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

BMC Genomics
Yu-Chen LiuHsien-Da Huang

Abstract

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. 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. 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.

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jan 10, 2003·Nucleic Acids Research·D KarolchikUNKNOWN University of California Santa Cruz
Dec 31, 2005·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Nov 11, 2010·Nucleic Acids Research·Rasko LeinonenUNKNOWN International Nucleotide Sequence Database Collaboration
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Dec 20, 2012·RNA·William R JeckNorman E Sharpless
Mar 1, 2013·Nature·Thomas B HansenJørgen Kjems
Mar 1, 2013·Nature·Sebastian MemczakNikolaus Rajewsky
Mar 7, 2013·Genetics·Johnny T Y KungJeannie T Lee
Apr 27, 2013·Science·Jeremy E Wilusz, Phillip A Sharp
Sep 17, 2013·Molecular Cell·Yang ZhangLing-Ling Chen
Sep 17, 2013·PLoS Genetics·Julia SalzmanPatrick O Brown
Jan 17, 2014·Nature·Yvonne TayPier Paolo Pandolfi
Mar 13, 2014·PloS One·Peter L WangJulia Salzman
Jul 30, 2014·Genome Biology·Junjie U GuoDavid P Bartel
Sep 23, 2014·RNA·Petar GlažarNikolaus Rajewsky
Sep 23, 2014·Molecular Cell·Reut Ashwal-FlussSebastian Kadener
Sep 23, 2014·Cell·Xiao-Ou ZhangLi Yang
Nov 8, 2014·Clinical Chemistry·Jae Hoon BahnXinshu Xiao
Mar 3, 2015·Journal of Molecular Biology·Steven KellyArgyris Papantonis
Mar 15, 2015·Cell·Simon J ConnGregory J Goodall
Apr 30, 2015·Molecular Cell·Agnieszka Rybak-WolfNikolaus Rajewsky
Sep 18, 2015·Circulation Research·Jes-Niels BoeckelStefanie Dimmeler
Oct 10, 2015·Nucleic Acids Research·Yu-Chen LiuHsien-Da Huang
Nov 12, 2015·Bioinformatics·Jun ChengChristoph Dieterich
Nov 22, 2015·Nucleic Acids Research·Chih-Hung ChouHsien-Da Huang
Dec 15, 2015·Nucleic Acids Research·Thomas B HansenJørgen Kjems
Feb 14, 2016·Nucleic Acids Research·Xiaofeng SongWange Lu
Apr 5, 2016·Nature Reviews. Genetics·Daniel W Thomson, Marcel E Dinger
Jun 19, 2016·Genome Biology·Yujiao DangJie Qiao
Jun 16, 2017·Journal of Clinical Laboratory Analysis·Mengqian TianBingxiu Xiao

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Citations

Jul 4, 2019·BMC Bioinformatics·Ya-Chi LinKuei-Yang Hsiao

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Methods Mentioned

BETA
RNA-Seq
465 transcriptome sequencing

Software Mentioned

CircRNA
Cufflinks
find
RefSeq
circ
ORCEL
CircNet
DAVID
UCSC genome browser
STAR

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