title: Tracking the evolution of epialleles during neural differentiation and brain development: D-Aspartate oxidase as a model gene.
abstract: We performed ultra-deep methylation analysis at single molecule level of the promoter region of developmentally regulated D-Aspartate oxidase (Ddo), as a model gene, during brain development and embryonic stem cell neural differentiation. Single molecule methylation analysis enabled us to establish the effective epiallele composition within mixed or pure brain cell populations. In this framework, an epiallele is defined as a specific combination of methylated CpG within Ddo locus and can represent the epigenetic haplotype revealing a cell-to-cell methylation heterogeneity. Using this approach, we found a high degree of polymorphism of methylated alleles (epipolymorphism) evolving in a remarkably conserved fashion during brain development. The different sets of epialleles mark stage, brain areas, and cell type and unravel the possible role of specific CpGs in favoring or inhibiting local methylation. Undifferentiated embryonic stem cells showed non-organized distribution of epialleles that apparently originated by stochastic methylation events on individual CpGs. Upon neural differentiation, despite detecting no changes in average methylation, we observed that the epiallele distribution was profoundly different, gradually shifting toward organized patterns specific to the glial or neuronal cell types. Our findings provide a deep view of gene methylation heterogeneity in brain cell populations promising to furnish innovative ways to unravel mechanisms underlying methylation patterns generation and alteration in brain diseases.
authors.affiliation: a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.|b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy.
authors.forename: Ermanno
authors.initials: E
authors.lastname: Florio
authors.affiliation: a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.|b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy.
authors.forename: Simona
authors.initials: S
authors.lastname: Keller
authors.affiliation: a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.|b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy.
authors.forename: Lorena
authors.initials: L
authors.lastname: Coretti
authors.affiliation: a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.|b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy.
authors.forename: Ornella
authors.initials: O
authors.lastname: Affinito
authors.affiliation: c Dipartimento di Fisica , Università degli Studi di Napoli "Federico II" and Istituto Nazionale di Fisica Nucleare , Sezione di Napoli, Naples , Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Scala
authors.affiliation: a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.|d CEINGE Biotecnologie Avanzate , Naples , Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Errico
authors.affiliation: e Institute of Genetics and Biophysics 'A. Buzzati-Traverso', Consiglio Nazionale delle Ricerche , Naples , Italy.
authors.forename: Annalisa
authors.initials: A
authors.lastname: Fico
authors.affiliation: f Department of Neuroscience , Reproductive and Dentistry Sciences, Università degli Studi di Napoli 'Federico II' , Naples , Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Boscia
authors.affiliation: f Department of Neuroscience , Reproductive and Dentistry Sciences, Università degli Studi di Napoli 'Federico II' , Naples , Italy.
authors.forename: Maria Josè
authors.initials: MJ
authors.lastname: Sisalli
authors.affiliation: g Department of Environmental , Biological and Pharmaceutical Science and Technologies, Second University of Naples , Caserta , Italy.
authors.forename: Mafalda Giovanna
authors.initials: MG
authors.lastname: Reccia
authors.affiliation: c Dipartimento di Fisica , Università degli Studi di Napoli "Federico II" and Istituto Nazionale di Fisica Nucleare , Sezione di Napoli, Naples , Italy.
authors.forename: Gennaro
authors.initials: G
authors.lastname: Miele
authors.affiliation: b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Monticelli
authors.affiliation: f Department of Neuroscience , Reproductive and Dentistry Sciences, Università degli Studi di Napoli 'Federico II' , Naples , Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Scorziello
authors.affiliation: h Dipartimento di Farmacia , Università degli Studi di Napoli 'Federico II' , Naples , Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Lembo
authors.affiliation: g Department of Environmental , Biological and Pharmaceutical Science and Technologies, Second University of Naples , Caserta , Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Colucci-D'Amato
authors.affiliation: e Institute of Genetics and Biophysics 'A. Buzzati-Traverso', Consiglio Nazionale delle Ricerche , Naples , Italy.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Minchiotti
authors.affiliation: a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.|b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy.
authors.forename: Vittorio Enrico
authors.initials: VE
authors.lastname: Avvedimento
authors.affiliation: d CEINGE Biotecnologie Avanzate , Naples , Italy.|g Department of Environmental , Biological and Pharmaceutical Science and Technologies, Second University of Naples , Caserta , Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Usiello
authors.affiliation: a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.
authors.forename: Sergio
authors.initials: S
authors.lastname: Cocozza
authors.affiliation: a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.|b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Chiariotti
mesh_terms: D000818:Animals; D000831:Animals, Newborn; D001921:Brain / Q000196:embryology* / Q000254:growth & development / Q000378:metabolism; D002454:Cell Differentiation / Q000235:genetics*; D002478:Cells, Cultured; D018899:CpG Islands; D050804:D-Aspartate Oxidase / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D004622:Embryo, Mammalian; D044127:Epigenesis, Genetic; D005260:Female; D018507:Gene Expression Regulation, Developmental; D015971:Gene Expression Regulation, Enzymologic; D051379:Mice; D008810:Mice, Inbred C57BL; D008954:Models, Biological; D058953:Neural Stem Cells / Q000502:physiology*; D011110:Polymorphism, Genetic; D011247:Pregnancy
chemical_list: D050804:D-Aspartate Oxidase
keywords: Brain DNA methylation; brain cells; epialleles; epigenetic dynamics; epipolymorphism