Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners.
The supernumerary chromosome 21 in Down syndrome differentially affects the methylation statuses at CpG dinucleotide sites and creates genome-wide transcriptional dysregulation of parental alleles, ultimately causing diverse pathologies. At present, it is unknown whether those effects are dependent or independent of the parental origin of the nondisjoined chromosome 21. Linkage analysis is a standard method for the determination of the parental origin of this aneuploidy, although it is inadequate in cases with deficiency of samples from the progenitors. Here, we assessed the reliability of the epigenetic 5mCpG imprints resulting in the maternally (oocyte)-derived allele methylation at a differentially methylated region (DMR) of the candidate imprinted WRB gene for asserting the parental origin of chromosome 21. We developed a methylation-sensitive restriction enzyme-specific PCR assay, based on the WRB DMR, across single nucleotide polymorphisms (SNPs) to examine the methylation statuses in the parental alleles. In genomic DNA from blood cells of either disomic or trisomic subjects, the maternal alleles were consistently methylated, while the paternal alleles were unmethylated. However, the supernumerary chromosome 21 did alter the methylation patterns at the RUNX1 (chromosome 21) and TMEM131 (chromosome 2) CpG sites in a parent-of-origin-independent manner. To evaluate the 5mCpG imprints, we conducted a computational comparative epigenomic analysis of transcriptome RNA sequencing (RNA-Seq) and histone modification expression patterns. We found allele fractions consistent with the transcriptional biallelic expression of WRB and ten neighboring genes, despite the similarities in the confluence of both a 17-histone modification activation backbone module and a 5-histone modification repressive module between the WRB DMR and the DMRs of six imprinted genes. We concluded that the maternally inherited 5mCpG imprints at the WRB DMR are uncoupled from the parental allele expression of WRB and ten neighboring genes in several tissues and that trisomy 21 alters DNA methylation in parent-of-origin-dependent and -independent manners.
Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil.|Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil.|Graduate Program in Biosciences and Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil.
Antônio Francisco
AF
Alves da Silva
Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil.|Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil.|Postgraduate Program in Biosciences and Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil.
Filipe Brum
FB
Machado
Faculdade de Medicina de São José do Rio Preto, São Paulo, Brazil.
Érika Cristina
ÉC
Pavarino
Faculdade de Medicina de São José do Rio Preto, São Paulo, Brazil.
Joice Matos
JM
Biselli-Périco
Faculdade de Medicina de São José do Rio Preto, São Paulo, Brazil.
Bruna Lancia
BL
Zampieri
Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil.|Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil.
Ronaldo
R
da Silva Francisco Junior
Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil.|Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil.
Pedro Thyago
PT
Mozer Rodrigues
Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil.|Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil.
Douglas
D
Terra Machado
Department of Genetics, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
Cíntia Barros
CB
Santos-Rebouças
Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, South Holland, The Netherlands.
Maria
M
Gomes Fernandes
Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, South Holland, The Netherlands.
Susana Marina
SM
Chuva de Sousa Lopes
Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil.
Álvaro Fabricio
ÁF
Lopes Rios
Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil.|Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil.|Graduate Program in Biosciences and Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil.
Enrique
0000-0002-2529-0548
E
Medina-Acosta
D000483:Alleles; D002460:Cell Line; D018899:CpG Islands / Q000235:genetics*; D004247:DNA / Q000235:genetics; D019175:DNA Methylation; D004314:Down Syndrome / Q000235:genetics*; D057890:Epigenomics / Q000379:methods; D005260:Female; D018392:Genomic Imprinting; D006657:Histones / Q000378:metabolism; D006801:Humans; D009865:Oocytes / Q000378:metabolism; D010290:Parents; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide
D006657:Histones; D004247:DNA