title: High-throughput DNA analysis shows the importance of methylation in the control of immune inflammatory gene transcription in chronic periodontitis.
abstract: BACKGROUND
  Chronic periodontitis represents a complex disease that is hard to control and is not completely understood. Evidence from past studies suggests that there is a key role for DNA methylation in the pathogenesis of periodontitis. However, all reports have applied technologies that investigate genes in a low throughput. In order to advance in the knowledge of the disease, we analyzed DNA methylation variations associated with gene transcription using a high-throughput assay. Infinium® HumanMethylation450 (Illumina) was performed on gingival samples from 12 periodontitis cases and 11 age-matched healthy individuals. Methylation data of 1,284 immune-related genes and 1,038 cell cycle-related genes from Gene Ontology (GO) and 575 genes from a dataset of stably expressed genes (genes with consistent expression in different physiological states and tissues) were extracted from a microarray dataset and analyzed using bioinformatics tools. DNA methylation variations ranging from -2,000 to +2,000 bp from the transcription start site (TSS) were analyzed, and the results were tested against a differential expression microarray dataset between healthy and periodontitis gingival tissues. Differences were evaluated using tests from the R Statistical Project.
  
  
  RESULTS
  The comparison of probes between periodontitis and normal gingival tissues showed that the mean methylation scores and the frequency of methylated probes were significantly lower in genes related to the immune process. In the immune group, these parameters were negatively correlated with gene expression (Mann-Whitney test, p < 2.2e - 16).
  
  
  CONCLUSIONS
  Our results show that variations in DNA methylation between healthy and periodontitis cases are higher in genes related to the immune-inflammatory process. Thus, DNA methylation must be modulating chromatin regions and, consequently, modulating the mRNA transcription of immune-inflammatory genes related with periodontitis, impacting the prognosis of disease.
authors.affiliation: Department of Morphology, School of Dentistry of Piracicaba, FOP-UNICAMP, University of Campinas, Av. Limeira 901, Piracicaba, SP 13414-018, Brazil.
authors.forename: Ana Paula
authors.initials: AP
authors.lastname: De Souza
authors.affiliation: Department of Morphology, School of Dentistry of Piracicaba, FOP-UNICAMP, University of Campinas, Av. Limeira 901, Piracicaba, SP 13414-018, Brazil ; Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON M5G 2M9, Canada.
authors.forename: Aline Cristiane
authors.initials: AC
authors.lastname: Planello
authors.affiliation: Department of Morphology, School of Dentistry of Piracicaba, FOP-UNICAMP, University of Campinas, Av. Limeira 901, Piracicaba, SP 13414-018, Brazil.
authors.forename: Marcelo Rocha
authors.initials: MR
authors.lastname: Marques
authors.affiliation: Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON M5G 2M9, Canada.
authors.forename: Daniel Diniz
authors.initials: DD
authors.lastname: De Carvalho
authors.affiliation: Department of Morphology, School of Dentistry of Piracicaba, FOP-UNICAMP, University of Campinas, Av. Limeira 901, Piracicaba, SP 13414-018, Brazil.
authors.forename: Sergio Roberto Peres
authors.initials: SR
authors.lastname: Line
keywords: Chronic periodontitis; DNA methylation; Epigenetics; Inflammation; Transcription