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Xrn1-sensitive lncRNAs accumulate upon inactivation of Dbp2 and Mtr4

ABSTRACT: Xrn1-sensitive lncRNAs accumulate upon inactivation of Dbp2 and Mtr4

PROVIDER: PRJNA986459 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24991444_1.fastq.gz	Fastqsanger.gz
	SRR24991444_2.fastq.gz	Fastqsanger.gz
	SRR24991445_1.fastq.gz	Fastqsanger.gz
	SRR24991445_2.fastq.gz	Fastqsanger.gz
	SRR24991446_1.fastq.gz	Fastqsanger.gz

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Xrn1-sensitive lncRNAs accumulate upon inactivation of Dbp2 and Mtr4

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Xrn1-sensitive lncRNAs are insensitive to Dbp2 nuclear depletion

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Nonsense-Mediated Decay restricts lncRNAs levels in yeast unless blocked by double-stranded RNA structure

Project description:Antisense long non-coding (aslnc)RNAs represent a substantial part of eukaryotic transcriptomes that are, in yeast, controlled by the Xrn1 exonuclease. Nonsense-Mediated Decay (NMD) destabilizes the Xrn1-sensitive aslncRNAs (XUT), but what determines their sensitivity remains unclear. We report that 3’ single-stranded (3’-ss) extension mediates XUTs degradation by NMD, assisted by the Mtr4 and Dbp2 helicases. Single-gene investigation, genome-wide RNA analyses and double-stranded (ds)RNA mapping revealed that 3'-ss extensions discriminate the NMD-targeted XUTs from stable lncRNAs. Ribosome profiling showed that XUT are translated locking them for NMD activity. Interestingly, mutants of the Mtr4 and Dbp2 helicases accumulated XUTs, suggesting that dsRNA unwinding is a critical step for degradation. Indeed, expression of anti-complementary transcripts protects cryptic intergenic lncRNAs from NMD. Our results indicate that aslncRNAs form dsRNA that are only translated and targeted to NMD if dissociated by Mtr4 and Dbp2. We propose that NMD buffers genome expression by discarding pervasive regulatory transcripts.

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tiling hen2 and mtr4-HEN2 is a cofactor of the nuclear exosome in Arabidopsis

Project description:til-ath-2011_3 - tiling hen2 and mtr4 - Identification and comparison of the RNA substrates that accumulate in hen2 and mtr4 mutants. Total RNA extracted from WT, hen2 and mtr4 mutants was used for oligo-dT primed cDNA preparation. Samples were hybridised to NimbleGen whole genome tiling arrays. 8 dye-swapped samples. Gene knockout, genotype comparison, normal vs. transgenic comparison.

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