5-hydroxymethylcytosine is highly dynamic across human fetal brain development

BackgroundEpigenetic processes play a key role in orchestrating transcriptional regulation during the development of the human central nervous system. We previously described dynamic changes in DNA methylation (5mC) occurring during human fetal brain development, but other epigenetic processes operating during this period have not been extensively explored. Of particular interest is DNA hydroxymethylation (5hmC), a modification that is enriched in the human brain and hypothesized to play an important role in neuronal function, learning and memory. In this study, we quantify 5hmC across the genome of 71 human fetal brain samples spanning 23 to 184 days post-conception.ResultsWe identify widespread changes in 5hmC occurring during human brain development, notable sex-differences in 5hmC in the fetal brain, and interactions between 5mC and 5hmC at specific sites. Finally, we identify loci where 5hmC in the fetal brain is associated with genetic variation.ConclusionsThis study represents the first systematic analysis of dynamic changes in 5hmC across human neurodevelopment and highlights the potential importance of this modification in the human brain. A searchable database of our fetal brain 5hmC data is available as a resource to the research community at http://www.epigenomicslab.com/online-data-resources.

[1]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[2]  J. Jui,et al.  Dynamics of 5-hydroxymethylcytosine and chromatin marks in Mammalian neurogenesis. , 2013, Cell reports.

[3]  Peng Jin,et al.  5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging , 2011, Nature Neuroscience.

[4]  Li-Huei Tsai,et al.  Tet1 Is Critical for Neuronal Activity-Regulated Gene Expression and Memory Extinction , 2013, Neuron.

[5]  Swati Kadam,et al.  Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine , 2010, Nucleic acids research.

[6]  J. Mill,et al.  Variation in 5-hydroxymethylcytosine across human cortex and cerebellum , 2016, Genome Biology.

[7]  Ruth Pidsley,et al.  A data-driven approach to preprocessing Illumina 450K methylation array data , 2013, BMC Genomics.

[8]  N. Heintz,et al.  The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain , 2009, Science.

[9]  J. Irudayaraj,et al.  Diversity of two forms of DNA methylation in the brain , 2014, Front. Genet..

[10]  Andrey A. Shabalin,et al.  Matrix eQTL: ultra fast eQTL analysis via large matrix operations , 2011, Bioinform..

[11]  Rong Li,et al.  Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain , 2013, Genome Biology.

[12]  D. Bates,et al.  Fitting Linear Mixed-Effects Models Using lme4 , 2014, 1406.5823.

[13]  G. Pfeifer,et al.  5-Hydroxymethylcytosine: a stable or transient DNA modification? , 2014, Genomics.

[14]  S. Balasubramanian,et al.  Accurate Measurement of 5-Methylcytosine and 5-Hydroxymethylcytosine in Human Cerebellum DNA by Oxidative Bisulfite on an Array (OxBS-Array) , 2015, PloS one.

[15]  David R. Liu,et al.  Conversion of 5-Methylcytosine to 5- Hydroxymethylcytosine in Mammalian DNA by the MLL Partner TET1 , 2009 .

[16]  Brent S. Pedersen,et al.  Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values , 2012, Bioinform..

[17]  Per B. Brockhoff,et al.  lmerTest Package: Tests in Linear Mixed Effects Models , 2017 .

[18]  Bing Ren,et al.  Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine , 2012, Nature Protocols.

[19]  Chongli Yuan,et al.  Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro. , 2014, Biochimica et biophysica acta.

[20]  S. Balasubramanian,et al.  Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution , 2012, Science.

[21]  S. Balasubramanian,et al.  oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips , 2015, Methods.

[22]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[23]  Pau Farré,et al.  Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array , 2013, Epigenetics & Chromatin.

[24]  A. H. Smits,et al.  Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives , 2013, Cell.

[25]  J. David Sweatt,et al.  TET1 Controls CNS 5-Methylcytosine Hydroxylation, Active DNA Demethylation, Gene Transcription, and Memory Formation , 2013, Neuron.

[26]  A. Lloyd,et al.  Differential effect of three base modifications on DNA thermostability revealed by high resolution melting. , 2012, Analytical chemistry.

[27]  P. Jin,et al.  Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine , 2011, Nature Biotechnology.

[28]  J. Mill,et al.  Methylation quantitative trait loci in the developing brain and their enrichment in schizophrenia-associated genomic regions , 2015, Nature neuroscience.

[29]  Cathryn M. Gould,et al.  Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA , 2017, Epigenetics & Chromatin.

[30]  N. Heintz,et al.  MeCP2 binds to 5hmc enriched within active genes and accessible chromatin in the nervous system , 2012, Cell.

[31]  Matthew D. Schultz,et al.  Global Epigenomic Reconfiguration During Mammalian Brain Development , 2013, Science.

[32]  David R. Liu,et al.  The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing , 2010, PloS one.

[33]  G. Hon,et al.  Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome , 2012, Cell.

[34]  John D. Davis,et al.  Upregulation of TET1 and downregulation of APOBEC3A and APOBEC3C in the parietal cortex of psychotic patients , 2012, Translational Psychiatry.

[35]  Shankar Balasubramanian,et al.  Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine , 2013, Nature Protocols.

[36]  Michael C O'Donovan,et al.  Methylomic trajectories across human fetal brain development , 2015, Genome research.

[37]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[38]  N. Sousa,et al.  TET enzymes and DNA hydroxymethylation in neural development and function - how critical are they? , 2014, Genomics.

[39]  E. Cook,et al.  Increased binding of MeCP2 to the GAD1 and RELN promoters may be mediated by an enrichment of 5-hmC in autism spectrum disorder (ASD) cerebellum , 2014, Translational Psychiatry.

[40]  Zachary D. Smith,et al.  Tet1 regulates adult hippocampal neurogenesis and cognition. , 2013, Cell stem cell.

[41]  Poshen B. Chen,et al.  Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells , 2011, Cell.

[42]  S. Horvath.  DNA methylation age of human tissues and cell types , 2013, Genome Biology.

[43]  P. Ainsworth,et al.  Anomalous migration of PCR products using nondenaturing polyacrylamide gel electrophoresis: the amelogenin sex-typing system. , 1994, Journal of forensic sciences.

[44]  P. Brockhoff,et al.  Tests in Linear Mixed Effects Models , 2015 .

[45]  S. Warren,et al.  Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice , 2014, BMC Genomics.

[46]  B. Blencowe,et al.  5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary , 2012, Nature Structural &Molecular Biology.

[47]  S. Balasubramanian,et al.  A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation , 2013, Genome Biology.

[48]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[49]  Eric-Wubbo Lameijer,et al.  Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array , 2013, Epigenetics & Chromatin.

[50]  E. Li,et al.  Establishment and Maintenance of Genomic Methylation Patterns in Mouse Embryonic Stem Cells by Dnmt3a and Dnmt3b , 2003, Molecular and Cellular Biology.

[51]  Wolfgang Schramm,et al.  Team , 2018, Spaces of Intensity.

[52]  R. Weksberg,et al.  Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray , 2013, Epigenetics.