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Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities
Pervasive transcription of genomes generates multiple classes of non-coding RNAs. One of these classes are stable long non-coding RNAs which overlap coding genes in antisense direction (asRNAs). The function of such asRNAs is not fully understood but several cases of antisense-dependent gene express...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737743/ https://www.ncbi.nlm.nih.gov/pubmed/28977638 http://dx.doi.org/10.1093/nar/gkx737 |
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author | Bunina, Daria Štefl, Martin Huber, Florian Khmelinskii, Anton Meurer, Matthias Barry, Joseph D. Kats, Ilia Kirrmaier, Daniel Huber, Wolfgang Knop, Michael |
author_facet | Bunina, Daria Štefl, Martin Huber, Florian Khmelinskii, Anton Meurer, Matthias Barry, Joseph D. Kats, Ilia Kirrmaier, Daniel Huber, Wolfgang Knop, Michael |
author_sort | Bunina, Daria |
collection | PubMed |
description | Pervasive transcription of genomes generates multiple classes of non-coding RNAs. One of these classes are stable long non-coding RNAs which overlap coding genes in antisense direction (asRNAs). The function of such asRNAs is not fully understood but several cases of antisense-dependent gene expression regulation affecting the overlapping genes have been demonstrated. Using high-throughput yeast genetics and a limited set of four growth conditions we previously reported a regulatory function for ∼25% of asRNAs, most of which repress the expression of the sense gene. To further explore the roles of asRNAs we tested more conditions and identified 15 conditionally antisense-regulated genes, 6 of which exhibited antisense-dependent enhancement of gene expression. We focused on the sporulation-specific gene SPS100, which becomes upregulated upon entry into starvation or sporulation as a function of the antisense transcript SUT169. We demonstrate that the antisense effect is mediated by its 3′ intergenic region (3′-IGR) and that this regulation can be transferred to other genes. Genetic analysis revealed that SUT169 functions by changing the relative expression of SPS100 mRNA isoforms from a short and unstable transcript to a long and stable species. These results suggest a novel mechanism of antisense-dependent gene regulation via mRNA isoform switching. |
format | Online Article Text |
id | pubmed-5737743 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-57377432018-01-04 Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities Bunina, Daria Štefl, Martin Huber, Florian Khmelinskii, Anton Meurer, Matthias Barry, Joseph D. Kats, Ilia Kirrmaier, Daniel Huber, Wolfgang Knop, Michael Nucleic Acids Res Gene regulation, Chromatin and Epigenetics Pervasive transcription of genomes generates multiple classes of non-coding RNAs. One of these classes are stable long non-coding RNAs which overlap coding genes in antisense direction (asRNAs). The function of such asRNAs is not fully understood but several cases of antisense-dependent gene expression regulation affecting the overlapping genes have been demonstrated. Using high-throughput yeast genetics and a limited set of four growth conditions we previously reported a regulatory function for ∼25% of asRNAs, most of which repress the expression of the sense gene. To further explore the roles of asRNAs we tested more conditions and identified 15 conditionally antisense-regulated genes, 6 of which exhibited antisense-dependent enhancement of gene expression. We focused on the sporulation-specific gene SPS100, which becomes upregulated upon entry into starvation or sporulation as a function of the antisense transcript SUT169. We demonstrate that the antisense effect is mediated by its 3′ intergenic region (3′-IGR) and that this regulation can be transferred to other genes. Genetic analysis revealed that SUT169 functions by changing the relative expression of SPS100 mRNA isoforms from a short and unstable transcript to a long and stable species. These results suggest a novel mechanism of antisense-dependent gene regulation via mRNA isoform switching. Oxford University Press 2017-11-02 2017-08-23 /pmc/articles/PMC5737743/ /pubmed/28977638 http://dx.doi.org/10.1093/nar/gkx737 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Gene regulation, Chromatin and Epigenetics Bunina, Daria Štefl, Martin Huber, Florian Khmelinskii, Anton Meurer, Matthias Barry, Joseph D. Kats, Ilia Kirrmaier, Daniel Huber, Wolfgang Knop, Michael Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities |
title | Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities |
title_full | Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities |
title_fullStr | Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities |
title_full_unstemmed | Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities |
title_short | Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities |
title_sort | upregulation of sps100 gene expression by an antisense rna via a switch of mrna isoforms with different stabilities |
topic | Gene regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737743/ https://www.ncbi.nlm.nih.gov/pubmed/28977638 http://dx.doi.org/10.1093/nar/gkx737 |
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