chromosome architecture by stabilizing chromatin loops of chromatin fibers through interaction with its unconventional HEAT-repeat DNA binding domain.

2014-05-16 | GSE55948 | GEO

Mitochondrial DNA rearrangements in a patient with mutations in Topoisomerase 3 alpha

Project description:Topoisomerase 3α is required for decatenation and segregation of human mitochondrial DNA

| PRJEB23559 | ENA

Interaction between TBP and condensing drives the organization and faithful segregation of mitotic chromosomes

Project description:Genome/chromosome organization is highly ordered and controls nuclear events. Here, we show that the TATA box-binding protein (TBP) interacts with the Cnd2 kleisin subunit of condensin to mediate interphase and mitotic chromosome organization in fission yeast. TBP recruits condensin onto RNA polymerase III-transcribed (Pol III) genes and highly transcribed Pol II genes; condensin in turn associates these genes with centromeres. Inhibition of the Cnd2-TBP interaction disrupts condensin localization across the genome and the proper assembly of mitotic chromosomes, leading to severe defects in chromosome segregation and eventually causing cellular lethality. We propose that the Cnd2-TBP interaction coordinates transcription with chromosomal architecture by linking dispersed gene loci with centromeres. This chromosome arrangement can contribute to the efficient transmission of physical force at the kinetochore to chromosomal arms, thereby supporting the fidelity of chromosome segregation. Genome-wide distributions of condensin and Pol III factors in fission yeast.

2015-08-12 | E-GEOD-60273 | biostudies-arrayexpress

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