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Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis

BACKGROUND: Emerging evidence indicates that Circular RNAs (circRNAs) exert post-transcriptional regulation of gene expression. A subclass of circRNA was found enriched with miRNA target sites. This evidence suggests that this kind of circRNA functions as natural miRNA sponge. Noticing the potential...

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Autores principales: Liu, Yu-Chen, Hong, Hsiao-Chin, Yang, Chi-Dung, Lee, Wei-Hsiang, Huang, Hsin-Tzu, Huang, Hsien-Da
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954272/
https://www.ncbi.nlm.nih.gov/pubmed/29764361
http://dx.doi.org/10.1186/s12864-018-4456-9
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author Liu, Yu-Chen
Hong, Hsiao-Chin
Yang, Chi-Dung
Lee, Wei-Hsiang
Huang, Hsin-Tzu
Huang, Hsien-Da
author_facet Liu, Yu-Chen
Hong, Hsiao-Chin
Yang, Chi-Dung
Lee, Wei-Hsiang
Huang, Hsin-Tzu
Huang, Hsien-Da
author_sort Liu, Yu-Chen
collection PubMed
description BACKGROUND: Emerging evidence indicates that Circular RNAs (circRNAs) exert post-transcriptional regulation of gene expression. A subclass of circRNA was found enriched with miRNA target sites. This evidence suggests that this kind of circRNA functions as natural miRNA sponge. Noticing the potential impacts of circular RNA research, we were motivated to identify novel circRNAs as well as putative circRNA-miRNA interactions through retroactive sourced transcriptome sequencing samples. RESULTS: Through the analysis in 465 RNA-seq runs and 22 reports published in recent years, putatively circRNA sponged miRNA that had been experimentally verified targeting circRNA host gene were found. From this observation, supporting evidence of the competitive endogenous relationship of circRNAs and miRNAs targeting circRNA host genes can be observed. Given the self-regulation and self-induction nature of these circRNAs, this kind of hypothetical phenomenon was hereby called Ouroboros Resembling Competitive Endogenous Loop (ORCEL) in circular RNAs. CONCLUSIONS: The fact that miRNA sponge circRNA originated from region miRNA target sites enriched regions, while genes encoded from these regions are conserved to be miRNA targets rationalize the existence of ORCEL. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4456-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-59542722018-05-21 Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis Liu, Yu-Chen Hong, Hsiao-Chin Yang, Chi-Dung Lee, Wei-Hsiang Huang, Hsin-Tzu Huang, Hsien-Da BMC Genomics Research BACKGROUND: Emerging evidence indicates that Circular RNAs (circRNAs) exert post-transcriptional regulation of gene expression. A subclass of circRNA was found enriched with miRNA target sites. This evidence suggests that this kind of circRNA functions as natural miRNA sponge. Noticing the potential impacts of circular RNA research, we were motivated to identify novel circRNAs as well as putative circRNA-miRNA interactions through retroactive sourced transcriptome sequencing samples. RESULTS: Through the analysis in 465 RNA-seq runs and 22 reports published in recent years, putatively circRNA sponged miRNA that had been experimentally verified targeting circRNA host gene were found. From this observation, supporting evidence of the competitive endogenous relationship of circRNAs and miRNAs targeting circRNA host genes can be observed. Given the self-regulation and self-induction nature of these circRNAs, this kind of hypothetical phenomenon was hereby called Ouroboros Resembling Competitive Endogenous Loop (ORCEL) in circular RNAs. CONCLUSIONS: The fact that miRNA sponge circRNA originated from region miRNA target sites enriched regions, while genes encoded from these regions are conserved to be miRNA targets rationalize the existence of ORCEL. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4456-9) contains supplementary material, which is available to authorized users. BioMed Central 2018-05-09 /pmc/articles/PMC5954272/ /pubmed/29764361 http://dx.doi.org/10.1186/s12864-018-4456-9 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Liu, Yu-Chen
Hong, Hsiao-Chin
Yang, Chi-Dung
Lee, Wei-Hsiang
Huang, Hsin-Tzu
Huang, Hsien-Da
Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis
title Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis
title_full Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis
title_fullStr Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis
title_full_unstemmed Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis
title_short Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis
title_sort ouroboros resembling competitive endogenous loop (orcel) in circular rnas revealed through transcriptome sequencing dataset analysis
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954272/
https://www.ncbi.nlm.nih.gov/pubmed/29764361
http://dx.doi.org/10.1186/s12864-018-4456-9
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