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Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells
Apoptosis is a form of regulated cell death that plays a critical role in survival and developmental homeostasis. There are numerous reports on regulation of apoptosis by protein-coding genes as well as small non-coding RNAs, such as microRNAs. However, there is no comprehensive investigation of cir...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6424894/ https://www.ncbi.nlm.nih.gov/pubmed/30918512 http://dx.doi.org/10.3389/fgene.2019.00176 |
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author | Yaylak, Bilge Erdogan, Ipek Akgul, Bunyamin |
author_facet | Yaylak, Bilge Erdogan, Ipek Akgul, Bunyamin |
author_sort | Yaylak, Bilge |
collection | PubMed |
description | Apoptosis is a form of regulated cell death that plays a critical role in survival and developmental homeostasis. There are numerous reports on regulation of apoptosis by protein-coding genes as well as small non-coding RNAs, such as microRNAs. However, there is no comprehensive investigation of circular RNAs (circRNA) that are differentially expressed under apoptotic conditions. We have performed a transcriptomics study in which we first triggered apoptosis in HeLa cells through treatment with four different agents, namely cisplatin, doxorubicin, TNF-α and anti-Fas mAb. Total RNAs isolated from control as well as treated cells were treated with RNAse R to eliminate the linear RNAs. The remaining RNAs were then subjected to deep-sequencing to identify differentially expressed circRNAs. Interestingly, some of the dys-regulated circRNAs were found to originate from protein-coding genes well-documented to regulate apoptosis. A number of candidate circRNAs were validated with qPCR with or without RNAse R treatment as well. We then took advantage of bioinformatics tools to investigate the coding potential of differentially expressed RNAs. Additionally, we examined the candidate circRNAs for the putative miRNA-binding sites and their putative target mRNAs. Our analyses point to a potential for circRNA-mediated sponging of miRNAs known to regulate apoptosis. In conclusion, this is the first transcriptomics study that provides a complete circRNA profile of apoptotic cells that might shed light onto the potential role of circRNAs in apoptosis. |
format | Online Article Text |
id | pubmed-6424894 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-64248942019-03-27 Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells Yaylak, Bilge Erdogan, Ipek Akgul, Bunyamin Front Genet Genetics Apoptosis is a form of regulated cell death that plays a critical role in survival and developmental homeostasis. There are numerous reports on regulation of apoptosis by protein-coding genes as well as small non-coding RNAs, such as microRNAs. However, there is no comprehensive investigation of circular RNAs (circRNA) that are differentially expressed under apoptotic conditions. We have performed a transcriptomics study in which we first triggered apoptosis in HeLa cells through treatment with four different agents, namely cisplatin, doxorubicin, TNF-α and anti-Fas mAb. Total RNAs isolated from control as well as treated cells were treated with RNAse R to eliminate the linear RNAs. The remaining RNAs were then subjected to deep-sequencing to identify differentially expressed circRNAs. Interestingly, some of the dys-regulated circRNAs were found to originate from protein-coding genes well-documented to regulate apoptosis. A number of candidate circRNAs were validated with qPCR with or without RNAse R treatment as well. We then took advantage of bioinformatics tools to investigate the coding potential of differentially expressed RNAs. Additionally, we examined the candidate circRNAs for the putative miRNA-binding sites and their putative target mRNAs. Our analyses point to a potential for circRNA-mediated sponging of miRNAs known to regulate apoptosis. In conclusion, this is the first transcriptomics study that provides a complete circRNA profile of apoptotic cells that might shed light onto the potential role of circRNAs in apoptosis. Frontiers Media S.A. 2019-03-13 /pmc/articles/PMC6424894/ /pubmed/30918512 http://dx.doi.org/10.3389/fgene.2019.00176 Text en Copyright © 2019 Yaylak, Erdogan and Akgul. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Yaylak, Bilge Erdogan, Ipek Akgul, Bunyamin Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells |
title | Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells |
title_full | Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells |
title_fullStr | Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells |
title_full_unstemmed | Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells |
title_short | Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells |
title_sort | transcriptomics analysis of circular rnas differentially expressed in apoptotic hela cells |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6424894/ https://www.ncbi.nlm.nih.gov/pubmed/30918512 http://dx.doi.org/10.3389/fgene.2019.00176 |
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