Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex

Genome Biology

Yuan Ran¹  Jian Chen¹  Changyu Tao²  Zelin Liu³  Ence Yang⁴  Sichen Li⁵ 

[1] 0000 0001 0198 0694, grid.263761.7, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, 215123, Suzhou, People’s Republic of China;0000 0001 2256 9319, grid.11135.37, Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, People’s Republic of China;0000 0001 2256 9319, grid.11135.37, Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, People’s Republic of China;0000 0001 2256 9319, grid.11135.37, Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, People’s Republic of China;0000 0001 2256 9319, grid.11135.37, Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, People’s Republic of China;0000 0004 0369 313X, grid.419897.a, Key Laboratory of Neuroscience (Peking University), Ministry of Education, 100191, Beijing, People’s Republic of China;0000000419368729, grid.21729.3f, Department of Industrial Engineering and Operations Research, School of Engineering and Applied Science, Columbia University, 10027, New York, NY, USA;

关键词: Circular RNA;    circQTLs;    Expression variation;    GWAS;   

DOI  :  10.1186/s13059-019-1701-8

来源: publisher

【 摘 要 】

BackgroundCircular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of complex traits and diseases.ResultsWe systematically characterize 10,559 high-quality circRNAs in 589 human dorsolateral prefrontal cortex samples. We identify biological and technical factors contributing to expression heterogeneity associated with the expression levels of many circRNAs, including the well-known circRNA CDR1as. Combining the expression levels of circRNAs with genetic cis-acting SNPs, we detect 196,255 circRNA quantitative trait loci (circQTLs). By characterizing circQTL SNPs, we find that partial circQTL SNPs might influence circRNA formation by altering the canonical splicing site or the reverse complementary sequence match. Additionally, we find that a subset of these circQTL SNPs is highly linked to genome-wide association study signals of complex diseases, especially schizophrenia, inflammatory bowel disease, and type II diabetes mellitus.ConclusionsOur results reveal technical, biological, and genetic factors affecting circRNA expression variation among individuals, which lead to further understanding of circRNA regulation and thus of the genetic architecture of complex traits or diseases.

【 授权许可】

CC BY