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Global RNA stability profiling reveals stabilization of P-body-enriched transcripts in the absence of human Dcp2

ABSTRACT: Global RNA stability profiling reveals stabilization of P-body-enriched transcripts in the absence of human Dcp2

PROVIDER: PRJNA601203 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10887642_1.fastq.gz	Fastqsanger.gz
	SRR10887642_2.fastq.gz	Fastqsanger.gz
	SRR10887643_1.fastq.gz	Fastqsanger.gz
	SRR10887643_2.fastq.gz	Fastqsanger.gz
	SRR10887644_1.fastq.gz	Fastqsanger.gz

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Global RNA stability profiling reveals stabilization of P-body-enriched transcripts in the absence of human Dcp2

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.

2020-05-06 | GSE143662 | 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.

2020-12-16 | GSE153258 | GEO

Klebsiella pneumoniae strain:DCP2 | isolate:DCP2

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Effects of Dcp1a and Dcp2 knockdown during mouse oocyte maturation

Project description:Oocyte maturation is accompanied by a transition from mRNA stability to instability. We investigated the role of DCP1A and DCP2, proteins responsible for mRNA decapping, in mRNA destabilization during mouse oocyte maturation. siRNA-mediated knockdown of both Dcp1a and Dcp2 transcripts prior to initiation of maturation inhibited the maturation-associated increase of DCP1A and DCP2, stabilized a set of maternal mRNAs that are normally degraded during maturation, and inhibited development beyond the 2-cell stage, likely a consequence of failure to activate fully the zygotic genome. Total RNA from 30 MII eggs was used in each sample. Three independent biological replicates were analyzed for each condition.

2013-02-06 | E-GEOD-27049 | biostudies-arrayexpress

mRNA sequencing analysis of zebrafish embryos, Dcp2 inhibition

Project description:we determined the contribution of the decapping enzyme Dcp2 to maternal mRNA clearance in zebrafish embryos by overexpressing a dominant-negative form of Dcp2.

2017-05-31 | GSE95679 | GEO

Effects of Dcp1a and Dcp2 knockdown during mouse oocyte maturation

2013-02-06 | GSE27049 | GEO

Global RNA stability profiling during selective chemical inhibition of human Dcp2

Project description:Global RNA stability profiling during selective chemical inhibition of human Dcp2

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3' RACE-seq of reporter LINE-1 and control mRNAs' 3' non-templated ends in 293T 'wild-type', XRN1 KO, DCP2 KO, DCP2 plus XRN1 KO cells

Project description:Human LINE-1 retrotransposons can mobilize in the human genome by a copy-and-paste machanism involving RNA intermediates. LINE-1 mRNA 3' ends play a major role in initiation of reverse transcription (a step retrotransposition). To assess the impact of RNA 3’ end dynamics of LINE-1 mRNA on its retrotransposition potential in human cells we analyzed 3' non-templated ends on LINE-1, and control GAPDH and PABPC4 mRNAs by 3' RACE-seq. RNA was retrieved from multiple clonal 293T cells wild-type or knock-out in eitehr XRN1, DCP2, or both (DCP2 plus XRN1). Publication: D Janecki, R Sen, N Szóstak, A Kajdasz, M Kordys, K Plawgo, D Pandakov, A Philips, Z Warkocki (2024): LINE-1 mRNA 3’ end dynamics shape its biology and retrotransposition potential. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad1251

2024-01-05 | GSE230464 | GEO

Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo

Project description:We have identified mRNAs whose abundance or translational efficiency is regulated in nutrient-rich medium by the Scd6 or Dhh1 protein in either wild-type cells or dcp2∆ cells lacking the decapping enzyme

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Stabilization competency signature

Project description:Comparison of gene expresion profile of 4 SC clones and 4 SI clones at different time points defined a stabilization competency signiture required for successful reprogramming mRNA profilling 4 SI clones at 5 time points, 4 SC clones at 6 time points, and 3 feeder samples.

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