长链非编码RNA lnc-DC的生物信息学分析与验证

Bioinformatics analysis and verification of the long non-coding RNA lnc-DC

目的通过生物信息学分析获取人类长链非编码RNA lnc-DC的相关信息,初步验证并讨论其意义。方法利用NCBI数据库获取lnc-DC的基本信息及其在人类正常组织中的表达数据;利用UCSC数据库获取lnc-DC基因上游5端启动子序列并通过JASPAR预测结合的转录因子;获取lnc-DC的二级结构并通过catRAPID预测其结合蛋白,利用富集工具Enrichr对lnc-DC结合蛋白进行富集分析;通过原位杂交(FISH)检验lnc-DC在皮肤组织中的表达;运用siRNA干扰和实时定量PCR检测验证转录因子GATA3对lnc-DC的调控作用。结果NCBI数据库显示长链非编码RNA lnc-DC在食管和皮肤中高表达,原位杂交确证lnc-DC在皮肤组织中高表达;软件预测显示GATA3等转录因子可结合到lnc-DC基因启动子区域,运用siRNA干扰表明GATA3确实可调控lnc-DC的表达;软件预测显示lnc-DC可与U2AF2、HNRDL、TIAR、PTBP1、TIA1等蛋白结合,其结合蛋白主要富集于RNA剪接通路,调控RNA加工成熟的过程。结论生物信息学分析能预测lnc-DC的转录调控因子及发挥作用的结合蛋白,表明lnc-DC可能在皮肤正常功能维持中发挥关键作用并受转录因子GATA3的调控。

Objective To obtain the relevant information of human long non-coding RNA lnc-DC by bioinformatical analysis and to confirm its expression and the regulator concerned in the skin.Methods The expression of lnc-DC in human normal tissues was downloaded from NCBI and confirmed by FISH;Transcription factors bind to lnc-DC promoter were predicted by JASPAR and confirmed by siRNA and qPCR;The proteins potential bind to lnc-DC were predicted by catRAPID;lnc-DC binding proteins were analyzed by Enrichr.Results lnc-DC was highly expressed in esophagus and skin;Transcription factors like GATA3 bound to lnc-DC promoter;RNA binding proteins U2AF2,HNRDL,TIAR,PTBP1 and TIA1 potential bound to lnc-DC.Conclusions The bioinformatics online tools may predict transcription regulators and molecular mechanisms of lnc-DC,indicating the important role of GATA3 regulated lnc-DC in the maintenance of normal skin function.