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Khare, Tarang; Pai, Shraddha; Koncevicius, Karolis; Pal, Mrinal; Kriukiene, Edita; Liutkeviciute, Zita; Irimia, Manuel; Jia, Peixin; Ptak, Carolyn; Xia, Menghang; Tice, Raymond; Tochigi, Mamoru; Moréra, Solange; Nazarians, Anaies; Belsham, Denise; Wong, Albert H C; Blencowe, Benjamin J; Wang, Sun Chong; Kapranov, Philipp; Kustra, Rafal; Labrie, Viviane; Klimasauskas, Saulius; Petronis, Arturas
Nature structural & molecular biology, 10/2012, Volume: 19, Issue: 10Journal Article
The 5-methylcytosine (5-mC) derivative 5-hydroxymethylcytosine (5-hmC) is abundant in the brain for unknown reasons. Here we characterize the genomic distribution of 5-hmC and 5-mC in human and mouse tissues. We assayed 5-hmC by using glucosylation coupled with restriction-enzyme digestion and microarray analysis. We detected 5-hmC enrichment in genes with synapse-related functions in both human and mouse brain. We also identified substantial tissue-specific differential distributions of these DNA modifications at the exon-intron boundary in human and mouse. This boundary change was mainly due to 5-hmC in the brain but due to 5-mC in non-neural contexts. This pattern was replicated in multiple independent data sets and with single-molecule sequencing. Moreover, in human frontal cortex, constitutive exons contained higher levels of 5-hmC relative to alternatively spliced exons. Our study suggests a new role for 5-hmC in RNA splicing and synaptic function in the brain.
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