Flinders Cancer Research, College of Medicine and Public Health, Flinders University, Bedford Park 5042, South Australia, Australia.
Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park 5042, South Australia, Australia.
Cells. 2020 Nov 16;9(11):2488. doi: 10.3390/cells9112488.
High-throughput RNA sequencing (RNA-seq) and dedicated bioinformatics pipelines have synergized to identify an expansive repertoire of unique circular RNAs (circRNAs), exceeding 100,000 variants. While the vast majority of these circRNAs comprise canonical exonic and intronic sequences, microexons (MEs)-which occur in 30% of functional mRNA transcripts-have been entirely overlooked. CircRNAs which contain these known MEs (ME-circRNAs) could be identified with commonly utilized circRNA prediction pipelines, CIRCexplorer2 and CIRI2, but were not previously recognized as ME-circRNAs. In addition, when employing a bespoke bioinformatics pipeline for identifying RNA chimeras, called Hyb, we could also identify over 2000 ME-circRNAs which contain novel MEs at their backsplice junctions, that are uncalled by either CIRCexplorer2 or CIRI2. Analysis of circRNA-seq datasets from gliomas of varying clinical grades compared with matched control tissue has shown circRNAs have potential as prognostic markers for stratifying tumor from healthy tissue. Furthermore, the abundance of microexon-containing circRNAs (ME-circRNAs) between tumor and normal tissues is correlated with the expression of a splicing associated factor, Serine/arginine repetitive matrix 4 (). Overexpressing SRRM4, known for regulating ME inclusion in mRNAs critical for neural differentiation, in human HEK293 cells resulted in the biogenesis of over 2000 novel ME-circRNAs, including , and changes in the abundance of many canonical circRNAs, including and . This shows SRRM4, in which its expression is correlated with poor prognosis in gliomas, acts as a bona fide circRNA biogenesis factor. Given the known roles of MEs and circRNAs in oncogenesis, the identification of these previously unrecognized ME-circRNAs further increases the complexity and functional purview of this non-coding RNA family.
高通量 RNA 测序（RNA-seq）和专用生物信息学管道协同作用，鉴定出大量独特的环状 RNA（circRNA），超过 100,000 种变体。虽然这些 circRNA 绝大多数由典型的外显子和内含子序列组成，但微外显子（ME）——出现在 30%的功能性 mRNA 转录本中——完全被忽视了。包含这些已知 ME 的 circRNA（ME-circRNA）可以通过常用的 circRNA 预测管道 CIRCexplorer2 和 CIRI2 识别，但以前并未被认为是 ME-circRNA。此外，当使用名为 Hyb 的定制生物信息学管道识别 RNA 嵌合体时，我们还可以识别超过 2000 个 ME-circRNA，它们的 backsplice 连接处包含新的 ME，这两个管道都无法识别。分析不同临床分级的胶质瘤与匹配的对照组织的 circRNA-seq 数据集表明，circRNA 具有作为区分肿瘤与健康组织的预后标志物的潜力。此外，肿瘤和正常组织之间含有微外显子的 circRNA（ME-circRNA）的丰度与剪接相关因子丝氨酸/精氨酸重复矩阵 4（）的表达相关。在人 HEK293 细胞中过表达 SRRM4，该基因已知可调节对神经分化至关重要的 mRNA 中的 ME 包含，导致超过 2000 个新的 ME-circRNA 的生物发生，包括 ，以及许多典型 circRNA 丰度的变化，包括 。这表明 SRRM4 作为 bona fide circRNA 生物发生因子，其表达与胶质瘤的不良预后相关。鉴于 ME 和 circRNA 在肿瘤发生中的已知作用，这些以前未被识别的 ME-circRNA 的鉴定进一步增加了这个非编码 RNA 家族的复杂性和功能范围。
