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

ABSTRACT: 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

ORGANISM(S): Mus musculus

SUBMITTER: Richard Young

PROVIDER: E-GEOD-33346 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2012-03-14 | GSE33346 | GEO

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

2012-02-09 | GSE30919 | GEO

Nucleosome eviction in mitosis assists condensin loading and chromosome condensation

Project description:The experiment was performed to assess the importance of nucleosome eviction for the binding of condensin to chromatin during mitosis. The condensin complex associates with chromatin during mitosis to ensure chromosome condensation and accurate segregation, but how this binding is achieved remains poorly understood. Our study indicates that transcription co-activators Gcn5 and Mst2 assist condensin binding during mitosis by evicting nucleosomes. To reach this conclusion, we mapped nucleosomes, during mitosis, in wild-type and gcn5mst2 mutant strains. This experiment allowed us (1) to identify nucleosome-depleted regions (ndrs) during mitosis and to show that condensin tends to colocalize with ndr at the 3ends of genes, and (2) to confirm the importance of nucleosome eviction from ndrs by gcn5 and mst2, during mitosis, for the binding of condensin to chromatin.this experiment determines the patterns of nucleosomes in wild type and mutant fission yeast cells arrested in early mitosis. We analysed wild-type cells, cells lacking Gcn5 histone acetylatransferase (gcn5D) and cells lacking both Gcn5 and Mst2 histone acetyltransferases (Gcn5Dmst2D). All cells used in this study expressed a GFP-tagged version of condensin (Cnd2-GFP) and were blocked in early mitosis at 19C by the nda3-KM311 mutation. Mitotic indexes were determined by scoring the accumulation of Cnd2-GFP in the nucleus. Mitotic cells were collected and chromatin was digested by increasing amount of MNase to produce mononucleosomes. Mononucleosomal DNA was purified on an agarose gel and sequence on an Illumina Nextseq 500 apparatus. Three replicates of wild type, gcn5D and gcn5Dmst2D were analysed. Nucleosome patterns were determined in wild-type cells, cells lacking Gcn5 and cells lacking both Gcn5 and Mst2.

2016-04-18 | E-MTAB-4620 | biostudies-arrayexpress

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

Condensin II complex mediates interactions of histone gene loci

Project description:Condensin complexes are known for their importance in chromosome condensation during mitosis. However, condensin II binds to the geome during interphase as well. The role of condensin II in genome organization in mammalian interphase nuclei is not characterized. Since condensin II binds to the promoters of the transcriptionally active promoters in interphase genome, the aim of this study is to uncover its role in mediating chromatin interactions between active gene promoters such as histone gene loci.

2017-06-01 | GSE80219 | GEO

Pol II Ser7phospho ChIP-seq in mES cells

Project description:RNA Polymerase II transcribes protein-coding and many non-coding RNA genes in eukaryotes. The largest subunit of RNA Polymerase II, Rpb1, contains a hepta-peptide repeat on its C-terminal tail with three potential phosphorylation sites (Serine 2, Serine 5 and Serine 7). Mammalian Rpb1 contains 52 repeats. The phosphorylation events are catalyzed by specific protein kinases where the phosphorylation of specific residues is coupled to the transcription cycle. For example, the Cdk7 subunit of TFIIH phosphorylates both Serine 5 and Serine 7 during intiation and the Cdk9 subunit of P-TEFb phosphorylates Serine 2 during the transition into productive elongation. The dataset presented here is the genome-wide distribution of RNA Pol II with Serine 7 of the CTD phosphorylated in murine embryonic stem cells. This data, in addition to phospho-specific datasets generated in the same cell type in Rahl et al. Cell 2010 and Seila et al. Science 2008, represents the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II. An antibody specific to RNA Pol II Serine 7 phosphorylated CTD (gift of Dirk Eick; Chapman et al. Science 2008) was used to enrich for DNA fragments associated with this Pol II isoform in murine embryonic stem cells. DNA was purified and prepared for Illumina/Solexa sequencing following their standard protocol. This is a single dataset but together with datasets from Rahl et al. Cell 2010 and Seila et al. Science 2008, these datasets represent the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II.

2010-05-20 | E-GEOD-21917 | biostudies-arrayexpress

RNA pol II transcript abundance controls condensin accumulation at mitotically upregulated and heat shock-inducible genes in fission yeast

Project description:Condensin plays fundamental roles in chromosome dynamics. In this study, we determined the binding sites of condensin on fission yeast (Schizosaccharomyces pombe) chromosomes at the level of nucleotide sequences using chromatin immunoprecipitation (ChIP) and ChIP-sequencing (ChIP-seq). We found that condensin binds to RNA polymerase I-, II- and III-transcribed genes during both mitosis and interphase, and we focused on pol II constitutive and inducible genes. Accumulation sites for condensin are distinct from those of cohesin and DNA topoisomerase II. Using cell cycle stage- and heat shock-inducible genes, we demonstrate that pol II-mediated transcripts cause condensin accumulation. First, condensin’s enrichment on mitotically activated genes was abolished by deleting the sep1+ gene that encodes an M-phase-specific forkhead transcription factor. Second, by raising the temperature, condensin accumulation was rapidly induced at heat shock protein genes in interphase and even during mid-mitosis. In interphase, condensin accumulates preferentially during the post-replicative phase. pol II-mediated transcription was neither repressed nor activated by condensin, as levels of transcripts per se did not change when mutant condensin failed to associate with chromosomal DNA. However, massive chromosome missegregation occurred, suggesting that abundant pol II transcription may require active condensin prior to proper chromosome segregation.

2015-04-15 | GSE65956 | GEO

Genome-wide binding of condensin II and TFIIIC in human HEK293 cells

Project description:Condensin complexes are highly conserved for chromosome compaction to ensure their faithful segregation in mitosis. However, little is known about the role of condensin complexes in interphase. Condensins exists in two complexes, condensins I and II, in higher eukayotic cells. During interphase, condensin II is predominantly localized in the nucleus throughout the cell cycle, whereas condensin I is localized at the cytoplasm in interphase. The distinct localization patterns suggest that condensin II, but not condensin I, may contribute to genome organization in interphase. Our results suggest that condensin II is associated with TFIIIC complex in humans.

2018-09-05 | GSE119418 | GEO

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

2013-10-28 | GSE46316 | GEO

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