title: Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis.
abstract: BACKGROUND
  DNA methylation is thought to be extensively involved in the pathogenesis of many diseases, including major psychosis. However, most studies focus on DNA methylation alteration at promoters of protein-coding genes, despite the poor correlation between DNA methylation and gene expression.
  
  
  METHODS
  We analyzed differentially methylated regions and differentially expressed genes in patients with schizophrenia and bipolar disorder and normal subjects. Gene expression and DNA methylation were analyzed with RNA-seq and MeDIP-seq of post-mortem brain tissue (brain region BA9) cohort in five schizophrenia, seven bipolar disorder cases and six controls, respectively.
  
  
  RESULTS
  Here, we performed a large-scale integrative analysis using MeDIP-seq, coupled with RNA-seq, on brain samples from major psychotic and normal subjects and observed obvious discrepancy between DNA methylation and gene expression. We found that differentially methylated regions (DMRs) were distributed across different types of genomic elements, especially introns. These intronic DMRs were significantly enriched for diverse regulatory elements, such as enhancers and binding sites of certain transcriptional factors (e.g., Pol3). Notably, we found that parts of intronic DMRs overlapped with some intragenic miRNAs, such as hsa-mir-7-3. These intronic DMR-related miRNAs were found to target many differentially expressed genes. Moreover, functional analysis demonstrated that differential target genes of intronic DMR-related miRNAs were sufficient to capture many important biological processes in major psychosis, such as neurogenesis, suggesting that miRNAs may function as important linkers mediating the relationships between DNA methylation alteration and gene expression changes.
  
  
  CONCLUSIONS
  Collectively, our study indicated that DNA methylation alteration could induce expression changes indirectly by affecting miRNAs and the exploration of DMR-related miRNAs and their targets enhanced understanding of the molecular mechanisms underlying major psychosis.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. zhy_sara@126.com.
authors.forename: Hongying
authors.initials: H
authors.lastname: Zhao
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. xujinyuan90@gmail.com.
authors.forename: Jinyuan
authors.initials: J
authors.lastname: Xu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. panglinpl@163.com.
authors.forename: Lin
authors.initials: L
authors.lastname: Pang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. zhangyunpeng_biocc@yahoo.cn.
authors.forename: Yunpeng
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. fanhuihui@hrbmu.edu.cn.
authors.forename: Huihui
authors.initials: H
authors.lastname: Fan
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. bioliul1012@126.com.
authors.forename: Ling
authors.initials: L
authors.lastname: Liu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. ltt.2007@163.com.
authors.forename: Tingting
authors.initials: T
authors.lastname: Liu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. yufulong421@gmail.com.
authors.forename: Fulong
authors.initials: F
authors.lastname: Yu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. sda910722@gmail.com.
authors.forename: Guanxiong
authors.initials: G
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. lanyousi_001@163.com.
authors.forename: Yujia
authors.initials: Y
authors.lastname: Lan
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. bai_jingbelieve@126.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Bai
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. lixia@hrbmu.edu.cn.
authors.forename: Xia
authors.initials: X
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. xiaoyun@ems.hrbmu.edu.cn.|Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China. xiaoyun@ems.hrbmu.edu.cn.
authors.forename: Yun
authors.initials: Y
authors.lastname: Xiao
mesh_terms: D001714:Bipolar Disorder / Q000235:genetics*; D001921:Brain / Q000378:metabolism; D016022:Case-Control Studies; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D023281:Genomics; D006801:Humans; D007438:Introns / Q000235:genetics*; D012559:Schizophrenia / Q000235:genetics*