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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:The protein p27Kip1 (p27), a member of the Cip-Kip family of cyclin-dependent kinase inhibitors, is involved in tumorigenesis and a correlation between reduced levels of this protein in human tumours and a worse prognosis has been established. Recent reports revealed that p27 also behaves as a transcriptional regulator. Thus, it has been postulated that the development of tumours with low amounts of p27 could be propitiated by deregulation of transcriptional programs under the control of p27. However, these programs 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 (p27-BSs) on the whole chromatin of quiescent mouse embryonic fibroblasts. The chromatin regions associated to p27 have been annotated to the most proximal genes and it has been considered that the expression of these genes could by regulated by p27. The identification of the chromatin p27-BSs has been performed by Chromatin Immunoprecipitation Sequencing (ChIP-seq). Results revealed that p27 associated with 1839 sites that were annotated to 1417 different genes being 852 of them protein coding genes. Interestingly, most of the p27-BSs 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. Finally, cell adhesion assays revealed that the adhesion of p27-/- cells to the plates was much higher that controls, revealing a role of p27 in the regulation of a transcriptional program involved in cell adhesion.

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

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Genome-wide profile of cJun and p27 in breast cancer cells

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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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p27 binds to promoters of multiple genes leading to their repression

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A Whole-Cell Screening Platform for Discovering Cell Adhesion Molecules Enabling Programmable Bacterial Cell-Cell Adhesion

Project description:A Whole-Cell Screening Platform for Discovering Cell Adhesion Molecules Enabling Programmable Bacterial Cell-Cell Adhesion

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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

p27-affinity-purified mass spectrometry anslysis

Project description:This project aims to identify p27 modification sites.

2023-01-05 | PXD039223 | Pride