Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses.
Organisms are often exposed to environmental pressures that affect homeostasis, so it is important to understand the biological basis of stress-response. Various biological mechanisms have evolved to help cells cope with potentially cytotoxic changes in their environment. miRNAs are small non-coding...
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2013
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oai:doaj.org-article:94d1d6f99caa459e962d88eb27e9de712021-11-18T08:46:22ZMeta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses.1932-620310.1371/journal.pone.0080844https://doaj.org/article/94d1d6f99caa459e962d88eb27e9de712013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24244721/?tool=EBIhttps://doaj.org/toc/1932-6203Organisms are often exposed to environmental pressures that affect homeostasis, so it is important to understand the biological basis of stress-response. Various biological mechanisms have evolved to help cells cope with potentially cytotoxic changes in their environment. miRNAs are small non-coding RNAs which are able to regulate mRNA stability. It has been suggested that miRNAs may tip the balance between continued cytorepair and induction of apoptosis in response to stress. There is a wealth of data in the literature showing the effect of environmental stress on miRNAs, but it is scattered in a large number of disparate publications. Meta-analyses of this data would produce added insight into the molecular mechanisms of stress-response. To facilitate this we created and manually curated the miRStress database, which describes the changes in miRNA levels following an array of stress types in eukaryotic cells. Here we describe this database and validate the miRStress tool for analysing miRNAs that are regulated by stress. To validate the database we performed a cross-species analysis to identify miRNAs that respond to radiation. The analysis tool confirms miR-21 and miR-34a as frequently deregulated in response to radiation, but also identifies novel candidates as potentially important players in this stress response, including miR-15b, miR-19b, and miR-106a. Similarly, we used the miRStress tool to analyse hypoxia-responsive miRNAs. The most frequently deregulated miRNAs were miR-210 and miR-21, as expected. Several other miRNAs were also found to be associated with hypoxia, including miR-181b, miR-26a/b, miR-106a, miR-213 and miR-192. Therefore the miRStress tool has identified miRNAs with hitherto unknown or under-appreciated roles in the response to specific stress types. The miRStress tool, which can be used to uncover new insight into the biological roles of miRNAs, and also has the potential to unearth potential biomarkers for therapeutic response, is freely available at http://mudshark.brookes.ac.uk/MirStress.Laura Ann JacobsFindlay Bewicke-CopleyMark Graham PoolmanRyan Charles PinkRyan Charles PinkLaura Ann MulcahyIsabel BakerEllie-May BeamanTravis BrooksDaniel Paul CaleyWilliam CowlingJames Michael Stevenson CurrieJessica HorsburghLottie KenehanEmma KeyesDaniel LeiteDavide MassaAdam McDermott-RousePriya SamuelHannah WoodMunira KadhimDavid Raul Francisco CarterPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 11, p e80844 (2013) |
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| collection |
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| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Laura Ann Jacobs Findlay Bewicke-Copley Mark Graham Poolman Ryan Charles Pink Ryan Charles Pink Laura Ann Mulcahy Isabel Baker Ellie-May Beaman Travis Brooks Daniel Paul Caley William Cowling James Michael Stevenson Currie Jessica Horsburgh Lottie Kenehan Emma Keyes Daniel Leite Davide Massa Adam McDermott-Rouse Priya Samuel Hannah Wood Munira Kadhim David Raul Francisco Carter Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses. |
| description |
Organisms are often exposed to environmental pressures that affect homeostasis, so it is important to understand the biological basis of stress-response. Various biological mechanisms have evolved to help cells cope with potentially cytotoxic changes in their environment. miRNAs are small non-coding RNAs which are able to regulate mRNA stability. It has been suggested that miRNAs may tip the balance between continued cytorepair and induction of apoptosis in response to stress. There is a wealth of data in the literature showing the effect of environmental stress on miRNAs, but it is scattered in a large number of disparate publications. Meta-analyses of this data would produce added insight into the molecular mechanisms of stress-response. To facilitate this we created and manually curated the miRStress database, which describes the changes in miRNA levels following an array of stress types in eukaryotic cells. Here we describe this database and validate the miRStress tool for analysing miRNAs that are regulated by stress. To validate the database we performed a cross-species analysis to identify miRNAs that respond to radiation. The analysis tool confirms miR-21 and miR-34a as frequently deregulated in response to radiation, but also identifies novel candidates as potentially important players in this stress response, including miR-15b, miR-19b, and miR-106a. Similarly, we used the miRStress tool to analyse hypoxia-responsive miRNAs. The most frequently deregulated miRNAs were miR-210 and miR-21, as expected. Several other miRNAs were also found to be associated with hypoxia, including miR-181b, miR-26a/b, miR-106a, miR-213 and miR-192. Therefore the miRStress tool has identified miRNAs with hitherto unknown or under-appreciated roles in the response to specific stress types. The miRStress tool, which can be used to uncover new insight into the biological roles of miRNAs, and also has the potential to unearth potential biomarkers for therapeutic response, is freely available at http://mudshark.brookes.ac.uk/MirStress. |
| format |
article |
| author |
Laura Ann Jacobs Findlay Bewicke-Copley Mark Graham Poolman Ryan Charles Pink Ryan Charles Pink Laura Ann Mulcahy Isabel Baker Ellie-May Beaman Travis Brooks Daniel Paul Caley William Cowling James Michael Stevenson Currie Jessica Horsburgh Lottie Kenehan Emma Keyes Daniel Leite Davide Massa Adam McDermott-Rouse Priya Samuel Hannah Wood Munira Kadhim David Raul Francisco Carter |
| author_facet |
Laura Ann Jacobs Findlay Bewicke-Copley Mark Graham Poolman Ryan Charles Pink Ryan Charles Pink Laura Ann Mulcahy Isabel Baker Ellie-May Beaman Travis Brooks Daniel Paul Caley William Cowling James Michael Stevenson Currie Jessica Horsburgh Lottie Kenehan Emma Keyes Daniel Leite Davide Massa Adam McDermott-Rouse Priya Samuel Hannah Wood Munira Kadhim David Raul Francisco Carter |
| author_sort |
Laura Ann Jacobs |
| title |
Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses. |
| title_short |
Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses. |
| title_full |
Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses. |
| title_fullStr |
Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses. |
| title_full_unstemmed |
Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses. |
| title_sort |
meta-analysis using a novel database, mirstress, reveals mirnas that are frequently associated with the radiation and hypoxia stress-responses. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2013 |
| url |
https://doaj.org/article/94d1d6f99caa459e962d88eb27e9de71 |
| work_keys_str_mv |
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