Whole transcriptome sequencing identifies key circRNAs, lncRNAs, and miRNAs regulating neurogenesis in developing mouse retina.
Whole transcriptome sequencing identifies key circRNAs, lncRNAs, and miRNAs regulating neurogenesis in developing mouse retina.
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全转录组测序鉴定了调节小鼠视网膜神经发生的关键 circRNA、lncRNA 和 miRNA
DOI：
10.1186/s12864-021-08078-z
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发表时间：
2021-10-30
期刊：
影响因子：
4.4
通讯作者：
Chi ZL
中科院分区：
文献类型：
--
作者：
Chen G;Qian HM;Chen J;Wang J;Guan JT;Chi ZL
神经视网膜发育的分子复杂性仍研究不足。对视网膜神经发生调控的认识有助于探索视网膜变性的治疗方法。因此，我们通过全转录组测序整合了发育中视网膜的circRNA、lncRNA、miRNA和mRNA的时间序列表达谱。确定了调控视网膜神经发生的关键功能性非编码RNA（ncRNA）以及竞争性内源性RNA（ceRNA）网络。
转录组分析确定circRNA是变化最为显著的ncRNA亚型。我们基于其多样的分子功能，采用不同策略筛选出一系列与神经发生相关的circRNA、lncRNA和miRNA。通过实时荧光定量PCR验证了circCDYL、circATXN1、circDYM、circPRGRIP、lncRNA Meg3和lncRNA Vax2os的表达。这些circRNA和lncRNA通过复杂的circRNA/lncRNA - miRNA - mRNA网络参与神经递质转运和多细胞生物体生长。
全转录组测序和生物信息学分析系统地筛选出视网膜神经发生中的关键ncRNA。经验证的ncRNA及其circRNA/lncRNA - miRNA - mRNA网络在视网膜发育过程中参与神经递质转运和多细胞生物体生长。
网络版包含补充材料，获取网址：10.1186/s12864 - 021 - 08078 - z 。
BackgroundThe 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.ResultsTranscriptomic 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.ConclusionWhole-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.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
3.7
作者：
Chen X;Zhou R;Shan K;Sun Y;Yan B;Sun X;Wang J
通讯作者：
Wang J
影响因子：
17.8
作者：
Corso-Díaz X;Jaeger C;Chaitankar V;Swaroop A
通讯作者：
Swaroop A
影响因子：
14.9
作者：
Harris, MA;Clark, J;White, R
通讯作者：
White, R
小鼠发育视网膜的圆形RNome
影响因子：
8.8
作者：
Chen, Xue-Jiao;Zhang, Zi-Cheng;Jin, Zi-Bing
通讯作者：
Jin, Zi-Bing