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Transcription-associated Loading and Translocation of Condensin II on Chromosome Arms in Embryonic Stem Cells (flavopiridol ChIP-Seq)

ABSTRACT: Condensin molecules are loaded onto the genome to mediate essential changes in chromosome condensation during mitosis, but it is not clear why there are two forms of vertebrate condensin that become differentially distributed on chromosomes. We report here that condensin II, the form of condensin present in the nucleus throughout the cell cycle, functions specifically at active genes. Condensin II is loaded at transcriptionally active promoters in embryonic stem cells (ESCs), migrates through these genes in a transcription-dependent fashion and accumulates in transcription termination regions. Unlike cohesin, which is also loaded at active promoters, condensin II has little influence on transcription. We conclude that condensin II is loaded and distributed across actively transcribed chromatin and thus serves to specifically condense this euchromatic portion of chromosomes during the cell division cycle.

ORGANISM(S): Mus musculus

PROVIDER: GSE30919 | GEO | 2012/02/09

SECONDARY ACCESSION(S): PRJNA146263

REPOSITORIES: GEO

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Transcription-associated Loading and Translocation of Condensin II on Chromosome Arms in Embryonic Stem Cells (flavopiridol ChIP-Seq)

Project description:Condensin molecules are loaded onto the genome to mediate essential changes in chromosome condensation during mitosis, but it is not clear why there are two forms of vertebrate condensin that become differentially distributed on chromosomes. We report here that condensin II, the form of condensin present in the nucleus throughout the cell cycle, functions specifically at active genes. Condensin II is loaded at transcriptionally active promoters in embryonic stem cells (ESCs), migrates through these genes in a transcription-dependent fashion and accumulates in transcription termination regions. Unlike cohesin, which is also loaded at active promoters, condensin II has little influence on transcription. We conclude that condensin II is loaded and distributed across actively transcribed chromatin and thus serves to specifically condense this euchromatic portion of chromosomes during the cell division cycle. ChIP-Seq data for Condensin II and Cohesin in v6.5 ESCs treated or not with the RNA polymerase II elongation inhibitor flavopiridol.

2012-02-09 | E-GEOD-30919 | biostudies-arrayexpress

Transcription-associated Loading of Condensin II on Chromosome Arms in Embryonic Stem Cells (nocodazole ChIP-Seq)

Project description:Vertebrate condensin I and II molecules are loaded onto the genome to mediate essential changes in chromosome condensation during mitosis, but it is not clear how the two forms of condensin become distributed on chromosomes. We report here that condensin II, the form of condensin present in the nucleus throughout the cell cycle, is loaded at transcriptionally active promoters, migrates through these genes in a transcription-dependent fashion and accumulates in transcription termination regions during interphase. During mitosis, condensin I is recruited to actively transcribed genes and replaces condensin II. We conclude that the two forms of condensin are loaded at different times during the cell division cycle at the promoters of actively transcribed genes. ChIP-Seq data for Condensin II in v6.5 ESCs treated or not with nocodazole

2012-03-14 | E-GEOD-33346 | biostudies-arrayexpress

Transcription-associated Loading of Condensin II on Chromosome Arms in Embryonic Stem Cells (nocodazole ChIP-Seq)

2012-03-14 | GSE33346 | GEO

Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus

Project description:Structural maintenance of chromosomes (SMC) complexes play critical roles in chromosome dynamics in virtually all organisms but how they function remains poorly understood. In Bacillus subtilis, SMC condensin complexes are topologically loaded at centromeric sites adjacent to the replication origin. Here we provide evidence that these ring-shaped assemblies tether the left and right chromosome arms together while traveling from the origin to the terminus (>2 Mb) at rates >50kb/min. Condensin movement scales linearly with time arguing for an active transport mechanism. These data support a model in which SMC complexes function by processively enlarging DNA loops. Loop formation followed by processive enlargement provides a mechanism for how condensin complexes compact and resolve sister chromatids in mitosis and how cohesin generates topologically associating domains (TADs) during interphase.

