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ATAC-seq of WT and p27KO

ABSTRACT: Cell differentiation involves profound changes in global gene expression that often have to occur in coordination with cell cycle exit. Because cyclin-dependent kinase inhibitor p27 reportedly regulates proliferation of neural progenitor cells in the subependymal neurogenic niche of the adult mouse brain, but can also have effects on gene expression, we decided to molecularly analyze its role in adult neurogenesis and oligodendrogenesis. At the cell level, we show that p27 restricts residual cyclin-dependent kinase activity after mitogen withdrawal to antagonize cycling, but is not essential for cell cycle exit. Contrasting gene expression with chromatin accessibility, we find that p27 is coincidentally necessary to globally repress many genes involved in the transit from multipotentiality to differentiation, including those coding for neural progenitor transcription factors SOX2, OLIG2, and ASCL1. Our data reveal both direct association of p27 with regulatory sequences in the three genes and an additional hierarchical relationship where p27 repression of the Sox2 gene leads to reduced levels of SOX2-downstream targets Olig2 and Ascl1. In vivo, p27 is also required for the regulation of the proper level of SOX2 necessary for neuroblasts and oligodendroglial progenitor cells to timely exit cell cycle in a lineage-dependent manner.

ORGANISM(S): Mus musculus

PROVIDER: GSE196285 | GEO | 2023/01/09

REPOSITORIES: GEO

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RNA-seq of WT and p27KO

Project description:Cell differentiation involves profound changes in global gene expression that often have to occur in coordination with cell cycle exit. Because cyclin-dependent kinase inhibitor p27 reportedly regulates proliferation of neural progenitor cells in the subependymal neurogenic niche of the adult mouse brain, but can also have effects on gene expression, we decided to molecularly analyze its role in adult neurogenesis and oligodendrogenesis. At the cell level, we show that p27 restricts residual cyclin-dependent kinase activity after mitogen withdrawal to antagonize cycling, but is not essential for cell cycle exit. Contrasting gene expression with chromatin accessibility, we find that p27 is coincidentally necessary to globally repress many genes involved in the transit from multipotentiality to differentiation, including those coding for neural progenitor transcription factors SOX2, OLIG2, and ASCL1. Our data reveal both direct association of p27 with regulatory sequences in the three genes and an additional hierarchical relationship where p27 repression of the Sox2 gene leads to reduced levels of SOX2-downstream targets Olig2 and Ascl1. In vivo, p27 is also required for the regulation of the proper level of SOX2 necessary for neuroblasts and oligodendroglial progenitor cells to timely exit cell cycle in a lineage-dependent manner.

2023-01-09 | GSE196328 | GEO

BAF subunit switching regulates chromatin accessibility to control cell cycle exit in the developing mammalian cortex [RNA-seq]

Project description:mSWI/SNF or BAF chromatin regulatory complexes are dosage-sensitive regulators of human neural development frequently mutated in autism and intellectual disability. Cell cycle exit and differentiation of neural stem/progenitor cells is accompanied by BAF subunit switching to generate neuron-specific nBAF complexes. We manipulated the timing of BAF subunit exchange in vivo and found that early loss of the npBAF subunit BAF53a stalls cell cycle exit to disrupt neurogenesis. Loss of BAF53a results in decreased chromatin accessibility at specific neural transcription factor binding sites, including the pioneer factors Sox2 and Ascl1, due to Polycomb accumulation. This results in repression of cell cycle genes, thereby blocking cell cycle progression and differentiation. Cell cycle block upon Baf53a deletion could be rescued by premature expression of the nBAF subunit BAF53b but not by other major drivers of proliferation or differentiation. Wnt, EGF, FGF, Sox2, myc or Pax6 all fail to maintain proliferation in the absence of BAF53a, highlighting a novel mechanism underlying neural progenitor cell cycle exit in the continued presence of extrinsic proliferative cues.

2021-01-18 | GSE164990 | GEO

BAF subunit switching regulates chromatin accessibility to control cell cycle exit in the developing mammalian cortex [ATAC-seq]

2021-01-18 | GSE164989 | GEO

Contact inhibition controls miR-223 stabilization via p27kip1 expression

Project description:The control of cell cycle progression mostly relays on the concerted activity of cyclins, CDKs and CDKs inhibitor. Recent data demonstrated that microRNAs, by regulating the expression of these proteins, contribute to the control of cell cycle progression. Here we provide evidences that the CDK inhibitor p27Kip1 directly regulates microRNAs stability thereby influencing cell cycle exit following contact inhibition. By the use of wild type and p27 knock-out cells we uncovered several microRNAs whose expression is linked to the cell cycle exit in a p27-dependent manner. By studying one of this microRNA, miR-223, we provide evidence that p27 is an RNA binding protein able to bind miR-223 to stabilize its expression. High miR-223 levels participate in the control of cell proliferation. Overall, we identify a previously completely unknown and conserved function of p27Kip1 that contributes to the proper regulation of cell cycle progression impinging on microRNA expression.

