Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

作者：Matthew N Davies, Manuela Volta, Ruth Pidsley, Katie Lunnon, Abhishek Dixit, Simon Lovestone, Cristian Coarfa, R. Alan Harris, Aleksandar Milosavljevic, Claire Troakes, Safa Al‐Sarraj, Richard Dobson, Leonard C. Schalkwyk, Jonathan Mill · 发表于：Genome biology · 年份：2012 · DOI：10.1186/gb-2012-13-6-r43 · 被引用次数：652 · 研究领域：Epigenetics and DNA Methylation、Cancer-related gene regulation、Genomics and Rare Diseases

BACKGROUND: Dynamic changes to the epigenome play a critical role in establishing and maintaining cellular phenotype during differentiation, but little is known about the normal methylomic differences that occur between functionally distinct areas of the brain. We characterized intra- and inter-individual methylomic variation across whole blood and multiple regions of the brain from multiple donors. RESULTS: Distinct tissue-specific patterns of DNA methylation were identified, with a highly significant over-representation of tissue-specific differentially methylated regions (TS-DMRs) observed at intragenic CpG islands and low CG density promoters. A large proportion of TS-DMRs were located near genes that are differentially expressed across brain regions. TS-DMRs were significantly enriched near genes involved in functional pathways related to neurodevelopment and neuronal differentiation, including BDNF, BMP4, CACNA1A, CACA1AF, EOMES, NGFR, NUMBL, PCDH9, SLIT1, SLITRK1 and SHANK3. Although between-tissue variation in DNA methylation was found to greatly exceed between-individual differences within any one tissue, we found that some inter-individual variation was reflected across brain and blood, indicating that peripheral tissues may have some utility in epidemiological studies of complex neurobiological phenotypes. CONCLUSIONS: This study reinforces the importance of DNA methylation in regulating cellular phenotype across tissues, and highlights genomic patterns of epigenet...