Hydroxymethylation Annotation in Brain Integrative Tool (HABIT)

Katie Lunnon1*, Eilis Hannon1, Emma Dempster1, Chloe Wong2, Joe Burrage1, Claire Troakes2, Safa Al-Sarraj2, Leonard Schalkwyk3 and Jonathan Mill1,2

  1. University of Exeter Medical School, RILD, Barrack Road, University of Exeter, Devon, UK.
  2. Institute of Psychiatry, Psychology & Neuroscience, King's College London, De Crespigny Park, London, UK
  3. School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK


The most widely utilized approaches for quantifying DNA methylation involve the treatment of genomic DNA with sodium bisulfite, although this method cannot distinguish between DNA methylation (5mC) and DNA hydroxymethylation (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 combined 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 (prefrontal cortex and cerebellum) dissected from multiple individuals.


We identified 37,145 and 65,563 sites with "detectable" levels of 5hmC in the prefrontal cortex and cerebellum respectively, with 23,445 loci common across both regions. Distinct patterns of 5hmC were 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 were subsequently confirmed in an independent set of prefrontal cortex and cerebellum samples. Our data are available as downloadable UCSC genome browser tracks and as strip charts on this webpage as a resource to the community.


Our 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.

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UCSC Genome Browser track:

Displays mean hydroxymethylation for cerebellum and prefrontal cortex. You can search for genes or 450k probe IDs.