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ChIP-seq analysis identifies p27(Kip1)-target genes involved in cell adhesion and cell signalling in mouse embryonic fibroblasts

ABSTRACT: ChIP-seq analysis identifies p27(Kip1)-target genes involved in cell adhesion and cell signalling in mouse embryonic fibroblasts

PROVIDER: PRJEB19264 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1815316.fastq.gz	Fastqsanger.gz
	ERR1815317.fastq.gz	Fastqsanger.gz

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ChIP-seq analysis identifies p27(Kip1)-target genes involved in cell adhesion and cell signalling in mouse embryonic fibroblasts

Project description:The protein p27(Kip1), a member of the Cip-Kip family of cyclin-dependent kinase inhibitors, has been recently identified as a transcriptional regulator. However, the transcriptional programs regulated by this protein, still remain mostly unknown. The aim of this study has been to define the transcriptional programs regulated by p27 by first identifying the p27-binding sites on the whole chromatin of quiescent mouse embryonic fibroblasts by Chromatin Immunoprecipitation Sequencing (ChIP-seq). Results revealed that most of the p27 binding sites were in distal intergenic regions and introns whereas, in contrast, its association with promoter regions was very low. Gene ontology analysis of the protein coding genes revealed a number of relevant transcriptional programs regulated by p27 as cell adhesion, intracellular signalling and neuron differentiation among others. We validated the interaction of p27 with different chromatin regions by ChIP followed by qPCR and demonstrated that the expressions of several genes belonging to these programs are actually regulated by p27.

2017-02-21 | E-MTAB-5105 | biostudies-arrayexpress

ChIP-Seq analysis identifies p27(Kip1)-target genes involved in cell adhesion and cell signalling in mouse embryonic fibroblasts.

Project description: Not available

| S-EPMC5695801 | biostudies-literature

p27 binds to promoters of multiple genes leading to their repression

2011-12-01 | GSE20068 | GEO

p27 binds to promoters of multiple genes leading to their repression

Project description:The role of the cyclin-cdk inhibitor p27 in tumorigenesis is still a controversial matter. We demonstrate here that p27 negatively regulates transcription of a number of genes (p27-target genes) involved in key cellular functions as RNA processing, translation, respiration and cell proliferation. Crosslinked chromatin from quiescent NIH3T3 cells was sonicated, incubated overnight with the rabbit anti-p27 and IgG antibodies as control

2011-12-01 | E-GEOD-20068 | biostudies-arrayexpress

Explore the molecular profile and properties of quiescent (P27+) and mitotic (P27-) glioma cell in diffuse low grade astrocytoma cell lines LGG275

Project description:Astrocytomas are known to present a cellular heterogeneity consisting of three identified subpopulations: "astrocyte-like", "oligodendrocyte-like" and "NPC-like" cells. It has also been shown that they contain a subpopulations of quiescent, or neural G0 cells, representing more than 90% of the tumor cells. The properties of this cell remain unclear due to the fact that it is difficult to isolate them. We used mVenus/P27 vector expression, constructed by Oki et al (2014), where P27 is fused to mVenus to highlight quiescent cells in LGG275 cell lines, a slow-growing astrocytoma. Then we used this reporter system to sort the mVenus/P27 expressing cells (quiescent) and the negative cells (mitotic) in aims to explore the properties of these two populations and validate the mVenus/P27 tool.

2026-01-13 | GSE306414 | GEO

Distribution of p27- and PCAF binding sites (BS) on the chromatin of HCT116 cell line

Project description:We analyzed the transcriptional programs regulated by PCAF and p27 in the colon cancer cell line HCT116 by ChIP-seq. We identified 269 protein-encoding genes that contain both p27 and PCAF binding sites being the majority of these sites different for PCAF and p27

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Cisplatin induces the rearrangement of RBPs on CDKN1B/p27 mRNA

Project description:Cisplatin (CP) is a chemotherapeutic drug that is used to cure different types of cancer. CP induces DNA damage and leads to cell cycle arrest. The cyclin-dependent kinase inhibitor 1B (CDKN1B), also termed p27, plays an important role in the drug response ; and increased levels of p27 correlated with CP resistance. In HEK293 cells, we observed that p27 mRNAs levels increased whereas protein level drastically decreased in cells treated with CP; suggesting post-transcriptional regulatory events. To further understand the underlying mechanisms, we applied a biochemical approach combined with mass-spectrometry to systematically identify the RNA-binding proteins (RBPs) that are bound to the 3’UTR of p27 mRNAs in CP-treated versus non-treated cells in vivo. We found that 24 proteins, most of them known RBPs such HuR, hNRNPD, changed their association with p27 mRNA upon CP treatement. Furthermore, knock-down of a subset of the identified RBPs led to the inhibition of the CP-induced increase of p27 mRNA levels. In conclusion, these results highlight substantial rearrangement between RBPs and p27 mRNA upon CP treatment and corroborate the importance of post-transcriptional control in cellular drug response.

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Activated leukocyte cell adhesion molecule on human oligodendrocytes mediates Th17 cell adhesion

Project description:Activated leukocyte cell adhesion molecule on human oligodendrocytes mediates Th17 cell adhesion

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Cell-surface proteomics identifies differences in signalling and adhesion protein expression between naive and primed human pluripotent stem cells

Project description:Naive and primed human pluripotent stem cells (hPSC) provide valuable models to study cellular and molecular developmental processes. The lack of detailed information about cell-surface protein expression in these two pluripotent cell types prevents an understanding of how the cells communicate and interact with their microenvironments. Here, we used plasma membrane profiling to directly measure cell-surface protein expression in naive and primed hPSC. This unbiased approach quantified over 1700 plasma membrane proteins including those involved in cell adhesion, signalling and cell interactions. Notably, multiple cytokine receptors upstream of JAK-STAT signalling were more abundant in naive hPSC. In addition, functional experiments showed that FOLR1 and SUSD2 proteins are highly expressed at the cell surface in naive hPSC but are not required to establish human naive pluripotency. This study provides a comprehensive stem cell proteomic resource that uncovers differences in signalling pathway activity and has identified new markers to define human pluripotent states.

2020-04-17 | PXD015359 | Pride

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