红系细胞发育相关miR-196b的靶基因预测及意义

Target gene prediction of erythroid cells-related miR-196b

目的预测红系细胞发育相关miR-196b的靶基因,并探讨其作用机制。方法应用miRbase数据库查找多物种已知的miR-196b成熟序列,比对后分析其在多物种间的保守性。应用miRanda、miRDB、Targetscan7.1、PITA和miRWalk数据库对miR-196b的靶基因进行预测,筛选重复率较高的靶基因。应用Cytoscape3.3.0和KEGG对重复率较高的靶基因进行GO分类富集分析和信号通路富集分析。查阅文献,再次筛选与红系细胞发育相关的靶基因,采用Targetscan7.1和RNA22分析其与miR-196b的结合情况。结果 22个物种具有miR-196b成熟序列,序列比对发现miR-196b在多物种间高度保守。靶基因预测结果显示,共得到5 004个miR-196b的靶基因,其中重复率较高的靶基因有302个。GO分类富集分析结果显示,miR-196b靶基因在生物学过程显著富集于发育过程、细胞过程和定位等,在分子功能显著富集于蛋白结合和物质转运等,在细胞组分显著富集于细胞突起和细胞器膜等(P均<0.05)。结合信号通路富集分析结果,筛选出43个与红系细胞发育相关miR-196b的靶基因,其信号通路富集于Ras信号通路、c AMP信号通路和PI3K-Akt信号通路等(P均<0.05)。结合文献,最终筛选出与红系细胞发育相关的miR-196b靶基因有5个,分别为GATA1、Cdkn1b、Pld1、Cdh1和Ntrk2,其中GATA1、Cdkn1b和Cdh1可与miR-196b直接结合。结论红系细胞发育相关miR-196b的靶基因可能为GATA1、Cdkn1b、Pld1、Cdh1和Ntrk2;miR-196b可能通过对上述靶基因的直接或间接作用激活相应信号通路,在红系细胞的发育过程中发挥生物学作用。

Objective To predict the target genes of miR-196b related to erythroid cells and to explore their mecha- nism. Methods We applied miRbase database to search for miR-196b mature sequence of multiple species and analyze its conservation. MiRanda, miRDB, Targetscan7.1, PITA and miRWalk databases were used to predict the target genes of miR-196b, and we screened the target genes with high repetition rate. GO annotation and signal pathway enrichment analy- sis on target genes with high repetition rate were performed using Cytoscape3.3.0 and KEGG. Combined with literature, the target .genes related to erythroid cells were screened out, and we applied Targetscan7.1 and RNA22 to analysis their combination with miR-196b. Results Twenty-two species had miR-196b mature sequence, and we found that miR-196b was highly conserved among different species by sequence alignment. Target gene prediction results showed that a total of 5 004 miR-196b target genes were chosen, of which 302 target genes had a high repetition rate. GO enrichment analysis showed that the target genes of miR-196 in biological process were significantly enriched in the developmental process, cel- lular process and localization; as for the molecular function, they were significantly enriched in protein binding and material transport, and as for the cell component, they were significantly enriched in cell projection and organelle membrane （ all P 〈 0.05）. Signal pathway enrichment analysis showed that 43 target genes-associated with cell development were screened out, and their signal pathways were enriched in Ras signaling pathway, cAMP signaling pathway and PI3K-Akt signaling pathway （P 〈0.05）. Finally, 5 target genes were screened out, which were Ntrk2, Cdknlb, Pldl, Cdhl and GATA1, in which Cdhl, Cdknlb and GATA1 could be directly combined with miR-196b. Conclusions The erythroid cells-related miR-196b target genes may be GATA1, Cdknlb, Pldl, Cdhl and Ntrk2. Meanwhile, miR-196b can activate the corre- sponding signaling pathway through the direct or indirect effect of the target genes, and plays a biological role in the devel- opment of erythroid cells.