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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

SUBMITTER: Richard Young

PROVIDER: E-GEOD-30920 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2012-05-30 | GSE30920 | GEO

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

2012-02-09 | GSE30919 | GEO

MicroRNA Clustering Assists Processing of Suboptimal MicroRNA Hairpins Through the Action of the ERH Protein

Project description:Microprocessor initiates processing of microRNAs (miRNAs) from hairpin regions of primary transcripts (pri-miRNAs). Pri-miRNAs often contain multiple miRNA hairpins, and this clustered arrangement can assist processing of otherwise defective hairpins. We find that miR-451, which derives from a hairpin with a suboptimal terminal loop and a suboptimal stem length, accumulates to 40-fold higher levels when clustered with a helper hairpin. This phenomenon tolerates changes in hairpin order, linker lengths, and the identities of the helper hairpin, the recipient hairpin, the linker-sequence, and the RNA polymerase that transcribes the hairpins. It can act reciprocally and need not occur co-transcriptionally. It requires Microprocessor recognition of the helper hairpin and linkage of the two hairpins, yet predominantly manifests after helper-hairpin processing. It also requires Enhancer of Rudimentary Homology (ERH), which copurifies with Microprocessor and can dimerize and interact with other proteins that can dimerize, suggesting a model in which Microprocessor recruits another Microprocessor.

2020-04-16 | GSE142818 | GEO

SMC Complexes Are Guarded by the SUMO Protease Ulp2 Against SUMO-Chain-Mediated Turnover

Project description:Structural maintenance of chromosomes (SMC) complexes, cohesin, condensin and Smc5/6, are essential for viability and participate in multiple processes, including sister chromatid cohesion, chromosome condensation, and DNA repair. Here we show that SUMO chains target all three SMC complexes and are antagonized by the SUMO protease Ulp2 to prevent their turnover. We uncover that the essential role of the cohesin-associated subunit Pds5 is to counteract SUMO chains jointly with Ulp2. Importantly, fusion of Ulp2 to kleisin Scc1 supports viability of PDS5 null cells and protects cohesin from proteasomal degradation mediated by the SUMO-targeted ubiquitin ligase Slx5/Slx8. The lethality of PDS5 deleted cells can also be bypassed by simultaneous loss of the PCNA unloader, Elg1, and the cohesin releaser, Wpl1, but only when Ulp2 is functional. Condensin and Smc5/6 complex are similarly guarded by Ulp2 against unscheduled SUMO-chain assembly, which we propose to time the availability of SMC complexes on chromatin.

2021-08-05 | PXD022717 | Pride

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

2013-10-28 | GSE46316 | GEO

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

MCPH1 inhibits condensin II during interphase by regulating its SMC2-kleisin interface

Project description:The dramatic change in morphology of chromosomal DNAs between interphase and mitosis is one of the defining features of the eukaryotic cell cycle. Two types of enzymes, namely cohesin and condensin confer the topology of chromosomal DNA by extruding DNA loops. While condensin normally configures chromosomes exclusively during mitosis, cohesin does so during interphase. The processivity of cohesin’s loop extrusion during interphase is limited by a regulatory factor called WAPL, which induces cohesin to dissociate from chromosomes via a mechanism that requires dissociation of its kleisin from the neck of SMC3. We show here that a related mechanism may be responsible for blocking condensin II from acting during interphase. Cells derived from patients affected by microcephaly caused by mutations in the MCPH1 gene undergo premature chromosome condensation but it has never been established for certain whether MCPH1 regulates condensin II directly. We show that deletion of Mcph1 in mouse embryonic stem cells unleashes an activity of condensin II that triggers formation of compact chromosomes in G1 and G2 phases, which is accompanied by enhanced mixing of A and B chromatin compartments, and that this occurs even in the absence of CDK1 activity. Crucially, inhibition of condensin II by MCPH1 depends on the binding of a short linear motif within MCPH1 to condensin II’s NCAPG2 subunit. We show that the activities of both Cohesin and Condensin II may be restricted during interphase by similar types of mechanisms as MCPH1’s ability to block condensin II’s association with chromatin is abrogated by the fusion of SMC2 with NCAPH2. Remarkably, in the absence of both WAPL and MCPH1, cohesin and condensin II transform chromosomal DNAs of G2 cells into chromosomes with a solenoidal axis showing that both cohesin and condensin must be tightly regulated to adjust the structure of chromatids for their successful segregation.

2021-11-19 | GSE188988 | GEO

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