Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes
- University of Tübingen, Germany
- Umeå University, Sweden
Abstract
Intron splicing increases proteome complexity, promotes RNA stability, and enhances transcription. However, introns and the concomitant need for splicing extend the time required for gene expression and can cause an undesirable delay in the activation of genes. Here, we show that the plant microRNA processing factor SERRATE (SE) plays an unexpected and pivotal role in the regulation of intronless genes. Arabidopsis SE associated with more than 1000, mainly intronless, genes in a transcription-dependent manner. Chromatin-bound SE liaised with paused and elongating polymerase II complexes and promoted their association with intronless target genes. Our results indicate that stress-responsive genes contain no or few introns, which negatively affects their expression strength, but that some genes circumvent this limitation via a novel SE-dependent transcriptional activation mechanism. Transcriptome analysis of a Drosophila mutant defective in ARS2, the metazoan homologue of SE, suggests that SE/ARS2 function in regulating intronless genes might be conserved across kingdoms.
Data availability
Raw data have been deposited under accession codes accession number ERP016859 (ENA), PXD006004 (Pride) and GSE99367 (Geo Omnibus).
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RNA-seq of se mutantsPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE99367).
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Transcriptomic comparison of Drosophila snRNP biogenesis mutants reveals mutant-specific changes in pre-mRNA processing: implications for Spinal Muscular AtrophyPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE81121).
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RNA-Seq analysis, transcriptome assembly and gene expression profile analysis for Zea may ssp. mexicana L. under cold and drought stressPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE76939).
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Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stressPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE57252).
Article and author information
Author details
Funding
Deutsche Forschungsgemeinschaft
- Sascha Laubinger
Max-Planck-Gesellschaft (Open-access funding)
- Sven zur Oven-Krockhaus
- York-Dieter Stierhof
- Sascha Laubinger
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Yijun Qi, School of Life Sciences, Tsinghua University, China
Version history
- Received: March 28, 2018
- Accepted: August 22, 2018
- Accepted Manuscript published: August 28, 2018 (version 1)
- Version of Record published: September 12, 2018 (version 2)
Copyright
© 2018, Speth et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes
eLife 7:e37078.
https://doi.org/10.7554/eLife.37078
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