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Author Notes:

Correspondence: Hongjun SONG shongju1@jhmi.edu, Peng JIN peng.jin@emory.edu

These authors contributed equally to this work: Junjie U. Guo and Keith E. Szulwach

H.S. and P.J. conceived the project. Y.S. prepared genomic DNA samples. K.E.S., Y.L. and Z.X. performed 5hmC-seq, data pre-processing, and qPCR validation. B.X. and Y.G. performed RNA-seq, J.U.G. and K.E.S. analyzed the data. J.U.G., K.E.S., B.Y., G.L.M., P.J., and H.S. wrote the manuscript.

We thank Cheryl Strauss and Kimberley Christian for critical reading of the manuscript.

Junjie Guo, Keith E. Szulwach, Yijing Su, Yujing Li, Bing Yao, Zihui Xu, Joo Heon Shin, Bing Xie, Yuan Gao, Guo-li Ming, Peng Jin and Hongjun Song declare that they have no conflict of interest.


Research Funding:

This study was supported in part by the National Institutes of Health (NS051630 and MH076090 to P.J.; NS047344, MH087874, ES021957 to H.S., HD0679184 and NS048271 to G.L.M.), the Emory Genetics Discovery Fund (P.J.), the Simons Foundation Autism Research Initiative (P.J. and H.S.), Dr. Miriam & Sheldon G. Adelson Medical Research Foundation (G.L.M.), Maryland Stem Cell Research Foundation (G.L.M.), and John Hopkins Brain Science Institute (G.L.M.).

J.U.G. was a Damon Runyon fellow supported by the Damon Runyon Cancer Research Foundation.

Y.S. was supported by a postdoctoral fellowship from Maryland Stem Cell Research Foundation.


  • TET
  • active DNA demethylation
  • dentate granule neuron
  • methylome

Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain

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Journal Title:

Frontiers in Biology


Volume 9, Number 1


, Pages 66-74

Type of Work:

Article | Post-print: After Peer Review


Mounting evidence points to critical roles for DNA modifications, including 5-methylcytosine (5mC) and its oxidized forms, in the development, plasticity and disorders of the mammalian nervous system. The novel DNA base 5- hydroxymethylcytosine (5hmC) is known to be capable of initiating passive or active DNA demethylation, but whether and how extensively 5hmC functions in shaping the post-mitotic neuronal DNA methylome is unclear. Here we report the genome-wide distribution of 5hmC in dentate granule neurons from adult mouse hippocampus in vivo. 5hmC in the neuronal genome is highly enriched in gene bodies, especially in exons, and correlates with gene expression. Direct genome-wide comparison of 5hmC distribution between embryonic stem cells and neurons reveals extensive differences, reflecting the functional disparity between these two cell types. Importantly, integrative analysis of 5hmC, overall DNA methylation and gene expression profiles of dentate granule neurons in vivo reveals the genome-wide antagonism between these two states of cytosine modifications, supporting a role for 5hmC in shaping the neuronal DNA methylome by promoting active DNA demethylation.

Copyright information:

© 2014 Higher Education Press and Springer-Verlag Berlin Heidelberg.

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