ARHGAP29内含子区域SNP位点的生物信息学分析

›› 2020, Vol. 11 ›› Issue (3): 147-150.

ARHGAP29内含子区域SNP位点的生物信息学分析

侯宇转¹,阮文彦¹,段小红²,黄永清³

1. 宁夏医科大学口腔医学院
2. 军事口腔国家重点实验室第四军医大学口腔医院
3. 宁夏医科大学总医院口腔医院口腔颌面外科

收稿日期:2020-07-22 修回日期:2020-08-13 出版日期:2020-09-25 发布日期:2020-09-30
通讯作者: 黄永清 E-mail:yongqinghuang_6510@126.com
基金资助:
国家自然科学基金

Bioinformatics analysis of SNPs in ARHGAP29 intron regions

Received:2020-07-22 Revised:2020-08-13 Online:2020-09-25 Published:2020-09-30

摘要/Abstract

摘要： 目的：通过生物信息学方法对全基因组关联分析（GWAS）得到的ARHGAP29内含子区域的单核苷酸多态性（SNP）进行深度分析，对目标SNP进行信息注释及功能预测。方法：根据病例对照实验筛选出4个有统计学意义的SNP位点，运用美国国家生物技术信息中心（NCBI）中的SNP数据库、3D SNP数据库，RegulomeDB数据库、LncSNP2.0数据库等多种信息分析方法对SNP的生物学信息及相关长链非编码RNA（LncRNA）的功能进行预测。结果：4个SNP（rs3814019、rs72964308、rs17396055、rs7540684）均位于1号染色体，rs72964308的次要等位基因频率（MAF）值小于0.05，在后续分析中将其排除。目标SNP可通过三维的染色质环与ABCA4、ARHGAP29相互作用，线性距离95~200 kb。SNP在多种组织中位于增强子区，在个别组织中属于转录起始位点。rs17396055的转录因子信息中DNA可接近性较高，表明其转录活性较强。rs17396055和rs7540684相关的LncRNA预测显示相关性最高的疾病为唇腭裂。结论：上述生物信息学方法表明rs3814019、rs17396055、rs7540684在多种细胞类型中发挥调控作用，与rs17396055、rs7540684相关的LncRNA可能与颅颌面发育有关。

关键词: 唇腭裂, ARHGAP29, 单核苷酸多态性, 长链非编码RNA, 生物信息学

Abstract: Objective: To analyze the four intron SNPs of ARHGAP29 from previously reported GWAS results by bioinformatics, and performing information annotation and function prediction of target SNPs. Methods: Four statistically significant SNP loci were selected from the case-control experiment. The biological information of SNPs and the functions of related LncRNAs were predicted by using SNP database in NCBI website, 3DSNP database, RegulomeDB database, and LncSNP2.0 database. Results: Minor allele frequency (MAF) of rs72964308 was lower than 0.05, be excluded in subsequent analysis. The analysis of chromatin state showed that SNPs mainly locate in the enhancer region in various cell types, and also in the transcription initiation sites of rare tissues. The high DNA accessibility of the transcription factors that interacted with rs17396055 indicates a strong transcriptional activity. The prediction of LncRNA related with rs17396055 and rs7540684 showed that the disease with the highest correlation was cleft lip and palate. Conclusions: Rs3814019, rs17396055 and rs7540684 play regulatory roles in various cell types, and the LncRNA related to rs17396055 and rs7540684 may be associated with craniofacial development.

Key words: cleft lip and palate, ARHGAP29, SNP, LncRNA, bioinformatics

侯宇转阮文彦段小红黄永清. ARHGAP29内含子区域SNP位点的生物信息学分析[J]. 口腔生物医学, 2020, 11(3): 147-150.

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