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Identification of well-differentiated gene expressions between Han Chinese and Japanese using genome-wide microarray data analysis
  1. Yuan Yuan1,2,
  2. Ling Yang1,
  3. Meng Shi1,
  4. Dongsheng Lu1,
  5. Haiyi Lou1,
  6. Yi-Ping Phoebe Chen2,
  7. Li Jin3,
  8. Shuhua Xu1
  1. 1Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
  2. 2Department of Computer Science and Computer Engineering, La Trobe University, Melbourne, Victoria, Australia
  3. 3State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
  1. Correspondence to Professor Shuhua Xu, Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; xushua{at}picb.ac.cn

Abstract

Background Investigating variations in gene expression, which can be quantitatively measured on a genome-wide scale, is essential to understand and interpret phenotypic differences among human populations. Several previous studies have examined and compared variations in gene expression between continental populations. However, differences in gene expression variation between closely related populations have not been studied yet.

Method We performed a genome-wide analysis and systematically compared expression profiles of Han Chinese with those of the Japanese population.

Results We identified 768 genes (4.4% of 17 354 expressed genes) which were expressed differentially between the two populations, with 165 showing highly differential expression and enriched in genes involved in the spliceosome pathway, mRNA processing, mRNA metabolic process, RNA processing, RNA splicing and mitochondrial transport. We further identified cis- and trans-variants that regulated these differential gene expressions, and found that cis-variants shared in the two populations were centred within a range of 200 kb around transcription start site. Our analysis indicated that genetic differences in the cis-associated genes between the two populations could explain 7–43% of the identified expression divergence.

Conclusions In summary, despite considerable heterogeneity, gene expression profiles between Han Chinese and Japanese did show an overall difference, with well-differentiated expressions regulated by genetic variants which have been reported associated with hematological and biochemical traits in Japanese populations. Our results supported that gene expression is regulated by genetic variants and there is a genetic basis for the phenotypic differences between Han Chinese and Japanese populations.

  • Gene expression
  • Han Chinese
  • Japanese
  • eQTL
  • Genetic differentiation

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