TY - JOUR
T1 - Interior circular RNA
AU - Liu, Xiaoxin
AU - Hu, Zhangfeng
AU - Zhou, Junfei
AU - Tian, Cheng
AU - Tian, Guangmei
AU - He, Miao
AU - Gao, Lifen
AU - Chen, Lihong
AU - Li, Tiantian
AU - Peng, Hai
AU - Zhang, Weixiong
N1 - Funding Information:
This work was supported in part by National Natural Science Foundation of China [grants 31601995 and 31601090] and United States National Institutes of Health [grant R01 GM100364].
Publisher Copyright:
© 2019, © 2019 Informa UK Limited, trading as Taylor & Francis Group.
PY - 2020/1/2
Y1 - 2020/1/2
N2 - Formed by back splicing or back fusion of linear RNAs, circular RNAs (circRNAs) constitute a new class of non-coding RNAs of eukaryotes. Recent studies reveal a spliceosome-dependent biogenesis of circRNAs where circRNAs arise at the intron-exon junctions of mRNAs. In this study, using a novel de novo identification method, we show that circRNAs can originate from the interior regions of exons, introns, and intergenic transcripts in human, mouse and rice, which were referred to as interior circRNAs (i-circRNAs). Many i-circRNAs have some remarkable characteristics: multiple i-circRNAs may arise from the same genomic locus; their back fusion points may not be associated with the AG/GT splicing sites, but rather a new pair of motif AC/CT, their back fusion points are adjacent to complementary sequences; and they may circulate on short homologous sequences. We validated several i-circRNAs in HeLa cells by Polymerase Chain Reaction followed by Sanger sequencing. Our results combined showed that i-circRNAs are bona fide circRNAs, indicated novel biogenesis pathways independent of the splicing apparatus, and expanded our understanding of the origin, diversity, and complexity of circRNAs.
AB - Formed by back splicing or back fusion of linear RNAs, circular RNAs (circRNAs) constitute a new class of non-coding RNAs of eukaryotes. Recent studies reveal a spliceosome-dependent biogenesis of circRNAs where circRNAs arise at the intron-exon junctions of mRNAs. In this study, using a novel de novo identification method, we show that circRNAs can originate from the interior regions of exons, introns, and intergenic transcripts in human, mouse and rice, which were referred to as interior circRNAs (i-circRNAs). Many i-circRNAs have some remarkable characteristics: multiple i-circRNAs may arise from the same genomic locus; their back fusion points may not be associated with the AG/GT splicing sites, but rather a new pair of motif AC/CT, their back fusion points are adjacent to complementary sequences; and they may circulate on short homologous sequences. We validated several i-circRNAs in HeLa cells by Polymerase Chain Reaction followed by Sanger sequencing. Our results combined showed that i-circRNAs are bona fide circRNAs, indicated novel biogenesis pathways independent of the splicing apparatus, and expanded our understanding of the origin, diversity, and complexity of circRNAs.
KW - PCR
KW - RNA
KW - RNA sequencing
KW - Sanger sequencing
KW - chimeric RNA
KW - circular RNA
UR - http://www.scopus.com/inward/record.url?scp=85073969632&partnerID=8YFLogxK
U2 - 10.1080/15476286.2019.1669391
DO - 10.1080/15476286.2019.1669391
M3 - Article
C2 - 31532701
AN - SCOPUS:85073969632
SN - 1547-6286
VL - 17
SP - 87
EP - 97
JO - RNA Biology
JF - RNA Biology
IS - 1
ER -