GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India.
Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India.
Sci Rep. 2019 Mar 5;9(1):3432. doi: 10.1038/s41598-019-39977-7.
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.
环状 RNA（circRNAs）是通过外显子的反向剪接和转录本的环化产生的转录本异构体。最近在人类和其他模式生物中创建的环状 RNA 的全基因组图谱促使我们探索了一种流行的模式生物斑马鱼中的环状 RNA 文库。我们生成了五个主要的斑马鱼组织（血液、大脑、心脏、鳃和肌肉）的 RNA-seq 数据。在参考映射到线性转录物后，使用拆分映射算法来识别独特的反向剪接外显子。我们的分析在斑马鱼中发现了 3428 个新的环状 RNA。进一步的深入分析表明，大多数环状 RNA 来自先前注释良好的蛋白质编码和长非编码 RNA 基因座。此外，许多环状 RNA 表现出广泛的组织特异性。我们使用聚合酶链反应（PCR）和不同的引物集独立验证了一部分环状 RNA。使用定量实时 PCR 进行的表达分析重现了研究候选物中的特定组织。这项研究提供了斑马鱼组织中环状 RNA 的全面全基因组图谱。
