Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis

BMC Medical Genomics

Volumn 8, Issue 1, 2015, Pages

  Zhao, Hongying ^a   Xu, Jinyuan ^a   Pang, Lin ^a   Zhang, Yunpeng ^a   Fan, Huihui ^a   Liu, Ling ^a   Liu, Tingting ^a   Yu, Fulong ^a   Zhang, Guanxiong ^a   Lan, Yujia ^a   Bai, Jing ^a   Li, Xia ^a   Xiao, Yun ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

DNA methylation; Major psychosis; MeDIP seq; MiRNA; RNA seq

Indexed keywords

MICRORNA; TRANSCRIPTOME;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BIPOLAR DISORDER; BRAIN REGION; CLINICAL ARTICLE; CONTROLLED STUDY; DNA METHYLATION; DOWN REGULATION; EPIGENETICS; GENE EXPRESSION; GENE FUNCTION; GENE MAPPING; GENE TARGETING; GENETIC ASSOCIATION; GENOME ANALYSIS; HUMAN; HUMAN TISSUE; INTRON; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; SCHIZOPHRENIA; BRAIN; CASE CONTROL STUDY; GENETIC EPIGENESIS; GENETICS; GENOMICS; METABOLISM;

BIPOLAR DISORDER; BRAIN; CASE-CONTROL STUDIES; DNA METHYLATION; EPIGENESIS, GENETIC; GENOMICS; HUMANS; INTRONS; SCHIZOPHRENIA;

EID: 84944097016     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/s12920-015-0139-4     Document Type: Article

References (56)

