Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners

• Published in: PloS one Vol. 11; no. 4; p. e0154108
• Main Authors: Alves da Silva, Antônio Francisco, Machado, Filipe Brum, Pavarino, Érika Cristina, Biselli-Périco, Joice Matos, Zampieri, Bruna Lancia, da Silva Francisco Junior, Ronaldo, Mozer Rodrigues, Pedro Thyago, Terra Machado, Douglas, Santos-Rebouças, Cíntia Barros, Gomes Fernandes, Maria, Chuva de Sousa Lopes, Susana Marina, Lopes Rios, Álvaro Fabricio, Medina-Acosta, Enrique
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 21-04-2016; Public Library of Science (PLoS)
• Subjects: Alleles; Analysis; Aneuploidy; Biology and life sciences; Biotechnology; Blood cells; Cell Line; Chromosome 2; Chromosome 21; Chromosomes; Computer applications; Confluence; Congenital diseases; CpG islands; CpG Islands - genetics; Defects; Deoxyribonucleic acid; DNA; DNA - genetics; DNA Methylation; Down syndrome; Down Syndrome - genetics; Down's syndrome; Embryology; Epigenetics; Epigenomics - methods; Female; Gene expression; Gene sequencing; Genes; Genetic aspects; Genetic regulation; Genetic testing; Genomes; Genomic Imprinting; Genomics; Histones - metabolism; Humans; Identification; Laboratories; Linkage analysis; Medicine and Health Sciences; Methylation; Oocytes - metabolism; Parents; Physiological aspects; Polymerase Chain Reaction - methods; Polymorphism, Single Nucleotide; Reliability analysis; Research and Analysis Methods; Ribonucleic acid; RNA; RNA modification; Runx1 protein; Single-nucleotide polymorphism; Supernumerary; Tissues; Transcription; Trisomy; Brazil; Netherlands; Rio de Janeiro Brazil
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0154108

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.