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An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation [RNA-seq]

ABSTRACT: An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation [RNA-seq]

PROVIDER: PRJNA593587 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10588338.fastq.gz	Fastqsanger.gz
	SRR10588339.fastq.gz	Fastqsanger.gz

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An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation

Project description:An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation

| PRJNA594049 | ENA

An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation [Amplicon-seq]

Project description:An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation [Amplicon-seq]

| PRJNA594048 | ENA

An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation [RNA-seq]

Project description:MYC controls the transcription of large numbers of long non-coding RNAs. Since MYC is a ubiquitous oncoprotein, some of these long non-coding RNAs (lncRNAs) probably play a significant role in cancer. We applied CRISPRi to the identification of MYC-regulated lncRNAs that are required for MYC-driven cell proliferation in the P493-6 and RAMOS human lymphoid cell lines. We identified 320 non-coding loci that play a positive role in cell growth. Transcriptional repression of any one of these lncRNAs reduces the proliferative capacity of the cells. Selected hits were validated by RTqPCR and in CRISPRi-competition assays with individual GFP-expressing sgRNA-constructs. We also showed binding of MYC to the promoter of two candidate genes by chromatin immunoprecipitation. In the course of our studies, we discovered that the repressor domain SID derived from the MXD1 protein is highly effective in P493-6 and RAMOS cells in terms of the number of guides depleted in library screening and the extent of the induced transcriptional repression. In the cell lines used, it is superior to the KRAB repressor domain which serves routinely as transcriptional repressor domain in CRISPRi. The SID transcriptional repressor domain is effective as a fusion to the MS2 aptamer binding protein MCP allowing the construction of a doxycycline regulatable CRISPRi-system that allows controlled repression of targeted genes and will facilitate the functional analysis of growth-promoting lncRNAs.

2020-04-06 | GSE141482 | GEO

An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation [Amplicon-seq]

2020-04-06 | GSE141491 | GEO

An MXD1-derived repressor peptide identifies noncoding mediators of MYC-driven cell proliferation.

Project description:MYC controls the transcription of large numbers of long noncoding RNAs (lncRNAs). Since MYC is a ubiquitous oncoprotein, some of these lncRNAs probably play a significant role in cancer. We applied CRISPR interference (CRISPRi) to the identification of MYC-regulated lncRNAs that are required for MYC-driven cell proliferation in the P493-6 and RAMOS human lymphoid cell lines. We identified 320 noncoding loci that play positive roles in cell growth. Transcriptional repression of any one of these lncRNAs reduces the proliferative capacity of the cells. Selected hits were validated by RT-qPCR and in CRISPRi competition assays with individual GFP-expressing sgRNA constructs. We also showed binding of MYC to the promoter of two candidate genes by chromatin immunoprecipitation. In the course of our studies, we discovered that the repressor domain SID (SIN3-interacting domain) derived from the MXD1 protein is highly effective in P493-6 and RAMOS cells in terms of the number of guides depleted in library screening and the extent of the induced transcriptional repression. In the cell lines used, SID is superior to the KRAB repressor domain, which serves routinely as a transcriptional repressor domain in CRISPRi. The SID transcriptional repressor domain is effective as a fusion to the MS2 aptamer binding protein MCP, allowing the construction of a doxycycline-regulatable CRISPRi system that allows controlled repression of targeted genes and will facilitate the functional analysis of growth-promoting lncRNAs.

| S-EPMC7104257 | biostudies-literature

An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-04-06 | GSE141615 | GEO

The MYCL and MXD1 transcription factors regulate the fitness of murine dendritic cells

Project description:The present study reveals LMYC and MXD1 as novel regulators of a transcriptional program that is modulated during the maturation of Batf3-dependent dendritic cells (also known as type I classical dendritic cells or cDC1s). We used microarray analysis with ERCC spike in controls to determine the transcriptional effects of MYCL and MXD1 deficiency at steady state and after activation with poly IC. Mycl-deficient mice are available from Jackson laboratories as B6.129S6(C)-Mycltm1.1Kmm/J. Mxd1-/- mice were provided by R. Eisenman.

2019-12-05 | GSE141492 | GEO

Mxd1

Project description:Rattus norvegicus Mxd1, max dimerization protein 1 [Source:RGD Symbol;Acc:1564525], is expressed in 3 baseline experiment(s);

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Project description:Rattus norvegicus Mxd1, max dimerization protein 1 [Source:RGD Symbol;Acc:1564525], is differentially expressed in 34 experiment(s);

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Project description:Monodelphis domestica MXD1, MAX dimerization protein 1 [Source:NCBI gene;Acc:100032835], is expressed in 2 baseline experiment(s);

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