Effects of ADARs on small RNA processing pathways in C. elegans. Caenorhabditis elegans

Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine to inosine in double-stranded RNA (dsRNA). To evaluate effects of ADARs on small RNAs that derive from dsRNA precursors, we performed deep-sequencing, comparing small RNAs from wildtype and ADAR mutant C. elegans. While editing in small RNAs was rare, at least 40% of microRNAs had altered levels in at least one ADAR mutant strain, and miRNAs with significantly altered levels had mRNA targets with correspondingly affected levels. About 40% of siRNAs derived from endogenous genes (endo-siRNAs) also had altered levels in at least one mutant strain, including 63% of Dicer-dependent endo-siRNAs. The 26G class of endo-siRNAs was significantly affected by ADARs, and many altered 26G loci had intronic reads, and histone modifications associated with transcriptional silencing. Our data indicate ADARs, through both direct and indirect mechanisms, are important for maintaining wildtype levels of many small RNAs in C. elegans. Overall design: Deep sequencing of small RNAs in wild-type (N2), adr-1 null, adr-2 null and adr-1;adr-2 null mixed stage C. elegans

作用于RNA的腺苷脱氨酶（ADARs）是一类可在双链RNA（dsRNA）中将腺苷脱氨修饰为肌苷的RNA编辑酶。为评估ADARs对源自双链RNA（dsRNA）前体的小RNA的调控效应，我们开展了深度测序实验，对比了野生型与ADAR突变型秀丽隐杆线虫的小RNA表达谱。尽管小RNA的编辑事件较为罕见，但至少40%的微小RNA（miRNAs）在至少一种ADAR突变菌株中出现了表达水平改变；且表达水平发生显著变化的miRNAs，其对应的mRNA靶标也呈现出相应的表达水平变化。约40%源自内源基因的小干扰RNA（endo-siRNAs）同样在至少一种突变菌株中出现了表达水平改变，其中包括63%的Dicer依赖型内源小干扰RNA。26G类内源小干扰RNA的表达水平显著受ADARs调控，多数表达水平改变的26G基因座存在内含子读段，且伴随与转录沉默相关的组蛋白修饰。本研究数据表明，ADARs可通过直接与间接两种机制，对维持秀丽隐杆线虫中众多小RNA的野生型表达水平发挥重要作用。总体实验设计：对野生型（N2）、adr-1敲除突变体、adr-2敲除突变体以及adr-1;adr-2双敲除突变体的混合发育阶段秀丽隐杆线虫进行小RNA深度测序。