MethylomeDB: a Database of DNA Methylation Profiles of the Brain

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Dec 6

PMID 22140101

Citations 23

Authors

Yurong Xin

Benjamin Chanrion

Anne H ODonnell

Maria Milekic

Ramiro Costa

Yongchao Ge

Fatemeh G Haghighi

Affiliations

Soon will be listed here.

Abstract

MethylomeDB (http://epigenomics.columbia.edu/methylomedb/index.html) is a new database containing genome-wide brain DNA methylation profiles. DNA methylation is an important epigenetic mark in the mammalian brain. In human studies, aberrant DNA methylation alterations have been associated with various neurodevelopmental and neuropsychiatric disorders such as schizophrenia, and depression. In this database, we present methylation profiles of carefully selected non-psychiatric control, schizophrenia, and depression samples. We also include data on one mouse forebrain sample specimen to allow for cross-species comparisons. In addition to our DNA methylation data generated in-house, we have and will continue to include published DNA methylation data from other research groups with the focus on brain development and function. Users can view the methylation data at single-CpG resolution with the option of wiggle and microarray formats. They can also download methylation data for individual samples. MethylomeDB offers an important resource for research into brain function and behavior. It provides the first source of comprehensive brain methylome data, encompassing whole-genome DNA methylation profiles of human and mouse brain specimens that facilitate cross-species comparative epigenomic investigations, as well as investigations of schizophrenia and depression methylomes.

Citing Articles

An Overview of the Epigenetic Modifications in the Brain under Normal and Pathological Conditions.

Lossi L, Castagna C, Merighi A Int J Mol Sci. 2024; 25(7).

PMID: 38612690 PMC: 11011998. DOI: 10.3390/ijms25073881.

MIAOME: Human microbiome affect the host epigenome.

Wang L, Zhang W, Wu X, Liang X, Cao L, Zhai J Comput Struct Biotechnol J. 2022; 20:2455-2463.

PMID: 35664224 PMC: 9136154. DOI: 10.1016/j.csbj.2022.05.024.

EWAS Data Hub: a resource of DNA methylation array data and metadata.

Xiong Z, Li M, Yang F, Ma Y, Sang J, Li R Nucleic Acids Res. 2019; 48(D1):D890-D895.

PMID: 31584095 PMC: 6943079. DOI: 10.1093/nar/gkz840.

DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database.

Xiong Y, Wei Y, Gu Y, Zhang S, Lyu J, Zhang B Nucleic Acids Res. 2016; 45(D1):D888-D895.

PMID: 27899673 PMC: 5210584. DOI: 10.1093/nar/gkw1123.

NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases.

Wang J, Cao Y, Zhang H, Wang T, Tian Q, Lu X Nucleic Acids Res. 2016; 45(D1):D902-D907.

PMID: 27899613 PMC: 5210534. DOI: 10.1093/nar/gkw1038.

References

Ongenaert M, Van Neste L, De Meyer T, Menschaert G, Bekaert S, Van Criekinge W . PubMeth: a cancer methylation database combining text-mining and expert annotation. Nucleic Acids Res. 2007; 36(Database issue):D842-6. PMC: 2238841. DOI: 10.1093/nar/gkm788. View

Kerkel K, Spadola A, Yuan E, Kosek J, Jiang L, Hod E . Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet. 2008; 40(7):904-8. DOI: 10.1038/ng.174. View

Klose R, Bird A . Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci. 2006; 31(2):89-97. DOI: 10.1016/j.tibs.2005.12.008. View

He X, Chang S, Zhang J, Zhao Q, Xiang H, Kusonmano K . MethyCancer: the database of human DNA methylation and cancer. Nucleic Acids Res. 2007; 36(Database issue):D836-41. PMC: 2238864. DOI: 10.1093/nar/gkm730. View

Edwards J, ODonnell A, Rollins R, Peckham H, Lee C, Milekic M . Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. Genome Res. 2010; 20(7):972-80. PMC: 2892098. DOI: 10.1101/gr.101535.109. View

Lister R, Ecker J . Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res. 2009; 19(6):959-66. PMC: 3807530. DOI: 10.1101/gr.083451.108. View

Weber M, Hellmann I, Stadler M, Ramos L, Paabo S, Rebhan M . Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet. 2007; 39(4):457-66. DOI: 10.1038/ng1990. View

Bath K, Lee F . Variant BDNF (Val66Met) impact on brain structure and function. Cogn Affect Behav Neurosci. 2006; 6(1):79-85. DOI: 10.3758/cabn.6.1.79. View

Khulan B, Thompson R, Ye K, Fazzari M, Suzuki M, Stasiek E . Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006; 16(8):1046-55. PMC: 1524864. DOI: 10.1101/gr.5273806. View

10.

Yoder J, Walsh C, Bestor T . Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997; 13(8):335-40. DOI: 10.1016/s0168-9525(97)01181-5. View

11.

Irizarry R, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg S, Jeddeloh J . Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 2008; 18(5):780-90. PMC: 2336799. DOI: 10.1101/gr.7301508. View

12.

Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E . Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet. 2006; 38(2):149-53. DOI: 10.1038/ng1719. View

13.

Li E, Bestor T, Jaenisch R . Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 1992; 69(6):915-26. DOI: 10.1016/0092-8674(92)90611-f. View

14.

Yuan E, Haghighi F, White S, Costa R, McMinn J, Chun K . A single nucleotide polymorphism chip-based method for combined genetic and epigenetic profiling: validation in decitabine therapy and tumor/normal comparisons. Cancer Res. 2006; 66(7):3443-51. DOI: 10.1158/0008-5472.CAN-05-3739. View

15.

Weber M, Davies J, Wittig D, Oakeley E, Haase M, Lam W . Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet. 2005; 37(8):853-62. DOI: 10.1038/ng1598. View

16.

Chen R, Pettersson U, Beard C, Jaenisch R . DNA hypomethylation leads to elevated mutation rates. Nature. 1998; 395(6697):89-93. DOI: 10.1038/25779. View

17.

Hernandez D, Nalls M, Gibbs J, Arepalli S, van der Brug M, Chong S . Distinct DNA methylation changes highly correlated with chronological age in the human brain. Hum Mol Genet. 2011; 20(6):1164-72. PMC: 3043665. DOI: 10.1093/hmg/ddq561. View

18.

Montagna M, Santacatterina M, Torri A, Menin C, Zullato D, Chieco-Bianchi L . Identification of a 3 kb Alu-mediated BRCA1 gene rearrangement in two breast/ovarian cancer families. Oncogene. 1999; 18(28):4160-5. DOI: 10.1038/sj.onc.1202754. View

19.

Mostafavi Abdolmaleky H, Cheng K, Russo A, Smith C, Faraone S, Wilcox M . Hypermethylation of the reelin (RELN) promoter in the brain of schizophrenic patients: a preliminary report. Am J Med Genet B Neuropsychiatr Genet. 2005; 134B(1):60-6. DOI: 10.1002/ajmg.b.30140. View

20.

Weaver I, Cervoni N, Champagne F, DAlessio A, Sharma S, Seckl J . Epigenetic programming by maternal behavior. Nat Neurosci. 2004; 7(8):847-54. DOI: 10.1038/nn1276. View