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Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci

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  • Atsushi Takata

    (Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute
    Yokohama City University Graduate School of Medicine)

  • Naomichi Matsumoto

    (Yokohama City University Graduate School of Medicine)

  • Tadafumi Kato

    (Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute)

Abstract

Detailed analyses of transcriptome have revealed complexity in regulation of alternative splicing (AS). These AS events often undergo modulation by genetic variants. Here we analyse RNA-sequencing data of prefrontal cortex from 206 individuals in combination with their genotypes and identify cis-acting splicing quantitative trait loci (sQTLs) throughout the genome. These sQTLs are enriched among exonic and H3K4me3-marked regions. Moreover, we observe significant enrichment of sQTLs among disease-associated loci identified by GWAS, especially in schizophrenia risk loci. Closer examination of each schizophrenia-associated loci revealed four regions (each encompasses NEK4, FXR1, SNAP91 or APOPT1), where the index SNP in GWAS is in strong linkage disequilibrium with sQTL SNP(s), suggesting dysregulation of AS as the underlying mechanism of the association signal. Our study provides an informative resource of sQTL SNPs in the human brain, which can facilitate understanding of the genetic architecture of complex brain disorders such as schizophrenia.

Suggested Citation

  • Atsushi Takata & Naomichi Matsumoto & Tadafumi Kato, 2017. "Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14519
    DOI: 10.1038/ncomms14519
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    Cited by:

    1. Ruo-Han Hao & Tian-Pei Zhang & Feng Jiang & Jun-Hui Liu & Shan-Shan Dong & Meng Li & Yan Guo & Tie-Lin Yang, 2024. "Revealing brain cell-stratified causality through dissecting causal variants according to their cell-type-specific effects on gene expression," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Anat Kreimer & Tal Ashuach & Fumitaka Inoue & Alex Khodaverdian & Chengyu Deng & Nir Yosef & Nadav Ahituv, 2022. "Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

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