Long non-coding RNA repertoire and regulation by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast-猫眼课题宝

DOI：

10.1101/158477

发表时间：

2017-07

期刊：

bioRxiv

影响因子：

--

通讯作者：

中科院分区：

其他

文献类型：

--

作者：

S. Atkinson;S. Marguerat;Danny A. Bitton;María Rodríguez-López;C. Rallis;J. Lemay;Cristina Cotobal;M. Malecki;J. Mata;F. Bachand;J. Bähler

转录组的特征是普遍存在但定义不明确的长非编码RNA（lncRNA）。我们在粟酒裂殖酵母中鉴定了5775个新的lncRNA，几乎是以前注释的lncRNA的4倍。大多数lncRNA在遗传和生理干扰下，特别是在减数分裂后期，变得去抑制。这些lncRNA通过三种RNA加工途径靶向：核外泌体、细胞质核酸外切酶和RNAi，途径之间具有实质性的协调和冗余。我们将lncRNA分为隐蔽的不稳定转录本（CUT），Xrn1敏感的不稳定转录本（XUT）和Dicer敏感的不稳定转录本（DUT）。XUT和DUT富含反义lncRNA，而CUT通常是双向的并且被主动翻译。细胞质核酸外切酶和RNAi抑制成千上万的减数分裂诱导的RNA。反义lncRNA和正义mRNA的表达在生理条件下通常呈负相关，但在遗传条件下不相关。基因间和双向lncRNA出现从核小体耗尽区域，定位核小体的上游。对S.粟酒裂殖酵母lncRNA库和特征为功能分析提供了丰富的资源。

Transcriptomes feature pervasive, but poorly defined long non-coding RNAs (lncRNAs). We identify 5775 novel lncRNAs in Schizosaccharomyces pombe, nearly 4-times the previously annotated lncRNAs. Most lncRNAs become derepressed under genetic and physiological perturbations, especially during late meiosis. These lncRNAs are targeted by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease and RNAi, with substantial coordination and redundancy among pathways. We classify lncRNAs into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease and RNAi repress thousands of meiotically induced RNAs. Antisense lncRNA and sense mRNA expression often negatively correlate in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. This broad survey of the S. pombe lncRNA repertoire and characteristics provides a rich resource for functional analyses.