XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast
E L van Dijk1, C L Chen, Y d'Aubenton-Carafa
1Centre de Génétique Moléculaire (CNRS UPR 3404), avenue de la Terrasse, 91198 Gif sur Yvette, France.
Nature
|June 24, 2011
Summary
Researchers discovered 1,658 novel unstable transcripts (XUTs) in yeast, with most acting as antisense regulators. These XUTs, sensitive to the Xrn1 exonuclease, reveal a new layer of gene regulation involving histone modifications and adaptive responses.
Area of Science:
- Molecular Biology
- Genetics
- Yeast Biology
Background:
- Non-coding RNAs (ncRNAs) are crucial for gene regulation, chromatin structure, and genome stability.
- Large ncRNAs influence processes like cancer development and X-chromosome inactivation.
- Genome-wide characterization of regulatory ncRNAs in Saccharomyces cerevisiae is limited, especially those sensitive to the Xrn1 exonuclease.
Purpose of the Study:
- To identify and characterize novel regulatory ncRNAs in Saccharomyces cerevisiae.
- To investigate the role of Xrn1-sensitive unstable transcripts (XUTs) in gene regulation.
- To elucidate the relationship between antisense XUTs, histone modifications, and gene silencing.
Main Methods:
- Strand-specific RNA sequencing (RNA-seq) to identify XUTs.
- Analysis of XUTs in lithium-containing media for adaptive responses.
- RNA polymerase II (RNAPII) chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) in Xrn1-deficient strains.
- Investigation of H3K4me3 marks and Set1 histone methyl-transferase activity.
Main Results:
- Identified 1,658 Xrn1-sensitive unstable transcripts (XUTs), with 66% antisense to open reading frames.
- XUTs are polyadenylated and dependent on RNAPII.
- Most XUTs accumulate in lithium media, suggesting a role in adaptive responses.
- Antisense XUTs lead to decreased RNAPII occupancy at target genes.
- H3K4me3 marks are associated with genes regulated by antisense XUTs, and antagonize their repressive activity.
Conclusions:
- Antisense ncRNA-mediated regulation is a widespread pathway in Saccharomyces cerevisiae.
- XUTs play a significant role in gene expression control and adaptive responses.
- The interplay between antisense XUTs and H3K4me3 methylation is critical for gene silencing.
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