基础医学与临床 ›› 2020, Vol. 40 ›› Issue (10): 1328-1334.

• 研究论文 • 上一篇    下一篇

长链非编码RNA lnc-DC的生物信息学分析与验证

胡雪停, 吴晓凤, 徐祥*   

  1. 陆军军医大学大坪医院 干细胞与再生医学科, 创伤、烧伤与复合伤国家重点实验室, 重庆 400042
  • 收稿日期:2020-04-02 修回日期:2020-07-01 出版日期:2020-10-05 发布日期:2020-09-29
  • 通讯作者: * xiangxu@tmmu.edu.cn
  • 基金资助:
    国家自然科学基金(81871568)

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

HU Xue-ting, WU Xiao-feng, XU Xiang*   

  1. State Key Laboratory of Trauma, Burns and Combined Injury, Deparment of Stem Cell and Regenerative Medicine, Daping Hospital,Army Medical University,Chongqing 400042, China
  • Received:2020-04-02 Revised:2020-07-01 Online:2020-10-05 Published:2020-09-29
  • Contact: * xiangxu@tmmu.edu.cn

摘要: 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。

关键词: 生物信息学, 长链非编码RNA lnc-DC, GATA3, 皮肤

Abstract: 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.

Key words: bioinformatics, long non-coding RNA lnc-DC, GATA3, skin

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