GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
Cells. 2020 Jul 30;9(8):1806. doi: 10.3390/cells9081806.
The sequencing of total RNA depleted for ribosomal sequences remains the method of choice for the study of circRNAs. Our objective was to characterize non-canonical circRNAs, namely not originating from back splicing and circRNA produced by non-coding genes. To this end, we analyzed a dataset from porcine testis known to contain about 100 intron-derived circRNAs. Labelling reads containing a circular junction and originating from back splicing provided information on the very small contribution of long non-coding genes to the production of canonical circRNAs. Analyses of the other reads revealed two origins for non-canonical circRNAs: (1) Intronic sequences for lariat-derived intronic circRNAs and intron circles, (2) Mono-exonic genes (mostly non-coding) for either a new type of circRNA (including only part of the exon: sub-exonic circRNAs) or, even more rarely, mono-exonic canonical circRNAs. The most complex set of sub-exonic circRNAs was produced by (ribozyme RNA). We specifically investigated the intronic circRNA of , which is probably an independently transcribed sisRNA (stable intronic sequence RNA). We may be witnessing the emergence of a new non-coding gene in the porcine genome. Our results are evidence that most non-canonical circRNAs originate from non-coding sequences.
对核糖体序列进行测序的总 RNA 仍然是研究 circRNAs 的首选方法。我们的目的是表征非规范的 circRNAs，即不是源自反向剪接和由非编码基因产生的 circRNA。为此，我们分析了一组来自猪睾丸的数据集，该数据集已知包含约 100 个内含子衍生的 circRNAs。标记包含圆形接头的读段并源自反向剪接，为长非编码基因对产生规范 circRNAs 的微小贡献提供了信息。对其他读段的分析揭示了非规范 circRNAs 的两种起源：（1）套索衍生内含子 circRNAs 和内含子环的内含子序列，（2）单外显子基因（主要是非编码），用于新的 circRNA 类型（仅包含外显子的一部分：亚外显子 circRNAs）或更罕见的单外显子规范 circRNAs。亚外显子 circRNAs 种类最多的是由 （核酶 RNA）产生的。我们特别研究了 的内含子 circRNA，它可能是一种独立转录的 sisRNA（稳定内含子序列 RNA）。我们可能正在见证猪基因组中一个新的非编码基因的出现。我们的结果表明，大多数非规范 circRNAs 源自非编码序列。
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