dsRNAs expressed in C. elegans development

Cellular RNAs containing double-stranded RNA (dsRNA) structures are subject to A-to-I RNA editing by the adenosine deaminases that act on RNA (ADARs). While A-to-I editing can alter mRNA coding potential, most editing is observed in non-coding sequences, the function of which remains poorly characterized. Using a dsRNA immunoprecipitation and high-thoughput sequencing (dsRIP-Seq) approach, we identify 1523 expressed A-to-I edited regions and characterize their expression during Caenorhabditis elegans development. We observe that edited regions are highly expressed in early development and are closely associated with protein-coding genes. Edited dsRNA structures give rise to abundant small interfering RNAs (siRNAs) that are negatively correlated with ADAR expression and regulate the developmental expression of associated genes. RNA-Seq of total RNA and RNA immunoprecipitated with a dsRNA-specific antibody (dsRIP) from whole C. elegans at four stages of development: embryos, early stage larvae (L1-L2), late stage larvae (L3-L4), and young adults.

含有双链RNA（double-stranded RNA, dsRNA）结构的细胞RNA，会被作用于RNA的腺苷脱氨酶（adenosine deaminases that act on RNA, ADARs）介导A-to-I RNA编辑。尽管A-to-I编辑可改变mRNA的编码潜能，但绝大多数编辑事件发生在非编码序列中，这类序列的功能目前仍未得到充分阐释。本研究采用双链RNA免疫沉淀结合高通量测序（dsRNA immunoprecipitation and high-throughput sequencing, dsRIP-Seq）技术，鉴定出1523个具有表达活性的A-to-I编辑区域，并解析了其在秀丽隐杆线虫（Caenorhabditis elegans）发育过程中的表达特征。研究发现，编辑区域在发育早期呈现高表达状态，且与蛋白质编码基因存在紧密关联。经编辑的dsRNA结构可产生大量小型干扰RNA（small interfering RNAs, siRNAs），这类siRNA的表达水平与ADAR的表达呈负相关，并可调控其关联基因的发育性表达。本研究对秀丽隐杆线虫四个发育阶段（胚胎期、早期幼虫期L1-L2、晚期幼虫期L3-L4以及年轻成虫期）的全虫体总RNA，以及通过dsRNA特异性抗体免疫沉淀（dsRIP）获取的RNA进行了RNA测序（RNA-Seq）。