Global epigenomic reconfiguration during mammalian brain development

Ryan Lister, Eran A. Mukamel, Joseph R. Nery, Mark Urich, Clare A. Puddifoot, Nicholas D. Johnson, Jacinta Lucero, Yun Huang, Andrew J. Dwork, Matthew D. Schultz, Miao Yu, Julian Tonti-Filippini, Holger Heyn, Shijun Hu, Joseph C. Wu, Anjana Rao, Manel Esteller, Chuan He, Fatemeh G. Haghighi, Terrence J. SejnowskiM. Margarita Behrens, Joseph R. Ecker

Research output: Contribution to journalArticlepeer-review

1410 Scopus citations


DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. During this period, highly conserved non-CG methylation (mCH) accumulates in neurons, but not glia, to become the dominant form of methylation in the human neuronal genome. Moreover, we found an mCH signature that identifies genes escaping X-chromosome inactivation. Last, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) maps revealed that hmC marks fetal brain cell genomes at putative regulatory regions that are CG-demethylated and activated in the adult brain and that CG demethylation at these hmC-poised loci depends on Tet2 activity.

Original languageEnglish
Article number1237905
Issue number6146
StatePublished - 2013
Externally publishedYes


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