Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat Rev Genet. 2009;10:252–63.
Article
CAS
PubMed
Google Scholar
Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, et al. Global epigenomic reconfiguration during mammalian brain development. Science. 2013;341:1237905.
Article
PubMed
PubMed Central
Google Scholar
Spiers H, Hannon E, Schalkwyk LC, Smith R, Wong CC, O'Donovan MC, Bray NJ, Mill J. Methylomic trajectories across human fetal brain development. Genome Res. 2015;25:338–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;324:930–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen T, Ueda Y, Dodge JE, Wang Z, Li E. Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol Cell Biol. 2003;23:5594–605.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science. 2009;324:929–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Khare T, Pai S, Koncevicius K, Pal M, Kriukiene E, Liutkeviciute Z, Irimia M, Jia P, Ptak C, Xia M, et al. 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nat Struct Mol Biol. 2012;19:1037–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, Bauer C, Munzel M, Wagner M, Muller M, Khan F, et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell. 2013;152:1146–59.
Article
CAS
PubMed
Google Scholar
Iurlaro M, Ficz G, Oxley D, Raiber EA, Bachman M, Booth MJ, Andrews S, Balasubramanian S, Reik W. A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation. Genome Biol. 2013;14:R119.
Article
PubMed
PubMed Central
Google Scholar
Jin SG, Kadam S, Pfeifer GP. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 2010;38:e125.
Article
PubMed
PubMed Central
Google Scholar
Yildirim O, Li R, Hung JH, Chen PB, Dong X, Ee LS, Weng Z, Rando OJ, Fazzio TG. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell. 2011;147:1498–510.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mellen M, Ayata P, Dewell S, Kriaucionis S, Heintz N. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell. 2012;151:1417–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Santiago M, Antunes C, Guedes M, Sousa N, Marques CJ. TET enzymes and DNA hydroxymethylation in neural development and function - how critical are they? Genomics. 2014;104:334–40.
Article
CAS
PubMed
Google Scholar
Kaas GA, Zhong C, Eason DE, Ross DL, Vachhani RV, Ming GL, King JR, Song H, Sweatt JD. TET1 controls CNS 5-methylcytosine hydroxylation, active DNA demethylation, gene transcription, and memory formation. Neuron. 2013;79:1086–93.
Article
CAS
PubMed
Google Scholar
Rudenko A, Dawlaty MM, Seo J, Cheng AW, Meng J, Le T, Faull KF, Jaenisch R, Tsai LH. Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Neuron. 2013;79:1109–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang RR, Cui QY, Murai K, Lim YC, Smith ZD, Jin S, Ye P, Rosa L, Lee YK, Wu HP, et al. Tet1 regulates adult hippocampal neurogenesis and cognition. Cell Stem Cell. 2013;13:237–45.
Article
PubMed
PubMed Central
Google Scholar
Wen L, Li X, Yan L, Tan Y, Li R, Zhao Y, Wang Y, Xie J, Zhang Y, Song C, et al. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain. Genome Biol. 2014;15:R49.
Article
PubMed
PubMed Central
Google Scholar
Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, Li Y, Chen CH, Zhang W, Jian X, et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol. 2011;29:68–72.
Article
CAS
PubMed
Google Scholar
Szulwach KE, Li X, Li Y, Song CX, Wu H, Dai Q, Irier H, Upadhyay AK, Gearing M, Levey AI, et al. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci. 2011;14:1607–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen Y, Damayanti NP, Irudayaraj J, Dunn K, Zhou FC. Diversity of two forms of DNA methylation in the brain. Front Genet. 2014;5:46.
PubMed
PubMed Central
Google Scholar
Zhubi A, Chen Y, Dong E, Cook EH, Guidotti A, Grayson DR. 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. Transl Psychiatry. 2014;4:e349.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dong E, Gavin DP, Chen Y, Davis J. Upregulation of TET1 and downregulation of APOBEC3A and APOBEC3C in the parietal cortex of psychotic patients. Transl Psychiatry. 2012;2:e159.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One. 2010;5:e8888.
Article
PubMed
PubMed Central
Google Scholar
Skvortsova K, Zotenko E, Luu PL, Gould CM, Nair SS, Clark SJ, Stirzaker C. Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA. Epigenetics Chromatin. 2017;10:16.
