Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Aichi 474-8511, Japan.
Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi 460-0001, Japan.
Database (Oxford). 2021 Nov 3;2021(2021). doi: 10.1093/database/baab072.
MicroRNAs (miRNAs) are small non-coding RNAs shown to regulate gene expression by binding to complementary transcripts. Genetic variants, including single-nucleotide polymorphisms and short insertions/deletions, contribute to traits and diseases by influencing miRNA expression. However, the association between genetic variation and miRNA expression remains to be elucidated. Here, by using genotype data and miRNA expression data from 3448 Japanese serum samples, we developed a computational pipeline to systematically identify genome-wide miRNA expression quantitative trait loci (miR-eQTLs). Not only did we identify a total of 2487 cis-miR-eQTLs and 3 155 773 trans-miR-eQTLs at a false discovery rate of <0.05 in six dementia types (Alzheimer's disease, dementia with Lewy bodies, vascular dementia, frontotemporal lobar degeneration, normal-pressure hydrocephalus and mild cognitive impairment) and all samples, including those from patients with other types of dementia, but also we examined the commonality and specificity of miR-eQTLs among dementia types. To enable data searching and downloading of these cis- and trans-eQTLs, we developed a user-friendly database named JAMIR-eQTL, publicly available at https://www.jamir-eqtl.org/. This is the first miR-eQTL database designed for dementia types. Our integrative and comprehensive resource will contribute to understanding the genetic basis of miRNA expression as well as to the discovery of deleterious mutations, particularly in dementia studies. Database URL: https://www.jamir-eqtl.org/.
微小 RNA（miRNAs）是一种小的非编码 RNA，通过与互补转录本结合来调节基因表达。包括单核苷酸多态性和短插入/缺失在内的遗传变异通过影响 miRNA 表达，从而导致性状和疾病的发生。然而，遗传变异与 miRNA 表达之间的关联仍有待阐明。在这里，我们通过使用来自 3448 个日本血清样本的基因型数据和 miRNA 表达数据，开发了一个计算流程，以系统地鉴定全基因组 miRNA 表达数量性状基因座（miR-eQTLs）。我们不仅在六种痴呆症（阿尔茨海默病、路易体痴呆、血管性痴呆、额颞叶变性、正常压力脑积水和轻度认知障碍）和所有样本（包括来自其他类型痴呆症患者的样本）中鉴定出总共 2487 个 cis-miR-eQTL 和 3155773 个 trans-miR-eQTL，假发现率<0.05，而且还研究了 miR-eQTL 在痴呆症类型之间的共性和特异性。为了能够搜索和下载这些 cis 和 trans-eQTL，我们开发了一个名为 JAMIR-eQTL 的用户友好型数据库，可在 https://www.jamir-eqtl.org/ 上公开获取。这是第一个为痴呆症类型设计的 miR-eQTL 数据库。我们的综合和全面的资源将有助于理解 miRNA 表达的遗传基础，并有助于发现有害突变，特别是在痴呆症研究中。数据库网址：https://www.jamir-eqtl.org/。
