东亚人群的胎盘表达定量性状位点

IF 3.3 Q2 GENETICS & HEREDITY
HGG Advances Pub Date : 2024-04-11 Epub Date: 2024-02-03 DOI:10.1016/j.xhgg.2024.100276
Jaeyong Choi, Seung Mi Lee, Errol R Norwitz, Ji Hoi Kim, Young Mi Jung, Chan-Wook Park, Jong Kwan Jun, Dakyung Lee, Yongjoon Jin, Sookyung Kim, Bukyoung Cha, Joong Shin Park, Jong-Il Kim
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引用次数: 0

摘要

表达量性状位点(eQTL)分析测量基因表达的遗传变异对复杂性状的影响。虽然这种方法已被用于研究多种人体组织中的基因调控,但实体组织中的 eQTL 研究却相对缺乏。我们对从东亚人群中采集的胎盘进行了 eQTL 分析,以确定该组织中的基因调控机制。提取 mRNA,用 NGS 测序,并与使用母体和新生儿脐带血进行的匹配母体和胎儿 DNA 阵列进行比较。使用 tensorQTL 进行线性回归建模。精细图谱和表观基因组注释被用来选择推定的功能变异。我们确定了 2703 个编码基因,其中至少包含一个具有统计学意义的 eQTL(假发现率为 0.1。其中,19%的基因位于基因组区域,公共胎盘表观基因组的证据表明它们可能与功能相关。例如,位于胎盘特异性调控区的变异体 rs28379289 改变了转录因子的结合亲和力,导致 LGALS3 的高表达,而 LGALS3 的表达已知会影响胎盘功能。这项研究扩展了人类胎盘内调控元件的知识库,并确定了 108 个以前未报道的胎盘 eQTL 信号,这些信号已被列入我们公开的 GMI eQTL 数据库。还需要进一步的研究来确定和描述影响正常妊娠和胎盘相关疾病中胎盘功能的遗传调控机制。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Placental expression quantitative trait loci in an East Asian population.

Expression quantitative trait loci (eQTL) analysis measures the contribution of genetic variation in gene expression on complex traits. Although this methodology has been used to examine gene regulation in numerous human tissues, eQTL research in solid tissues is relatively lacking. We conducted eQTL analysis on placentas collected from an East Asian population in an effort to identify gene regulatory mechanisms in this tissue. Placentas (n = 102) were collected at the time of cesarean delivery. mRNA was extracted, sequenced with NGS, and compared with matched maternal and fetal DNA arrays performed using maternal and neonatal cord blood. Linear regression modeling was performed using tensorQTL. Fine-mapping along with epigenomic annotation was used to select putative functional variants. We identified 2,703 coding genes that contained at least one eQTL with statistical significance (false discovery rate <0.05). After fine-mapping, we found 108 previously unreported eQTL variants with posterior inclusion probability >0.1. Of these, 19% were located in genomic regions with evidence from public placental epigenome suggesting that they may be functionally relevant. For example, variant rs28379289 located in the placenta-specific regulatory region changes the binding affinity of transcription factor leading to higher expression of LGALS3, which is known to affect placental function. This study expands the knowledge base of regulatory elements within the human placenta and identifies 108 previously unreported placenta eQTL signals, which are listed in our publicly available GMI eQTL database. Further studies are needed to identify and characterize genetic regulatory mechanisms that affect placental function in normal pregnancy and placenta-related diseases.

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来源期刊
HGG Advances
HGG Advances Biochemistry, Genetics and Molecular Biology-Molecular Medicine
CiteScore
4.30
自引率
4.50%
发文量
69
审稿时长
14 weeks
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