ArticleNature2011
XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast.
Article in Nature, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 224 papers.
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Who cites it
224 citing papers in PubMed, 370 citations in OpenAlex.
- Genetic landscape of an in vivo protein interactome.Nature genetics · 2026Article
- TRiC/CCT chaperonin governs RNA polymerase II activity in the nucleus to support RNA homeostasis.Molecular cell · 2026Article
- A systematic interactome ofeLife · 2026Article
- The hidden power of antisense long non-coding RNAs: a dive into a novel regulatory layer mediated by double-stranded RNA formation.RNA biology · 2025Review
- Identification and Functions of lncRNAs in Fungi.Non-coding RNA · 2025Review
- Functional analysis and transcriptional profiling of non-coding RNAs in yeast.The Biochemical journal · 2025Review
- Identification of translation events that drive nonsense-mediated mRNA decay reveals functional roles for noncoding RNAs.bioRxiv : the preprint server for biology · 2025Article
- Precise measurement of molecular phenotypes with barcode-based CRISPRi systems.Genome biology · 2025Article
- Pervasive formation of double-stranded RNAs by overlapping sense/antisense transcripts in budding yeast mitosis and meiosis.RNA (New York, N.Y.) · 2025Article
- Proper 5'-3' cotranslational mRNA decay in yeast requires import of Xrn1 to the nucleus.PloS one · 2025Article
- Transcriptome-Wide Analysis of the 5' Cap Status of RNA Using 5' Monophosphate-Dependent Exonuclease Digestion and RNA Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- RNA degradation triggered by decapping is largely independent of initial deadenylation.The EMBO journal · 2024Article
- The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging.Nature communications · 2024Article
- Spt5 orchestrates cryptic transcript suppression and transcriptional directionality.Communications biology · 2024Article
- Natural antisense transcripts as versatile regulators of gene expression.Nature reviews. Genetics · 2024Review
- Article
- Pervasive translation of Xrn1-sensitive unstable long noncoding RNAs in yeast.RNA (New York, N.Y.) · 2024Article
- In silico genome wide identification of long non-coding RNAs differentially expressed during Candida auris host pathogenesis.Archives of microbiology · 2024Article
- XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells.Cell reports · 2024Article
- Post-transcriptional regulation shapes the transcriptome of quiescent budding yeast.Nucleic acids research · 2024Article
164 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-coding (nc)RNAs are key players in numerous biological processes such as gene regulation, chromatin domain formation and genome stability. Large ncRNAs interact with histone modifiers and are involved in cancer development, X-chromosome inactivation and autosomal gene imprinting. However, despite recent evidence showing that pervasive transcription is more widespread than previously thought, only a few examples mediating gene regulation in eukaryotes have been described. In Saccharomyces cerevisiae, the bona-fide regulatory ncRNAs are destabilized by the Xrn1 5'-3' RNA exonuclease (also known as Kem1), but the genome-wide characterization of the entire regulatory ncRNA family remains elusive. Here, using strand-specific RNA sequencing (RNA-seq), we identify a novel class of 1,658 Xrn1-sensitive unstable transcripts (XUTs) in which 66% are antisense to open reading frames. These transcripts are polyadenylated and RNA polymerase II (RNAPII)-dependent. The majority of XUTs strongly accumulate in lithium-containing media, indicating that they might have a role in adaptive responses to changes in growth conditions. Notably, RNAPII chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) analysis of Xrn1-deficient strains revealed a significant decrease of RNAPII occupancy over 273 genes with antisense XUTs. These genes show an unusual bias for H3K4me3 marks and require the Set1 histone H3 lysine 4 methyl-transferase for silencing. Furthermore, abolishing H3K4me3 triggers the silencing of other genes with antisense XUTs, supporting a model in which H3K4me3 antagonizes antisense ncRNA repressive activity. Our results demonstrate that antisense ncRNA-mediated regulation is a general regulatory pathway for gene expression in S. cerevisiae.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.