title: DNA methylation patterns of protein coding genes and long noncoding RNAs in female schizophrenic patients.
abstract: Schizophrenia (SCZ) is a complex mental disorder contributed by both genetic and epigenetic factors. Long noncoding RNAs (lncRNAs) was recently found playing an important regulatory role in mental disorders. However, little was known about the DNA methylation of lncRNAs, although numerous SCZ studies have been performed on genetic polymorphisms or epigenetic marks in protein coding genes. We presented a comprehensive genome wide DNA methylation study of both protein coding genes and lncRNAs in female patients with paranoid and undifferentiated SCZ. Using the methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq), 8,163 and 764 peaks were identified in paranoid and undifferentiated SCZ, respectively (p < 1 × 10-5). Gene ontology analysis showed that the hypermethylated regions were enriched in the genes related to neuron system and brain for both paranoid and undifferentiated SCZ (p < 0.05). Among these peaks, 121 peaks were located in gene promoter regions that might affect gene expression and influence the SCZ related pathways. Interestingly, DNA methylation of 136 and 23 known lncRNAs in Refseq database were identified in paranoid and undifferentiated SCZ, respectively. In addition, ∼20% of intergenic peaks annotated based on Refseq genes were overlapped with lncRNAs in UCSC and gencode databases. In order to show the results well for most biological researchers, we created an online database to display and visualize the information of DNA methyation peaks in both types of SCZ (http://www.bioinfo.org/scz/scz.htm). Our results showed that the aberrant DNA methylation of lncRNAs might be another important epigenetic factor for SCZ.
authors.affiliation: Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Liao
authors.affiliation: Department of Neurology, The 148 Central Hospital of PLA, Zibo, Shandong, China. Electronic address: wangyunliang81@163.com.
authors.forename: Yunliang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.
authors.forename: Dongjun
authors.initials: D
authors.lastname: Dai
authors.affiliation: Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.
authors.forename: Xingyu
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Department of Neurology, The 148 Central Hospital of PLA, Zibo, Shandong, China.
authors.forename: Yuzheng
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China. Electronic address: gaoshugui@sina.com.
authors.forename: Shugui
authors.initials: S
authors.lastname: Gao
authors.affiliation: Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China. Electronic address: duanshiwei@nbu.edu.cn.
authors.forename: Shiwei
authors.initials: S
authors.lastname: Duan
mesh_terms: D000328:Adult; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D063990:Gene Ontology; D006801:Humans; D011401:Promoter Regions, Genetic; D062085:RNA, Long Noncoding / Q000235:genetics*; D012559:Schizophrenia / Q000235:genetics*; D055815:Young Adult
chemical_list: D062085:RNA, Long Noncoding
keywords: DNA methylation; Epigenetic; Long noncoding RNAs (lncRNAs); Schizophrenia (SCZ)