2017-02-03 | GSE85612 | GEO

Transcription-dependent positioning of Structural Maintenance of Chromosome complexes across the genome: RNA-Seq

Project description:The Structural Maintenance of Chromosomes (SMC) complexes regulate the chromosome structures essential for proper genome regulation and cell viability. In mammals, the coordinated actions of the SMC complexes condensin I, condensin II and cohesin regulate dynamic chromosome structures throughout the cell cycle, but it is not clear how these complexes are positioned across the genome. We report here that condensin I, condensin II and cohesin occupy active euchromatic regions of the embryonic stem cell genome, but not heterochromatic regions. Like cohesin, we find that condensin II is deposited at active genes by the SMC loading factor Nipbl. The recruitment of Condensin II to active genes is dependent on their transcriptional activation. Subsequent transcriptional elongation by RNA polymerase II distributes condensin II across gene bodies. During mitosis, condensin I occupies the same set of active genes occupied by condensin II during interphase. Thus, SMC complexes are positioned in the genome by transcription-dependent processes, indicating that condensin-dependent condensation mechanisms are preferentially utilized in euchromatic regions. RNA-seq in mES cells after known-down of Smc1, CapH2 or Smc2.

2013-10-28 | E-GEOD-46316 | biostudies-arrayexpress

Transcription-dependent positioning of Structural Maintenance of Chromosome complexes across the genome: RNA-Seq

2013-10-28 | GSE46316 | GEO

Transcription-associated Loading and Translocation of Condensin II on Chromosome Arms in Embryonic Stem Cells (RNA)

2012-05-30 | GSE30920 | GEO

Centromeres license the mitotic condensation of yeast chromosome arms

Project description:During mitosis, chromatin condensation shapes chromosomes as separate, rigid and compacted sister-chromatids to facilitate their segregation. Here, we show that unlike wild type yeast chromosomes, non-chromosomal DNA circles and chromosomes lacking a centromere fail to condense during mitosis. Genetics and ChIP-seq experiments establish that the centromere functions in chromosome condensation upstream of the kinases Aurora B and Bub1. Downstream of Aurora B and Bub1, Shugoshin and the deacetylase Hst2 facilitated spreading of the condensation signal from the pericentromeric region to the chromosome arms. Targeting Aurora B to DNA circles or centromere-ablated chromosomes, or releasing Shugoshin from PP2A-dependent inhibition bypassed the centromere requirement for condensation and enhanced the mitotic stability of DNA circles. Our data indicate that yeast cells license in a centromere-dependent manner the chromosome-autonomous condensation of their chromatin, excluding non-centromeric DNA from this process and thereby inhibiting their propagation.

2018-10-11 | GSE100643 | GEO

Transcription-associated Loading and Translocation of Condensin II on Chromosome Arms in Embryonic Stem Cells (RNA)

Project description:The precise control of gene expression programs is critical for maintenance of cell state in emryonic stem cells. Cohesin has been shown to play an important role in maintaining gene expression programs by contributing to DNA loops between enhancers and promoters of active genes. The influence of condensin on gene expression is not well understood. We used microarrays to detail the changes to the global gene expression program of mouse embryonic stem cells upon depletion of cohesin or condensin II. Mouse embryonic stem cells were treated with shRNA constructs targeting CapH2 (2 hairpins), Smc2 (2 hairpins), Smc1 (1 hairpin, 2 biological replicates) and GFP control (1 hairpin, 2 biological replicates) for a total of 8 samples. After 5 days RNA was extracted from the depleted cells and hybridized to Affymetrix microarrays.

2012-05-29 | E-GEOD-30920 | biostudies-arrayexpress

Condensin II Counters Cohesin and RNA Polymerase II in 3D Chromatin Organization

Project description:CTCF is present at the anchors of thousands of loops likely formed via cohesin-mediated loop extrusion in mammalian cells. Interaction domains present in D. melanogaster chromosomes form via the segregation of active and inactive chromatin in the absence of CTCF looping, but the role of transcription versus other architectural proteins in chromatin organization is unclear. Here we find that positioning of RNAPII via transcription elongation is essential in the formation of gene loops, which in turn interact to form compartmental domains. Inhibition of transcription elongation or depletion of cohesin decreases gene looping and formation of active compartmental domains. In contrast, depletion of condensin II, which also localizes to active chromatin, results in increased gene looping, formation of compartmental domains, and stronger intra-chromosomal compartmental interactions. Condensin II has a similar role in maintaining inter-chromosomal interactions responsible for pairing between homologous chromosomes, whereas inhibition of transcription elongation or cohesin depletion has little effect on homolog pairing. The results suggest distinct roles for cohesin and condensin II in the establishment of 3D nuclear organization in Drosophila.

2019-03-11 | GSE118756 | GEO

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