1. Craddock N, O'Donovan MC, Owen MJ. Genes for schizophrenia and bipolar disorder? Implications for psychiatric nosology. Schizophr Bull. 2006;32(1):9-16.
2. State MW, Levitt P. The conundrums of understanding genetic risks for autism spectrum disorders. Nat Neurosci. 2011;14(12):1499-506.
3. Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature. 2007;447(7143):425-32. Zhao et al. BMC Medical Genomics (2015) 8:62 Page 10 of 12
4. Abdolmaleky HM, Thiagalingam S, Wilcox M. Genetics and Epigenetics in Major Psychiatric Disorders. Am J Pharmacogenomics. 2005;5(3):149-60.
5. Rao JS, Keleshian VL, Klein S, Rapoport SI. Epigenetic modifications in frontal cortex from Alzheimer's disease and bipolar disorder patients. Translational psychiatry. 2012;2:e132. doi:10.1038/tp.2012.55.
6. Kuratomi G, Iwamoto K, Bundo M, Kusumi I, Kato N, Iwata N, et al. Aberrant DNA methylation associated with bipolar disorder identified from discordant monozygotic twins. Mol Psychiatry. 2007;13(4):429-41.
7. Tamura Y, Kunugi H, Ohashi J, Hohjoh H. Epigenetic aberration of the human REELIN gene in psychiatric disorders. Mol Psychiatry. 2007;12(6):519. 93-600.
8. Iwamoto K, Bundo M, Yamada K, Takao H, Iwayama-Shigeno Y, Yoshikawa T, et al. DNA methylation status of SOX10 correlates with its downregulation and oligodendrocyte dysfunction in schizophrenia. The Journal of neuroscience. 2005;25(22):5376-81.
9. Abdolmaleky HM, Cheng K-h, Faraone SV, Wilcox M, Glatt SJ, Gao F, et al. Hypomethylation of MB-COMT promoter is a major risk factor for schizophrenia and bipolar disorder. Hum Mol Genet. 2006;15(21):3132-45.
10. Gavin DP, Sharma RP. Histone modifications, DNA methylation, and schizophrenia. Neurosci Biobehav Rev. 2010;34(6):882-8.
11. Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, et al. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet. 2008;82(3):696-711.
12. Xiao Y, Camarillo C, Ping Y, Arana TB, Zhao H, Thompson PM, et al. The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder. PLoS One. 2014;9(4), e95875.
13. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet. 2007;39(4):457-66.
14. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484-92.
15. Simmer F, Brinkman AB, Assenov Y, Matarese F, Kaan A, Sabatino L, et al. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics. 2012;7(12):1355-67.
16. Moreau MP, Bruse SE, David-Rus R, Buyske S, Brzustowicz LM. Altered microRNA expression profiles in postmortem brain samples from individuals with schizophrenia and bipolar disorder. Biol Psychiatry. 2011;69(2):188-93.
17. Xiao Y, Guan J, Ping Y, Xu C, Huang T, Zhao H, et al. Prioritizing cancerrelated key miRNA-target interactions by integrative genomics. Nucleic Acids Res. 2012;40(16):7653-65.
18. Xiao Y, Ping Y, Fan H, Xu C, Guan J, Zhao H, et al. Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma. Neuro-Oncology. 2013;15(7):818-28. doi:10.1093/neuonc/not018.
19. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A. 2006;103(7):2257-61.
20. Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell. 2005;122(6):947-56.
21. Zhao H, Liu T, Liu L, Zhang G, Pang L, Yu F, et al. Chromatin states modify network motifs contributing to cell-specific functions. Sci Rep. 2015;5:11938. doi:10.1038/srep11938.
22. Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet. 2010;11(3):191-203.
23. Kim AH, Reimers M, Maher B, Williamson V, McMichael O, McClay JL, et al. MicroRNA expression profiling in the prefrontal cortex of individuals affected with schizophrenia and bipolar disorders. Schizophr Res. 2010;124(1):183-91.
24. Sheehan DV, Lecrubier Y, Sheehan KH, Amorim P, Janavs J, Weiller E, et al. The Mini-International Neuropsychiatric Interview (M.I.N.I.): the development and validation of a structured diagnostic psychiatric interview for DSM-IV and ICD-10. J Clin Psychiatry. 1998;59 Suppl 20:22-33.
25. Rajkowska G, Goldman-Rakic PS. Cytoarchitectonic definition of prefrontal areas in the normal human cortex: II. Variability in locations of areas 9 and 46 and relationship to the Talairach Coordinate System. Cereb Cortex. 1995;5(4):323-37.
26. Miller CL, Diglisic S, Leister F, Webster M, Yolken RH. Evaluating RNA status for RT-PCR in extracts of postmortem human brain tissue. Biotechniques. 2004;36(4):628-33.
27. Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell. 2012;149(7):1635-46.
28. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22(9):1760-74.
29. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011;473(7345):43-9.
30. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011;39(Database issue):D152-7. doi:10.1093/nar/gkq1027.
31. Chien CH, Sun YM, Chang WC, Chiang-Hsieh PY, Lee TY, Tsai WC, et al. Identifying transcriptional start sites of human microRNAs based on highthroughput sequencing data. Nucleic Acids Res. 2011;39(21):9345-56.
32. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120(1):15-20.
33. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25(15):1966-7.
34. Chavez L, Jozefczuk J, Grimm C, Dietrich J, Timmermann B, Lehrach H, et al. Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res. 2010;20(10):1441-50.
35. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562-78.
36. Levesque D, Rouillard C. Nur77 and retinoid X receptors: crucial factors in dopamine-related neuroadaptation. Trends Neurosci. 2007;30(1):22-30.
37. Xing G, Zhang L, Russell S, Post R. Reduction of dopamine-related transcription factors Nurr1 and NGFI-B in the prefrontal cortex in schizophrenia and bipolar disorders. Schizophr Res. 2006;84(1):36-56.
38. Severino G, Manchia M, Contu P, Squassina A, Lampus S, Ardau R, et al. Association study in a Sardinian sample between bipolar disorder and the nuclear receptor REV-ERBalpha gene, a critical component of the circadian clock system. Bipolar Disord. 2009;11(2):215-20.
39. Maia BM, Rocha RM, Calin GA. Clinical significance of the interaction between non-coding RNAs and the epigenetics machinery: challenges and opportunities in oncology. Epigenetics. 2014;9(1):75-80.
40. Lorincz MC, Dickerson DR, Schmitt M, Groudine M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol. 2004;11(11):1068-75.
41. Papp B, Plath K. Epigenetics of reprogramming to induced pluripotency. Cell. 2013;152(6):1324-43. doi:10.1016/j.cell.2013.02.043.
42. Rylski M, Kaczmarek L. Ap-1 targets in the brain. Front Biosci. 2004;9:8-23.
43. Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.
44. Kaltschmidt B, Baeuerle PA, Kaltschmidt C. Potential involvement of the transcription factor NF-κB in neurological disorders. Mol Asp Med. 1993;14(3):171-90.
45. Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, et al. Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol. 2010;17(5):620-8.
46. Borchert GM, Lanier W, Davidson BL. RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol. 2006;13(12):1097-101.
47. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 2004;14(10A):1902-10.
48. Perkins DO, Jeffries CD, Jarskog LF, Thomson JM, Woods K, Newman MA, et al. microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder. Genome Biol. 2007;8(2):R27.
49. Kocerha J, Kauppinen S, Wahlestedt C. microRNAs in CNS disorders. Neruomol Med. 2009;11(3):162-72.
50. Villa C, Fenoglio C, De Riz M, Clerici F, Marcone A, Benussi L, et al. Role of hnRNP-A1 and miR-590-3p in neuronal death: genetics and expression analysis in patients with Alzheimer disease and frontotemporal lobar degeneration. Rejuvenation Res. 2011;14(3):275-81.
51. Beveridge N, Gardiner E, Carroll A, Tooney P, Cairns M. Schizophrenia is associated with an increase in cortical microRNA biogenesis. Mol Psychiatry. 2009;15(12):1176-89.
52. Sokolov BP. Oligodendroglial abnormalities in schizophrenia, mood disorders and substance abuse. Comorbidity, shared traits, or molecular phenocopies? Int J Neuropsychopharmacol Neuropsychopharmacologicum (CINP). 2007;10(4):547-55.
53. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466(7303):253-7.
54. Miller BH, Wahlestedt C. MicroRNA dysregulation in psychiatric disease. Brain Res. 2010;1338:89-99.
55. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010;28(10):1045-8.
56. Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011;146(3):353-8.