Profiling of oxBS-450K 5-hydroxymethylcytosine in human placenta and brain reveals enrichment at imprinted loci

References

• Monk D. Germline-derived DNA methylation and early embryo epigenetic reprogramming: The selected survival of imprints. Int J Biochem Cell Biol. 2015;67:128–138. doi:10.1016/j.biocel.2015.04.014. PMID:25966912
   PubMed Web of Science ®Google Scholar
• Globisch D, Münzel M, Müller M, et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One. 2010;5:e15367. doi:10.1371/journal.pone.0015367. PMID:21203455
   PubMed Web of Science ®Google Scholar
• Nestor CE, Ottaviano R, Reddington J, et al. Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res. 2012;22:467–477. doi:10.1101/gr.126417.111. PMID:22106369
   PubMed Web of Science ®Google Scholar
• Tahiliani M, Koh KP, Shen Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;324:930–935. doi:10.1126/science.1170116. PMID:19372391
   PubMed Web of Science ®Google Scholar
• He YF, Li BZ, Li Z, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science. 2011;333:1303–1307. doi:10.1126/science.1210944. PMID:21817016
   PubMed Web of Science ®Google Scholar
• Valinluck V, Sowers LC. Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res. 2007;67:946–950. doi:10.1158/0008-5472.CAN-06-3123. PMID:17283125
   PubMed Web of Science ®Google Scholar
• Wen L, Li X, Yan L, et al. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain. Genome Biol. 2014;15:R49. doi:10.1186/gb-2014-15-3-r49. PMID:24594098
   PubMed Web of Science ®Google Scholar
• Mellén M, Ayata P, Dewell S, et al. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell. 2012;151:1417–1430. doi:10.1016/j.cell.2012.11.022. PMID:23260135
   PubMed Web of Science ®Google Scholar
• Spruijt CG, Gnerlich F, Smits AH, et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell. 2013;152:1146–1159. doi:10.1016/j.cell.2013.02.004. PMID:23434322
   PubMed Web of Science ®Google Scholar
• Frommer M, McDonald LE, Millar DS, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992;89:1827–1831. doi:10.1073/pnas.89.5.1827. PMID:1542678
   PubMed Web of Science ®Google Scholar
• Huang Y, Pastor WA, Shen Y, et al. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One. 2010;5:e8888. doi:10.1371/journal.pone.0008888. PMID:20126651
   PubMed Web of Science ®Google Scholar
• Booth MJ, Marsico G, Bachman M, et al. Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution. Nat Chem. 2014;6:435–440. doi:10.1038/nchem.1893. PMID:24755596
   PubMed Web of Science ®Google Scholar
• Stewart SK, Morris TJ, Guilhamon P, et al. oxBS-450K: a method for analysing hydroxymethylation using 450K BeadChips. Methods. 2015;72:9–15. doi:10.1016/j.ymeth.2014.08.009. PMID:25175075
   PubMed Web of Science ®Google Scholar
• Lunnon K, Hannon E, Smith RG, et al. Variation in 5-hydroxymethylcytosine across human cortex and cerebellum. Genome Biol. 2016;17:27. doi:10.1186/s13059-016-0871-x. PMID:26883014
   PubMed Web of Science ®Google Scholar
• Green BB, Houseman EA, Johnson KC, et al. Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression. FASEB J. 2016;30:2874–2884. doi:10.1096/fj.201600310R. PMID:27118675
   PubMed Web of Science ®Google Scholar
• Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science. 2009;324:929–930. doi:10.1126/science.1169786. PMID:19372393
   PubMed Web of Science ®Google Scholar
• Bachman M, Uribe-Lewis S, Yang X, et al. 5-Formylcytosine can be a stable DNA modification in mammals. Nat Chem Biol. 2015;11:555–557. doi:10.1038/nchembio.1848. PMID:26098680
   PubMed Web of Science ®Google Scholar
• Fuke C, Shimabukuro M, Petronis A, et al. Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: an HPLC-based study. Ann Hum Genet. 2004;68:196–204. doi:10.1046/j.1529-8817.2004.00081.x. PMID:15180700
   PubMed Web of Science ®Google Scholar
• Court F, Tayama C, Romanelli V, et al. Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment. Genome Res. 2014;24:554–569. doi:10.1101/gr.164913.113. PMID:24402520
   PubMed Web of Science ®Google Scholar
• Sandoval J, Heyn H, Moran S, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics. 2011;6:692–702. doi:10.4161/epi.6.6.16196. PMID:21593595
