Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress
Oxidative stress (OS) is caused by an imbalance between pro- and anti-oxidant reactions leading to accumulation of reactive oxygen species within cells. We here investigate the effect of OS on the transcriptome of human fibroblasts. OS causes a rapid and transient global induction of transcription c...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2015
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| Online Access: | https://hdl.handle.net/10356/105695 http://hdl.handle.net/10220/26058 |
| _version_ | 1826120847718350848 |
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| author | Kuznetsov, Vladimir Andreevich Vardy, Leah Anne Ivshina, Anna Vladimirovna Giannakakis, Antonis Zhang, Jingxian Jenjaroenpun, Piroon Nama, Srikanth Zainolabidin, Norliyana Aau, Mei Yee Yarmishyn, Aliaksandr A. Vaz, Candida Grinchuk, Oleg V. Voorhoeve, Mathijs Sampath, Prabha Kurochkin, Igor V. Guccione, Ernesto |
| author2 | School of Computer Engineering |
| author_facet | School of Computer Engineering Kuznetsov, Vladimir Andreevich Vardy, Leah Anne Ivshina, Anna Vladimirovna Giannakakis, Antonis Zhang, Jingxian Jenjaroenpun, Piroon Nama, Srikanth Zainolabidin, Norliyana Aau, Mei Yee Yarmishyn, Aliaksandr A. Vaz, Candida Grinchuk, Oleg V. Voorhoeve, Mathijs Sampath, Prabha Kurochkin, Igor V. Guccione, Ernesto |
| author_sort | Kuznetsov, Vladimir Andreevich |
| collection | NTU |
| description | Oxidative stress (OS) is caused by an imbalance between pro- and anti-oxidant reactions leading to accumulation of reactive oxygen species within cells. We here investigate the effect of OS on the transcriptome of human fibroblasts. OS causes a rapid and transient global induction of transcription characterized by pausing of RNA polymerase II (PolII) in both directions, at specific promoters, within 30 minutes of the OS response. In contrast to protein-coding genes, which are commonly down-regulated, this novel divergent, PolII pausing-phenomenon leads to the generation of thousands of long noncoding RNAs (lncRNAs) with promoter-associated antisense lncRNAs transcripts (si-paancRNAs) representing the major group of stress-induced transcripts. OS causes transient dynamics of si-lncRNAs in nucleus and cytosol, leading to their accumulation at polysomes, in contrast to mRNAs, which get depleted from polysomes. We propose that si-lncRNAs represent a novel component of the transcriptional stress that is known to determine the outcome of immediate-early and later cellular stress responses and we provide insights on the fate of those novel mature lncRNA transcripts by showing that their association with polysomal complexes is significantly increased in OS. |
| first_indexed | 2024-10-01T05:23:09Z |
| format | Journal Article |
| id | ntu-10356/105695 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:23:09Z |
| publishDate | 2015 |
| record_format | dspace |
| spelling | ntu-10356/1056952023-02-28T16:55:55Z Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress Kuznetsov, Vladimir Andreevich Vardy, Leah Anne Ivshina, Anna Vladimirovna Giannakakis, Antonis Zhang, Jingxian Jenjaroenpun, Piroon Nama, Srikanth Zainolabidin, Norliyana Aau, Mei Yee Yarmishyn, Aliaksandr A. Vaz, Candida Grinchuk, Oleg V. Voorhoeve, Mathijs Sampath, Prabha Kurochkin, Igor V. Guccione, Ernesto School of Computer Engineering School of Biological Sciences DRNTU::Science::Biological sciences::Genetics Oxidative stress (OS) is caused by an imbalance between pro- and anti-oxidant reactions leading to accumulation of reactive oxygen species within cells. We here investigate the effect of OS on the transcriptome of human fibroblasts. OS causes a rapid and transient global induction of transcription characterized by pausing of RNA polymerase II (PolII) in both directions, at specific promoters, within 30 minutes of the OS response. In contrast to protein-coding genes, which are commonly down-regulated, this novel divergent, PolII pausing-phenomenon leads to the generation of thousands of long noncoding RNAs (lncRNAs) with promoter-associated antisense lncRNAs transcripts (si-paancRNAs) representing the major group of stress-induced transcripts. OS causes transient dynamics of si-lncRNAs in nucleus and cytosol, leading to their accumulation at polysomes, in contrast to mRNAs, which get depleted from polysomes. We propose that si-lncRNAs represent a novel component of the transcriptional stress that is known to determine the outcome of immediate-early and later cellular stress responses and we provide insights on the fate of those novel mature lncRNA transcripts by showing that their association with polysomal complexes is significantly increased in OS. ASTAR (Agency for Sci., Tech. and Research, S’pore) Published version 2015-06-25T01:36:03Z 2019-12-06T21:55:59Z 2015-06-25T01:36:03Z 2019-12-06T21:55:59Z 2015 2015 Journal Article Giannakakis, A., Zhang, J., Jenjaroenpun, P., Nama, S., Zainolabidin, N., Aau, M. Y., et al. (2015). Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress. Scientific Reports, 5, 9737-. 2045-2322 https://hdl.handle.net/10356/105695 http://hdl.handle.net/10220/26058 10.1038/srep09737 26024509 en Scientific Reports This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ application/pdf |
| spellingShingle | DRNTU::Science::Biological sciences::Genetics Kuznetsov, Vladimir Andreevich Vardy, Leah Anne Ivshina, Anna Vladimirovna Giannakakis, Antonis Zhang, Jingxian Jenjaroenpun, Piroon Nama, Srikanth Zainolabidin, Norliyana Aau, Mei Yee Yarmishyn, Aliaksandr A. Vaz, Candida Grinchuk, Oleg V. Voorhoeve, Mathijs Sampath, Prabha Kurochkin, Igor V. Guccione, Ernesto Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress |
| title | Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress |
| title_full | Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress |
| title_fullStr | Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress |
| title_full_unstemmed | Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress |
| title_short | Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress |
| title_sort | contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress |
| topic | DRNTU::Science::Biological sciences::Genetics |
| url | https://hdl.handle.net/10356/105695 http://hdl.handle.net/10220/26058 |
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