全转录组测序鉴定了调控发育中鼠视网膜神经发生的关键 circRNAs、lncRNAs 和 miRNAs。

Whole transcriptome sequencing identifies key circRNAs, lncRNAs, and miRNAs regulating neurogenesis in developing mouse retina.

机构信息

State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital of Wenzhou Medical University, Wenzhou, China.

出版信息

BMC Genomics. 2021 Oct 30;22(1):779. doi: 10.1186/s12864-021-08078-z.

BACKGROUND

The molecular complexity of neural retina development remains poorly studied. Knowledge of retinal neurogenesis regulation sheds light on retinal degeneration therapy exploration. Therefore, we integrated the time-series circRNA, lncRNA, miRNA, and mRNA expression profiles of the developing retina through whole-transcriptome sequencing. The key functional ncRNAs and the ceRNA network regulating retinal neurogenesis were identified.

RESULTS

Transcriptomic analysis identified circRNA as the most variable ncRNA subtype. We screened a series of neurogenesis-related circRNAs, lncRNAs, and miRNAs using different strategies based on their diversified molecular functions. The expression of circCDYL, circATXN1, circDYM, circPRGRIP, lncRNA Meg3, and lncRNA Vax2os was validated by quantitative real-time PCR. These circRNAs and lncRNAs participate in neurotransmitter transport and multicellular organism growth through the intricate circRNA/lncRNA-miRNA-mRNA network.

CONCLUSION

Whole-transcriptome sequencing and bioinformatics analysis systematically screened key ncRNAs in retinal neurogenesis. The validated ncRNAs and their circRNA/lncRNA-miRNA-mRNA network involve neurotransmitter transport and multicellular organism growth during retinal development.

背景

神经视网膜发育的分子复杂性仍未得到充分研究。对视网膜神经发生调控的了解为视网膜变性治疗的探索提供了线索。因此，我们通过全转录组测序整合了发育中视网膜的时序 circRNA、lncRNA、miRNA 和 mRNA 表达谱。鉴定了关键的功能性 ncRNA 以及调控视网膜神经发生的 ceRNA 网络。

结果

转录组分析表明 circRNA 是最具变异性的 ncRNA 亚型。我们使用不同的策略，基于其多样化的分子功能，筛选了一系列与神经发生相关的 circRNA、lncRNA 和 miRNA。circCDYL、circATXN1、circDYM、circPRGRIP、lncRNA Meg3 和 lncRNA Vax2os 的表达通过定量实时 PCR 得到验证。这些 circRNAs 和 lncRNAs 通过复杂的 circRNA/lncRNA-miRNA-mRNA 网络参与神经递质运输和多细胞生物生长。