2015-12-31 | E-GEOD-45538 | biostudies-arrayexpress

Contact inhibition controls miR-223 stabilization via p27kip1 expression

2015-12-31 | GSE45538 | GEO

The STRIPAK complex regulates response to chemotherapy through p21 and p27

Project description:We report that loss of a component of the STRIPAK complex in MDA-MB-231 cells known as STRIP1 causes cell cycle arrest and decreased proliferation due to increased expression of cyclin dependent kinase inhibitors, p21 and p27. This change in p21 and p27 expression results in a subset of cells forgoing therapy-induced senescence and becoming proliferative.

2020-03-17 | GSE145618 | GEO

ChIP-seq on Olig2, Ascl1, Tcf3, Max, NFI, Sox2, Sox9 and Sox21 in mouse neural stem cells

Project description:Definition of genome wide binding profile of Olig2, Ascl1, Tcf3, Max, NFI, Sox2, Sox9 and Sox21 in mouse neural stem cells. Three sets of processed data files, together with a README file (README_E-MTAB-2228.docx) describing the source and content of each file, are provided as additional files to this ArrayExpress submission and can be found in https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2228 .

2014-09-19 | E-MTAB-2228 | biostudies-arrayexpress

Molecular characterization of quiescent melanoma cells

Project description:Cancer dormancy is closely associated with cellular quiescence, a state whereby cells exit the cell cycle and are reversibly arrested in G0 phase. Curative cancer treatment thus requires therapies that either sustain the dormant state of quiescent cancer cells, or preferentially, eliminate them. However, the mechanisms responsible for the quiescent survival of these cells remain obscure. We took advantage that quiescent cells characteristically negative for the proliferation marker Ki67 and express high levels of the cyclin-dependent kinase (CDK) inhibitor p27 to develop a CRISPR/Cas9-based system to fuse a green fluorescent protein (EGFP) gene with endogenous CDKN1B, the gene encoding p27, and a red fluorescent protein (mCherry) gene with endogenous MKI67, the gene encoding Ki67 in the genome of human melanoma cells. Flow cytometry were used to isolate the viable quiescent (p27high/Ki67low) cells. The isolated quiescent and cycling cancer cells were subjected to RNA-seq

2021-05-18 | GSE174520 | GEO

p27Kip1 regulates cell cycle progression by modulating the expression of p21Cip1

Project description:In addition to its classical role as a CDK inhibitor, p27 also acts as a transcriptional regulator. We found that at early passages, embryonic fibroblasts from p27-/- mouse show reduced expression of genes involved in DNA replication and progress slowly through the cell cycle. These cells have high levels of p21 that associate with cyclin-cdk2 complexes and reduce their activity. Decreasing p21 in these cells elevates cdk2 activity and DNA replication. We observed that silencing p27 in cells induces p21 transcription. Interestingly, the transcription factor Pitx2 is up-regulated in p27-/- cells. We found that p27 associates with a regulatory domain of the Pitx2 gene and represses its expression. In turn, Pitx2 associates with p21 promoter and induces its transcription. Moreover, reducing Pitx2 in p27-/- cells decreases p21 levels. These findings indicate that p27 controls cell cycle progression by regulating Pitx2-mediated expression of p21.

2016-06-09 | E-MTAB-2790 | biostudies-arrayexpress

Rapid differentiation of hiPSCs into functional oligodendrocytes using an OLIG2 synthetic modified messenger RNARapid differentiation of hiPSCs into functional oligodendrocytes using an OLIG2 synthetic modified messenger RNA

Project description:We show that a synthetic modified messenger RNA (smRNA)-based reprogramming method that leads to the generation of transgene-free OLs has been developed. An smRNA encoding a modified form of OLIG2, a key TF in OL development, in which the serine 147 phosphorylation site is replaced with alanine, OLIG2S147A, is designed to reprogram hiPSCs into OLs. We demonstrate that repeated administration of the smRNA encoding OLIG2 S147A lead to higher and more stable protein expression. Using the single-mutant OLIG2 smRNA morphogen, we establish a 6-day smRNA transfection protocol, and glial induction lead to rapid NG2+ OL progenitor cell (OPC) generation (> 70% purity) from hiPSC-derived neural progenitor cells (NPCs). The smRNA-induced NG2+ OPCs can mature into functional OLs in vitro and promote remyelination in vivo. Proteomic analysis of OLIG2-binding proteins indicates that OLIG2 is bound by the heat shock protein 70 (HSP70) complex. The HSP70 complex is bound more strongly to OLIG2 with the modified phosphorylation site than to wild-type OLIG2.

2023-03-10 | PXD036975 | Pride

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