A genome-wide map of circular RNAs in adult zebrafish

被引：19

作者：

Sharma, Disha ^{[1
,3
]}

Sehgal, Paras ^{[2
,3
]}

Mathew, Samatha ^{[2
,3
]}

Vellarikkal, Shamsudheen Karuthedath ^{[2
,3
]}

Singh, Angom Ramcharan ^{[2
]}

Kapoor, Shruti ^{[1
,3
]}

Jayarajan, Rijith ^{[2
]}

Scaria, Vinod ^{[1
,3
]}

Sivasubbu, Sridhar ^{[2
,3
]}

机构：

[1] CSIR, IGIB, GN Ramachandran Knowledge Ctr Genome Informat, Mathura Rd, Delhi 110025, India

[2] CSIR, Inst Genom & Integrat Biol, Genom & Mol Med, Mathura Rd, Delhi 110025, India

[3] CSIR, Inst Genom & Integrat Biol, Acad Sci & Innovat Res, South Campus,Mathura Rd, Delhi 110025, India

来源：

SCIENTIFIC REPORTS | 2019年 / 9卷 / 1期

关键词：

SEQUENCE; EFFICIENT; TRANSCRIPTION; DATABASE;

D O I：

10.1038/s41598-019-39977-7

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Circular RNAs (circRNAs) are transcript isoforms generated by back-splicing of exons and circularisation of the transcript. Recent genome-wide maps created for circular RNAs in humans and other model organisms have motivated us to explore the repertoire of circular RNAs in zebrafish, a popular model organism. We generated RNA-seq data for five major zebrafish tissues - Blood, Brain, Heart, Gills and Muscle. The repertoire RNA sequence reads left over after reference mapping to linear transcripts were used to identify unique back-spliced exons utilizing a split-mapping algorithm. Our analysis revealed 3,428 novel circRNAs in zebrafish. Further in-depth analysis suggested that majority of the circRNAs were derived from previously well-annotated protein-coding and long noncoding RNA gene loci. In addition, many of the circular RNAs showed extensive tissue specificity. We independently validated a subset of circRNAs using polymerase chain reaction (PCR) and divergent set of primers. Expression analysis using quantitative real time PCR recapitulate selected tissue specificity in the candidates studied. This study provides a comprehensive genome-wide map of circular RNAs in zebrafish tissues.

引用

页数：11

共 35 条

[1] Correlation of circular RNA abundance with proliferation - exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues [J].