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RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis

ABSTRACT: RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis

PROVIDER: PRJNA795486 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17487763.fastq.gz	Fastqsanger.gz
	SRR17487764.fastq.gz	Fastqsanger.gz
	SRR17487765.fastq.gz	Fastqsanger.gz
	SRR17487766.fastq.gz	Fastqsanger.gz
	SRR17487767.fastq.gz	Fastqsanger.gz

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RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis

Project description:To gain insight into the functional role of DNE1 in cytoplasmic mRNA decay, we performed Parallel Analysis of RNA Ends (PARE) and Global Mapping of Uncapped and Cleaved Transcripts (GMUCT) analysis to identify DNE1-dependent cleavage sites based on their sensitivity to XRN4 within the Arabidopsis transcriptome

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RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis.

Project description:In plants, cytoplasmic mRNA decay is critical for posttranscriptionally controlling gene expression and for maintaining cellular RNA homeostasis. Arabidopsis DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a cytoplasmic mRNA decay factor that interacts with proteins involved in mRNA decapping and nonsense-mediated mRNA decay (NMD). There is limited information on the functional role of DNE1 in RNA turnover, and the identities of its endogenous targets are unknown. In this study, we utilized RNA degradome approaches to globally investigate DNE1 substrates. Monophosphorylated 5' ends, produced by DNE1, should accumulate in mutants lacking the cytoplasmic exoribonuclease XRN4, but be absent from DNE1 and XRN4 double mutants. In seedlings, we identified over 200 such transcripts, most of which reflect cleavage within coding regions. While most DNE1 targets were NMD-insensitive, some were upstream ORF (uORF)-containing and NMD-sensitive transcripts, indicating that this endoribonuclease is required for turnover of a diverse set of mRNAs. Transgenic plants expressing DNE1 cDNA with an active-site mutation in the endoribonuclease domain abolished the in planta cleavage of transcripts, demonstrating that DNE1 endoribonuclease activity is required for cleavage. Our work provides key insights into the identity of DNE1 substrates and enhances our understanding of DNE1-mediated mRNA decay.

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Regulated endocleavage balances the degradation of nonsense-mediated decay substrates

Project description:Nonsense-mediated mRNA decay (NMD) controls gene expression by eliminating mRNAs with premature or aberrant translation termination. Degradation of NMD substrates is initiated by the central NMD factor UPF1, which recruits the endonuclease SMG6 and the deadenylation-promoting SMG5/7 complex. Here we map transcriptome-wide sites of SMG6-mediated endocleavage via 3′ fragment capture and degradome sequencing.

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