Article
PubMed
PubMed Central
Google Scholar
Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science. 2012;336:934–7.
Article
CAS
PubMed
Google Scholar
Booth MJ, Ost TW, Beraldi D, Bell NM, Branco MR, Reik W, Balasubramanian S. Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat Protoc. 2013;8:1841–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lunnon K, Hannon E, Smith RG, Dempster E, Wong C, Burrage J, Troakes C, Al-Sarraj S, Kepa A, Schalkwyk L, Mill J. Variation in 5-hydroxymethylcytosine across human cortex and cerebellum. Genome Biol. 2016;17:27.
Article
PubMed
PubMed Central
Google Scholar
Hahn MA, Qiu R, Wu X, Li AX, Zhang H, Wang J, Jui J, Jin SG, Jiang Y, Pfeifer GP, Lu Q. Dynamics of 5-hydroxymethylcytosine and chromatin marks in mammalian neurogenesis. Cell Rep. 2013;3:291–300.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chopra P, Papale LA, White AT, Hatch A, Brown RM, Garthwaite MA, Roseboom PH, Golos TG, Warren ST, Alisch RS. Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice. BMC Genomics. 2014;15:131.
Article
PubMed
PubMed Central
Google Scholar
Field SF, Beraldi D, Bachman M, Stewart SK, Beck S, Balasubramanian S. Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA by oxidative bisulfite on an array (OxBS-array). PLoS One. 2015;10:e0118202.
Article
PubMed
PubMed Central
Google Scholar
Stewart SK, Morris TJ, Guilhamon P, Bulstrode H, Bachman M, Balasubramanian S, Beck S. oxBS-450K: a method for analysing hydroxymethylation using 450K BeadChips. Methods. 2015;72:9–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu M, Hon GC, Szulwach KE, Song CX, Jin P, Ren B, He C. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat Protoc. 2012;7:2159–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pedersen BS, Schwartz DA, Yang IV, Kechris KJ. Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinformatics. 2012;28:2986–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Slieker RC, Bos SD, Goeman JJ, Bovee JV, Talens RP, van der Breggen R, Suchiman HE, Lameijer EW, Putter H, van den Akker EB, et al. Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. Epigenetics Chromatin. 2013;6:26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hahn MA, Szabo PE, Pfeifer GP. 5-Hydroxymethylcytosine: a stable or transient DNA modification? Genomics. 2014;104:314–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
Article
PubMed
PubMed Central
Google Scholar
Hannon E, Spiers H, Viana J, Pidsley R, Burrage J, Murphy TM, Troakes C, Turecki G, O'Donovan MC, Schalkwyk LC, et al. Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. Nat Neurosci. 2016;19(1):48–54.
Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell. 2012;149:1368–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lopez CM, Lloyd AJ, Leonard K, Wilkinson MJ. Differential effect of three base modifications on DNA thermostability revealed by high resolution melting. Anal Chem. 2012;84:7336–42.
Article
PubMed
Google Scholar
Mendonca A, Chang EH, Liu W, Yuan C. Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro. Biochim Biophys Acta. 1839;2014:1323–9.
Google Scholar
Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14:R115.
Article
PubMed
PubMed Central
Google Scholar
Pidsley R, Y Wong CC, Volta M, Lunnon K, Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics. 2013;14:293.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eng B, Ainsworth P, Waye JS. Anomalous migration of PCR products using nondenaturing polyacrylamide gel electrophoresis: the amelogenin sex-typing system. J Forensic Sci. 1994;39:1356–9.
Article
CAS
PubMed
Google Scholar
R Development Core Team. R: A Language and Environment for Statistical Computing. Austria: the R Foundation for Statistical Computing; 2011. Available online at http://www.R-project.org/.
Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S, Hudson TJ, Weksberg R. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics. 2013;8:203–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price ME, Cotton AM, Lam LL, Farre P, Emberly E, Brown CJ, Robinson WP, Kobor MS. Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. Epigenetics Chromatin. 2013;6:4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shabalin AA. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics. 2012;28:1353–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bates D, Maechler M, Bolker B, Walker S. Fitting linear mixed-effects models using lme4. J Stat Softw. 2015;67:1–48.
Article
Google Scholar
lmerTest: Tests in Linear Mixed Effects Models v. R package version 2.0–30. 2016. https://cran.r-project.org/web/packages/lmerTest/index.html.