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Global RNA stability profiling in human NBDY knockout using TimeLapse-seq

ABSTRACT: Global RNA stability profiling in human NBDY knockout using TimeLapse-seq

PROVIDER: PRJNA607951 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11139039_1.fastq.gz	Fastqsanger.gz
	SRR11139039_2.fastq.gz	Fastqsanger.gz
	SRR11139040_1.fastq.gz	Fastqsanger.gz
	SRR11139040_2.fastq.gz	Fastqsanger.gz
	SRR11139041_1.fastq.gz	Fastqsanger.gz

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Global RNA stability profiling in human NBDY knockout using TimeLapse-seq

Project description:We previously identified a conserved human microprotein NoBody/NBDY that can interact with the mRNA decapping complex through EDC4 and affects the expression of an NMD (nonsense-mediated decay) substrate. However, it remains unclear the exact mechanism of NBDY-regulated RNA stability change and whether this is the direct cause/consequence of its modulation of P-body structure/numbers. Here we present a global profile of RNA stability in human NBDY knockout cells via TimeLapse-seq. By comparing this dataset to our previous work done in DCP2 KO cells, we demonstrate that NBDY is a specificity factor of the 5'-3' RNA decay. In addition, these data indicate a role of NBDY in cell cycle and other signaling transduction processes as well.

2020-12-16 | GSE145682 | GEO

Global RNA stability profiling in HEK293T cells under EGF treatment using TimeLapse-seq

Project description:Global RNA stability profiling in HEK293T cells under EGF treatment using TimeLapse-seq

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Global RNA stability profiling in HEK293T cells under EGF treatment using TimeLapse-seq

Project description:We discovered through LC-MS/MS followed by biochemical assays and immunofluorescence that human microprotein NoBody/NBDY can be phosphorylated during EGF signaling transduction, and that this single post-translational modification of the smallest decapping complex component known to date is necessary to the observed disappearance of P-bodies under EGF treatment. RNA stability measurement of a known hDcp2 substrate, RRP41, showed decreased RNA life-time under EGF treatment. We hence wish to investigate the effect of this phospho-NBDY mediated P-body disassembly on global RNA turnover. Here we present a global profile of RNA stability in human HEK293 cells under EGF treatment via TimeLapse-seq. By comparing this dataset to our previous and current work done in DCP2 KO and in NBDY KO cells, respectively, we demonstrate that P-body dissociation observed during EGF signaling does not cause RNA stability change globally except for a few known EGF regulated transcripts.

2021-12-31 | GSE146213 | GEO

Global RNA stability profiling during selective chemical inhibition of human Dcp2

Project description:Multiple RNA decapping enzymes coexist in mammalian cells to regulate decay of partially overlapping sets of cellular transcripts, but a comprehensive understanding of cellular substrate selectivity of each enzyme is yet to be achieved. Previously we demonstrate the utility of TimeLapse-seq in global profiling of RNA stability changes in human Dcp2 knockout cells. However, secondary transcriptional changes and upregulation of alternative decay pathways have obscured complete mapping of Dcp2 substrates. Here, we present the discovery and first application of a cell-permeable, highly selective Dcp2 ligand in the chemical genetic study of its RNA substrates.

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Project description:Multiple RNA decapping enzymes coexist in mammalian cells to regulate decay of distinct subsets of cellular transcripts, but their specificity remains incompletely defined to date. Here we present a global profile of RNA stability changes in human Dcp2 knockout cells via TimeLapse-seq. We demonstrate that P-body enrichment is the strongest correlate of Dcp2-dependent RNA decay, and that post-transcriptional modifications such as m6A present additive effect for Dcp2 targeting. Importantly, our data support a model in which P-bodies are sites that sort translationally repressed transcripts for cytoplasmic decay through additional molecular marks.

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