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Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics

ABSTRACT: Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics

PROVIDER: PRJNA549287 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9312960.fastq.gz	Fastqsanger.gz
	SRR9312961.fastq.gz	Fastqsanger.gz
	SRR9312962.fastq.gz	Fastqsanger.gz
	SRR9312963.fastq.gz	Fastqsanger.gz
	SRR9312964.fastq.gz	Fastqsanger.gz

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Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics

Project description:NFkB RelA is the potent transcriptional activator of inflammatory response genes. We stringently defined a list of direct RelA target genes by integrating physical (ChIPseq) and functional (RNAseq in knockouts) datasets. We then dissected each gene's regulatory strategy by testing RelA variants in a novel primary-cell genetic complementation assay. All endogenous target genes required that RelA makes DNA-base-specific contacts, and none could be activated by the DNA binding domain alone. However, endogenous target genes differed widely in how they employ the two transactivation domains. Through model-aided analysis of the dynamic timecourse data we reveal gene-specific synergy and redundancy of TA1 and TA2. Given that post-translational modifications control TA1 activity and intrinsic affinity for coactivators determines TA2 activity, the differential TA logics suggests context-dependent vs. context-independent control of endogenous RelA-target genes. While some inflammatory initiators appear to require co-stimulatory TA1 activation, inflammatory resolvers are a part of the NFkB RelA core response.

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Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics [caRNAseq]

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Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics [MEF]

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Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics (ChIP-seq.WT.MEFs)

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Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics (RNA-seq.WT.p53ko.MEFs_4)

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Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics [ChIP-seq RNAPII]

Project description:NFkB RelA is the potent transcriptional activator of inflammatory response genes. We stringently defined a list of direct RelA target genes by integrating physical (ChIPseq) and functional (RNAseq in knockouts) datasets. We then dissected each gene’s regulatory strategy by testing RelA variants in a novel primary-cell genetic complementation assay. All endogenous target genes required that RelA makes DNA-base-specific contacts, and none could be activated by the DNA binding domain alone. However, endogenous target genes differed widely in how they employ the two transactivation domains. Through model-aided analysis of the dynamic timecourse data we reveal gene-specific synergy and redundancy of TA1 and TA2. Given that post-translational modifications control TA1 activity and intrinsic affinity for coactivators determines TA2 activity, the differential TA logics suggests context-dependent vs. context-independent control of endogenous RelA-target genes. While some inflammatory initiators appear to require co-stimulatory TA1 activation, inflammatory resolvers are a part of the NFkB RelA core response.

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Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics

Project description:Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics

| PRJNA548321 | ENA

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