   PubMed Web of Science ®Google Scholar
• Yu M, Hon GC, Szulwach KE, et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell. 2012;149:1368–1380. doi:10.1016/j.cell.2012.04.027. PMID:22608086
   PubMed Web of Science ®Google Scholar
• Aryee MJ, Jaffe AE, Corrada-Bravo H, et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30:1363–1369. doi:10.1093/bioinformatics/btu049. PMID:24478339
   PubMed Web of Science ®Google Scholar
• Zhu L, Lv R, Kong L, et al. Genome-Wide Mapping of 5 mC and 5hmC identified differentially modified genomic regions in late-onset severe preeclampsia: A pilot study. PLoS One. 2015;10:e0134119. doi:10.1371/journal.pone.0134119. PMID:26214307
   PubMed Web of Science ®Google Scholar
• Matsubara K, Kagami M, Nakabayashi K, et al. Exploration of hydroxymethylation in Kagami-Ogata syndrome caused by hypermethylation of imprinting control regions. Clin Epigenetics. 2015;7:90. doi:10.1186/s13148-015-0124-y. PMID:26322139
   PubMed Web of Science ®Google Scholar
• Sanchez-Delgado M, Martin-Trujillo A, Tayama C, et al. Absence of Maternal Methylation in Biparental Hydatidiform Moles from Women with NLRP7 Maternal-effect mutations reveals widespread placenta-specific imprinting. PLoS Genet. 2015;11:e1005644. doi:10.1371/journal.pgen.1005644. PMID:26544189
   PubMed Web of Science ®Google Scholar
• Cavaillé J, Seitz H, Paulsen M, et al. Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region. Hum Mol Genet. 2002;11:1527–1538. doi:10.1093/hmg/11.13.1527. PMID:12045206
   PubMed Web of Science ®Google Scholar
• Cavaillé J, Buiting K, Kiefmann M, et al. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc Natl Acad Sci U S A. 2000;97:14311–14316. doi:10.1073/pnas.250426397. PMID:11106375
   PubMed Web of Science ®Google Scholar
• Guo L, Choufani S, Ferreira J, et al. Altered gene expression and methylation of the human chromosome 11 imprinted region in small for gestational age (SGA) placentae. Dev Biol. 2008;320:79–91. doi:10.1016/j.ydbio.2008.04.025. PMID:18550048
   PubMed Web of Science ®Google Scholar
• Piyasena C, Reynolds RM, Khulan B, et al. Placental 5-methylcytosine and 5-hydroxymethylcytosine patterns associate with size at birth. Epigenetics. 2015;10:692–697. doi:10.1080/15592294.2015.1062963. PMID:26091021
   PubMed Web of Science ®Google Scholar
• Turan S, Bastepe M. GNAS spectrum of disorders. Curr Osteoporos Rep. 2015;13:146–158. doi:10.1007/s11914-015-0268-x. PMID:25851935
   PubMed Web of Science ®Google Scholar
• Sanchez-Delgado M, Court F, Vidal E, et al. Human oocyte-derived methylation differences persist in the placenta revealing widespread transient imprinting. PLoS Genet. 2016;12:e1006427. doi:10.1371/journal.pgen.1006427. PMID:27835649
   PubMed Web of Science ®Google Scholar
• Zhang T, Termanis A, Özkan B, et al. G9a/GLP Complex maintains imprinted DNA methylation in embryonic stem cells. Cel Reports. 2016;77–85. doi:10.1016/j.celrep.2016.03.007. PMID: 27052169
   PubMed Web of Science ®Google Scholar
• Vitali P, Royo H, Marty V, et al. Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays. J Cell Sci. 2010;123:70–83. doi:10.1242/jcs.054957. PMID:20016068
   PubMed Web of Science ®Google Scholar
• Pastor WA, Pape UJ, Huang Y, et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. 2011;473:394–397. doi:10.1038/nature10102. PMID:21552279
   PubMed Web of Science ®Google Scholar
• Bortolin-Cavaillé ML, Dance M, Weber M, et al. C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts. Nucleic Acids Res. 2009;37:3464–3473. doi:10.1093/nar/gkp205. PMID:19339516
   PubMed Web of Science ®Google Scholar
• Noguer-Dance M, Abu-Amero S, Al-Khtib M, et al. The primate-specific microRNA gene cluster (C19MC) is imprinted in the placenta. Hum Mol Genet. 2010;19:3566–3582. doi:10.1093/hmg/ddq272. PMID:20610438
   PubMed Web of Science ®Google Scholar
• López-Abad M, Iglesias-Platas I, Monk D. Epigenetic characterization of CDKN1C in Placenta samples from non-syndromic intrauterine growth restriction. Front Genet. 2016;7:62. doi:10.3389/fgene.2016.00062. PMID:27200075
   PubMed Web of Science ®Google Scholar