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YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [RNA-Seq]

ABSTRACT: YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [RNA-Seq]

PROVIDER: PRJNA634098 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11818032.fastq.gz	Fastqsanger.gz
	SRR11818033.fastq.gz	Fastqsanger.gz
	SRR11818034.fastq.gz	Fastqsanger.gz
	SRR11818035.fastq.gz	Fastqsanger.gz
	SRR11818036.fastq.gz	Fastqsanger.gz

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Similar Datasets

YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [PAR-CLIP]

Project description:The RNA- and DNA-binding protein YBX1 is involved in various cellular processes. We here focused on investigating its role in posttranscriptional gene regulation in medulloblastoma, in which CRISPR screens have shown its essentiality for cellular survival. We found that YBX1 knockdown leads to broad upregulation of genes related to neuroinflammation, and directly regulates mRNA stability of various mRNA targets. More specifically, target CBX5, also called heterochromatin-protein 1 alpha (HP1-alpha), is downregulated upon YBX1 KD. It associates strongly with heterochromatin, and upon downregulation allows for upregulation of heterochromatin repressed genes related to inflammation.

2020-06-26 | GSE150925 | GEO

YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [RNA-Seq]

2020-06-26 | GSE150924 | GEO

YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [PAR-CLIP]

Project description:YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [PAR-CLIP]

| PRJNA634100 | ENA

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA.

Project description:Medulloblastomas arise from undifferentiated precursor cells in the cerebellum and account for about 20% of all solid brain tumors during childhood; standard therapies include radiation and chemotherapy, which oftentimes come with severe impairment of the cognitive development of the young patients. Here, we show that the posttranscriptional regulator Y-box binding protein 1 (YBX1), a DNA- and RNA-binding protein, acts as an oncogene in medulloblastomas by regulating cellular survival and apoptosis. We observed different cellular responses upon YBX1 knockdown in several medulloblastoma cell lines, with significantly altered transcription and subsequent apoptosis rates. Mechanistically, PAR-CLIP for YBX1 and integration with RNA-Seq data uncovered direct posttranscriptional control of the heterochromatin-associated gene CBX5; upon YBX1 knockdown and subsequent CBX5 mRNA instability, heterochromatin-regulated genes involved in inflammatory response, apoptosis and death receptor signaling were de-repressed. Thus, YBX1 acts as an oncogene in medulloblastoma through indirect transcriptional regulation of inflammatory genes regulating apoptosis and represents a promising novel therapeutic target in this tumor entity.

| S-EPMC7352269 | biostudies-literature

YBX1 HITS-CLIP

Project description:In order to identify YBX1 binding sites on endogenous RNA, we performed HITS-CLIP on endogenous YBX1 We used a previously published method to perform HITS-CLIP on endogenous YBX1 (Licatalosi D, et al. 2008, Nature 456:464-U22)

2015-05-08 | E-GEOD-63604 | biostudies-arrayexpress

YBX1 small-RNA HITS-CLIP

Project description:In order to identify YBX1 binding sites on tRNA fragments, we performed small-RNA HITS-CLIP on endogenous YBX1 We used a previously published method to perform HITS-CLIP on endogenous YBX1 (Chi SW, et al. 2009, Nature 460:479)

2015-05-08 | E-GEOD-63597 | biostudies-arrayexpress

Chip-chip from HCT116 cells with YBX1

Project description:YBX1 is a multifunctional protein involved in the control of transcription and translation. We identified YBX1 as an target of MEK/ERK signaling in colorectal cancer cell lines. We performed a ChIP-chip analysis of HCT116 cells to identify new potential target genes of YBX1. Comparison of input DNA fragments with fragments coprecipitated with YBX1 in HCT116 cells.

2010-10-09 | E-GEOD-18337 | biostudies-arrayexpress

YBX1-dependent hypoxia-induced modulation of gene expression

Project description:In order to identify YBX1-dependent targets that are modulated under hypoxic conditions, we used control and YBX1 knockdown cells grown under normoxia and hypoxia to profile gene expression levels. Control and YBX1-knockdown cells were grown and profiled under hypoxia and normoxia to identify YBX1-dependent hypoxia-induced target transcripts.

2015-05-08 | E-GEOD-63562 | biostudies-arrayexpress

BRD4 represses CBX5

Project description:BRD4 is amplified and/or up-regiulated in a subset of ovarian cancer which correlates with a poor survival siRNA sensitization screens in the presence of CHK1 inhibitor, LY2606368, identify BRD4 as a therapeutic target in ovarian cancer. BRD4 suppression by either siRNA or using JQ1 increases CBX5 expression

2016-05-01 | GSE78704 | GEO

YBX1-dependent LNA-tRF-mediated modulation of gene expression

Project description:In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by microarray profiling. Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr were transfected into control and YBX1-knockdown cells to identify YBX1-dependent targets that are modulated due to tRF loss-of-function.

2015-05-08 | E-GEOD-63564 | biostudies-arrayexpress

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