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Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [m6A-RIP-seq]

ABSTRACT: Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [m6A-RIP-seq]

PROVIDER: PRJNA681201 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13156881_1.fastq.gz	Fastqsanger.gz
	SRR13156881_2.fastq.gz	Fastqsanger.gz
	SRR13156882_1.fastq.gz	Fastqsanger.gz
	SRR13156882_2.fastq.gz	Fastqsanger.gz
	SRR13156883_1.fastq.gz	Fastqsanger.gz

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Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [m6A-RIP-seq]

Project description:Total RNAs were isolated from WT_CON, KO_CON, WT_LPS and KO_LPS Raw 264.7 cells, subjected to standard m6A RIP protocol. The libraries were generated with IPed and Input RNAs and subjected to Sequencing. Raw sequencing reads were aligned to the mouse genome (mm10) with Tophat , and gene expression levels were measured by Cufflinks.

2021-04-30 | GSE162254 | GEO

Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation

Project description:Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation

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Pooled CRISPR screening identifies m6A as a positive regulator of macrophage activation.

Project description:m6A RNA modification is implicated in multiple cellular responses. However, its function in the innate immune cells is poorly understood. Here, we identified major m6A "writers" as the top candidate genes regulating macrophage activation by LPS in an RNA binding protein focused CRISPR screening. We have confirmed that Mettl3-deficient macrophages exhibited reduced TNF-α production upon LPS stimulation in vitro. Consistently, Mettl3flox/flox;Lyzm-Cre mice displayed increased susceptibility to bacterial infection and showed faster tumor growth. Mechanistically, the transcripts of the Irakm gene encoding a negative regulator of TLR4 signaling were highly decorated by m6A modification. METTL3 deficiency led to the loss of m6A modification on Irakm mRNA and slowed down its degradation, resulting in a higher level of IRAKM, which ultimately suppressed TLR signaling-mediated macrophage activation. Our findings demonstrate a previously unknown role for METTL3-mediated m6A modification in innate immune responses and implicate the m6A machinery as a potential cancer immunotherapy target.

| S-EPMC8081357 | biostudies-literature

Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [Amplicon-seq]

Project description:Customized pooled RNA Binding Protein (RBP) CRISPR libraries were applied to macrophage cell line Raw 264.7 cells to identify RBPs that are critical for LPS activated TNFa production.sgRNAs that enriched in TNFa-low, TNFa-High and pre-sort populations were sequenced and significant enriched genes were retrieved with MAGeCK test subcommand.

2021-04-30 | GSE162469 | GEO

Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [RNA-seq]

Project description:The involvement of m6A modification in macrophage activation has been validated in our study that the expression of TNF-α in Mettl3-depleted Raw 264.7 cells stimulated with LPS were markedly reduced in comparison to control cells. To further explore the biological effects of m6A deficiency macrophages, we performed RNA sequencing analysis of Mettl3-KO and WT control Raw 264.7 cells upon LPS treatment. The GO enrichment analysis documented that the downregulated transcripts in Mettl3-KO Raw 264.7 cells were enriched in innate immune response related to defense and external stimulus. Notably, transcripts of the downstream components of the TLR4 signaling pathway, such as proinflammatory cytokines (Tnf-α, Il-6, Il-1β, Il-18,and Il-23) and co-stimulation molecules (Cd86), were downregulated in Mettl3-deficient cells, suggesting that METTL3 has a critical function in controlling the innate immune response of Raw 264.7 macrophages.

2021-04-30 | GSE162248 | GEO

Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [Amplicon-seq]

Project description:Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [Amplicon-seq]

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Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [RNA-seq]

Project description:Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [RNA-seq]

| PRJNA681200 | ENA

m6A-RIP-seq of Ascl1-induced neurons.

Project description:We performed m6A-RIPs in Ascl1-induced neurons (iNeurons) to investigate the neuronal m6A epitranscriptome. Immunoprecipitation was done twice using two different antibodies, acquired from Abcam and Synaptic Systems (SySy), allowing for a more robust detection of m6A modification marks. Additionally, RIP-seq was performed separately with intact and fragmented RNA. The former approach allowed to identify proportions of m6A-modified transcripts among the total number, while the latter approach provided the information to identify genomic coordinates of m6A peaks.

2023-07-12 | E-MTAB-9542 | biostudies-arrayexpress

Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation

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

2021-04-30 | GSE162255 | GEO

m6A-RIP seq of Huh7 cells

Project description:m6A-RIP seq of Huh7 cells

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