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Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast

ABSTRACT: Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast

PROVIDER: PRJNA839354 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19266831_1.fastq.gz	Fastqsanger.gz
	SRR19266831_2.fastq.gz	Fastqsanger.gz
	SRR19266832_1.fastq.gz	Fastqsanger.gz
	SRR19266832_2.fastq.gz	Fastqsanger.gz
	SRR19266833_1.fastq.gz	Fastqsanger.gz

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Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast

Project description:Despite being predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensitive lncRNAs (XUTs) are targeted by the Nonsense-Mediated mRNA Decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. We show that XUTs globally accumulate upon translation elongation inhibition, but not when initial ribosome loading is impaired. Ribo-Seq confirmed ribosomes binding to XUTs and identified ribosome-associated 5’-proximal small ORFs. Mechanistically, the NMD-sensitivity of XUTs mainly depends on the 3’-untranslated region length. Finally, we show that the peptide resulting from the translation of an NMD-sensitive XUT reporter exists in NMD-competent cells. Our work highlights the role of translation in the post-transcriptional metabolism of XUTs. We propose that XUT-derived peptides could be exposed to the natural selection, while NMD restricts XUTs levels.

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Translational landscape of Xrn1-sensitive lncRNAs in yeast

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Translational landscape of Xrn1-sensitive lncRNAs in yeast

Project description:Translational landscape of Xrn1-sensitive lncRNAs in yeast

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Project description:To determine the effects of inactivation of both the nosense-mediated mRNA decay pathway and the general 5' to 3' decay pathway on yeast mRNA decay, we compared the expression profiles of the wild-type, xrn1, xrn1 upf1, xrn1 nmd2, and xrn1 upf3 strains.

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Xrn1-sensitive lncRNAs are insensitive to Dbp2 nuclear depletion

Project description:Xrn1-sensitive lncRNAs are insensitive to Dbp2 nuclear depletion

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Silencing Xrn1 by dox-inducible shRNA

Project description:Xrn1 is a cytoplasmic 5’-3’ exoribonuclease responsible for degradation of multiple types of RNA. Data obtained on yeast model described Xrn1 function in degradation of messenger (m)RNA, Rapid transfer (t)RNA Decay (RTD) of hypomodified and unstable tRNA transcripts as well as maturation of 25S ribosomal (r)RNA and small nucleolar (sno)RNAs. Our group discovered previously that deletion of Xrn1 gene results in stabilization of a group of long non-coding RNAs which are often transcribed antisense to protein-coding genes and may regulate their expression on transcriptional level. However much less is known about human (h)Xrn1 function. Data available from human cell lines confirm involvement of hXrn1 in degradation of mRNA, initiator tRNA methionine and some miRNA. The high sequence similarity of Xrn1 between yeast and man suggests that also its function should be well conserved for hXrn1. Therefore, in this experiment using inducible shRNA we want to define hXrn1 targets by analyzing RNAs that are stabilized after Xrn1 silencing with focus on both coding and non-coding transcripts.

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Xrn1-sensitive lncRNAs are globally insensitive to the cytoplasmic helicases Ecm32, Ski2, Slh1, Dbp1 and Dhh1

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