Genome-wide comparison of allele-specific gene expression between African and European populations
Genome-wide comparison of allele-specific gene expression between African and European populations
复制标题
非洲和欧洲人群等位基因特异性基因表达的全基因组比较
DOI：
10.1093/hmg/ddy027
复制
发表时间：
2018-03
影响因子：
3.5
通讯作者：
Xu Shuhua
中科院分区：
文献类型：
--
作者：
Tian Lei;Khan Asifullah;Ning Zhilin;Yuan Kai;Zhang Chao;Lou Haiyi;Yuan Yuan;Xu Shuhua
人类群体中的转录组多样性反映了不同的调节机制。等位基因不平衡表达是导致人类表型变异的一种遗传调控机制。为了系统地研究全基因组等位基因特异性表达（ASE），我们分析了Geuvadis项目提供的欧洲和非洲人群的RNA-Seq数据。我们在欧洲人和非洲人的8个基因中发现了11个ASE位点，在9个基因中发现了9个群体特异性ASE位点，包括新的和已知的ASE信号。值得注意的是，在DNAJC 15中观察到洲际人群之间分化的ASE的最高信号，其中rs 12015的衍生等位基因（单核苷酸多态性（SNP））显示出比欧洲个体中的祖先等位基因显着更高的表达。我们确定了一个独特的单倍型DNAJC 15，其中一些SNPs高度分化的欧洲和非洲人口之间的强有力的联系与高ASE的网站。其中，SNP rs 17553284影响几种转录因子的结合以及DNAJC 15的基因型依赖性表达。因此，我们推测rs 17553284可能是介导rs 12015的ASE的调节性因果变体。我们发现了几个不同的洲际人群之间的ASE。高度分化的ASE基因在这里确定可能牵连在人口之间的表型变异，既进化和医学上的重要性。
Transcriptomic diversity across human populations reflects differential regulatory mechanisms. Allelic-imbalanced gene expression is a genetic regulatory mechanism that contributes to human phenotypic variation. To systematically investigate genome-wide allele-specific expression (ASE), we analyzed RNA-Seq data from European and African populations provided by the Geuvadis project. We identified 11 sites in 8 genes showing ASE in both Europeans and Africans, and 9 sites in 9 genes showing population-specific ASE, including both novel and known ASE signals. Notably, the top signal of differentiated ASE between inter-continental populations was observed in DNAJC15, of which the derived allele of rs12015, a single nucleotide polymorphism (SNP), showed significantly higher expression than did the ancestral allele specifically in European individuals. We identified a unique haplotype of DNAJC15, where a few SNPs highly differentiated between European and African populations were strongly linked to sites with high ASE. Among these, SNP rs17553284 affected the binding of several transcription factors as well as the genotype-dependent expression of DNAJC15. Therefore, we speculated that rs17553284 could be a regulatory causal variant that mediates the ASE of rs12015. We found several variations in ASE between intercontinental populations. The highly differentiated ASE genes identified here may implicate in the phenotypic variations among populations that are both evolutionarily and medically important.
登录
查看更多内容
影响因子：
12.3
作者：
Castel SE;Levy-Moonshine A;Mohammadi P;Banks E;Lappalainen T
通讯作者：
Lappalainen T
影响因子：
3.4
作者：
Sato MP;Makino T;Kawata M
通讯作者：
Kawata M
影响因子：
30.8
作者：
Pala M;Zappala Z;Marongiu M;Li X;Davis JR;Cusano R;Crobu F;Kukurba KR;Gloudemans MJ;Reinier F;Berutti R;Piras MG;Mulas A;Zoledziewska M;Marongiu M;Sorokin EP;Hess GT;Smith KS;Busonero F;Maschio A;Steri M;Sidore C;Sanna S;Fiorillo E;Bassik MC;Sawcer SJ;Battle A;Novembre J;Jones C;Angius A;Abecasis GR;Schlessinger D;Cucca F;Montgomery SB
通讯作者：
Montgomery SB
影响因子：
12.3
作者：
McLaren W;Gil L;Hunt SE;Riat HS;Ritchie GR;Thormann A;Flicek P;Cunningham F
通讯作者：
Cunningham F
影响因子：
4.5
作者：
Kabza M;Kubiak MR;Danek A;Rosikiewicz W;Deorowicz S;Polański A;Makałowska I
通讯作者：
Makałowska I