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

doi:10.1007/s11515-014-1295-1

Front. Biol.

2014, Vol. 9

Issue (1) : 66-74 https://doi.org/10.1007/s11515-014-1295-1

RESEARCH ARTICLE

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

Junjie U. GUO^1,^2,³,Keith E. SZULWACH⁴,Yijing SU^1,³,Yujing LI⁴,Bing YAO⁴,Zihui XU⁴,Joo Heon SHIN⁵,Bing XIE⁵,Yuan GAO^1,⁵,Guo-li MING^1,^2,³,Peng JIN^4,^*(

),Hongjun SONG^1,^2,^3,^*(

)

1. Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
2. The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
3. Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
4. Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
5. Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA

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Abstract

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.

Keywords dentate granule neuron active DNA demethylation TET methylome

Corresponding Author(s): Peng JIN

Issue Date: 13 May 2014

Cite this article:

Junjie U. GUO,Keith E. SZULWACH,Yijing SU, et al. Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain[J]. Front. Biol., 2014, 9(1): 66-74.

URL:

https://academic.hep.com.cn/fib/EN/10.1007/s11515-014-1295-1
https://academic.hep.com.cn/fib/EN/Y2014/V9/I1/66

Fig.1 Distribution of 5hmC in the genome of dentate granule neurons (DGNs) in vivo. (A) Correlation between 5hmC-seq results from two biologic replicates. Pearson’s correlation was calculated using non-overlapping 10-kb windows. (B) qPCR validation of DGN 5hmC-marked regions detected by 5hmC-seq. Regions 1-17 were those marked with 5hmC. Neg was a negative control region with no significant 5hmC. (C) Chromosome-wide 5hmC levels normalized by an input library. Note the lower abundance in the mitochondrial genome and sex chromosomes. (D) 5hmC levels within different genic regions, compared to intergenic regions. E, Meta-gene (left), meta-exon (middle), and meta-intron analyses of 5hmC levels.

Fig.2 Relationship between 5hmC, gene expression, and protein-DNA interaction in DGNs. (A) Meta-gene analysis of 5hmC levels correlated with gene expression. 5hmC levels were averaged across all genes stratified by their expression rank (top). Spearman’s correlations in 500 bp windows were shown (bottom). (B) 5hmC levels near the binding sites of four neuronal DNA-interacting factors previously determined in cultured mouse cortical neurons (Kim et al., 2010).

Fig.3 Comparison of 5hmC distributions between DGNs and ESCs. (A) A correlation matrix of 5hmC-seq results from two DGN replicates and on ESC sample. Pearson’s correlations were shown. (B) A scatter plot of DGN and ESC gene-body 5hmC levels. DGN- and ESC-specific 5hmC-marked genes were indicated by blue and red circles, respectively. (C) Examples of DGN-specific 5hmC-marked genes (top) and ESC-specific 5hmC-marked genes (bottom). (D) Gene ontology analysis of 1129 DGN-specific 5hmC-marked genes (left) and 1004 ESC-specific 5hmC-marked genes (right).

Fig.4 Global antagonism between 5hmC and overall DNA methylation in both DGNs and ESCs. (A) A chromosome-wide view of 5hmC (top) and overall DNA methylation (bottom) levels. Signals were moving-averaged using 10-kb windows. (B) A density plots of genome-wide paired values of DGN overall DNA methylation and 5hmC levels of 10-kb windows. (C) Boxplots of gene-body DNA methylation (left) and 5hmC (right) levels stratified by the expression ranks of all genes. Spearman’s correlations were shown at the bottom. (D) A density plots of genome-wide paired values of ESC overall DNA methylation and 5hmC levels of 10-kb windows. 5hmC levels were log10-transformed.

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