title: Variation in 5-hydroxymethylcytosine across human cortex and cerebellum.
abstract: BACKGROUND
  The most widely utilized approaches for quantifying DNA methylation involve the treatment of genomic DNA with sodium bisulfite; however, this method cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Previous studies have shown that 5hmC is enriched in the brain, although little is known about its genomic distribution and how it differs between anatomical regions and individuals. In this study, we combine oxidative bisulfite (oxBS) treatment with the Illumina Infinium 450K BeadArray to quantify genome-wide patterns of 5hmC in two distinct anatomical regions of the brain from multiple individuals.
  
  
  RESULTS
  We identify 37,145 and 65,563 sites passing our threshold for detectable 5hmC in the prefrontal cortex and cerebellum respectively, with 23,445 loci common across both brain regions. Distinct patterns of 5hmC are identified in each brain region, with notable differences in the genomic location of the most hydroxymethylated loci between these brain regions. Tissue-specific patterns of 5hmC are subsequently confirmed in an independent set of prefrontal cortex and cerebellum samples.
  
  
  CONCLUSIONS
  This study represents the first systematic analysis of 5hmC in the human brain, identifying tissue-specific hydroxymethylated positions and genomic regions characterized by inter-individual variation in DNA hydroxymethylation. This study demonstrates the utility of combining oxBS-treatment with the Illumina 450k methylation array to systematically quantify 5hmC across the genome and the potential utility of this approach for epigenomic studies of brain disorders.
authors.affiliation: University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK. k.lunnon@exeter.ac.uk.
authors.forename: Katie
authors.initials: K
authors.lastname: Lunnon
authors.affiliation: University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK.
authors.forename: Eilis
authors.initials: E
authors.lastname: Hannon
authors.affiliation: University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK.
authors.forename: Rebecca G
authors.initials: RG
authors.lastname: Smith
authors.affiliation: University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK.
authors.forename: Emma
authors.initials: E
authors.lastname: Dempster
authors.affiliation: Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK.
authors.forename: Chloe
authors.initials: C
authors.lastname: Wong
authors.affiliation: University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK.
authors.forename: Joe
authors.initials: J
authors.lastname: Burrage
authors.affiliation: Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK.
authors.forename: Claire
authors.initials: C
authors.lastname: Troakes
authors.affiliation: Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK.
authors.forename: Safa
authors.initials: S
authors.lastname: Al-Sarraj
authors.affiliation: Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Kepa
authors.affiliation: University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
authors.forename: Leonard
authors.initials: L
authors.lastname: Schalkwyk
authors.affiliation: University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK.|Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Mill
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism* / Q000031:analogs & derivatives; D002525:Cerebellar Cortex / Q000378:metabolism; D002531:Cerebellum / Q000378:metabolism; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D004247:DNA / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D015894:Genome, Human; D006801:Humans; D017422:Sequence Analysis, DNA; D013447:Sulfites
chemical_list: D013447:Sulfites; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA; C009279:sodium bisulfite