Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives

Abstract

Background: The Encyclopedia of DNA Elements (ENCODE) project has advanced our knowledge of the functional elements in the genome and epigenome. The aim of this article was to provide the comprehension about current research trends from ENCODE project and establish the link between epigenetics and periodontal diseases based on epigenome studies and seek the future direction.

Main body: Global epigenome research projects have emphasized the importance of epigenetic research for understanding human health and disease, and current international consortia show an improved interest in the importance of oral health with systemic health. The epigenetic studies in dental field have been mainly conducted in periodontology and have focused on DNA methylation analysis. Advances in sequencing technology have broadened the target for epigenetic studies from specific genes to genome-wide analyses.

Conclusions: In line with global research trends, further extended and advanced epigenetic studies would provide crucial information for the realization of comprehensive dental medicine and expand the scope of ongoing large-scale research projects.

Keywords: Chronic disease; ENCODE project; Epigenetics; Next-generation sequencing; Periodontology; Personalized medicine.

Fig. 1

Periodontal disease: development and progression. Generally, periodontal disease is initiated by microbial challenges and progresses with an immuno-inflammatory response, which deteriorates connective tissue and causes bone destruction. During this process, genetic risk factors work in conjunction with epigenetic factors, and disease phenotype appears as comprehensive product of genotypic, environmental, and biological interaction. Ab, antibody; PMNs, polymorphonuclear cells; Ag, antigen; LPS, lipopolysaccharides; CK, cytokine; PG, prostaglandin; MMP, matrix metalloproteinases

Fig. 2

Mechanisms of epigenetics. The epigenetic modifications cause alterations in gene expression without directly altering the DNA sequence. In general, DNA methylation causes a segment of DNA to associate more closely with a histone complex. This prevents transcription factors from binding to a DNA sequence, such as a promoter, resulting in reduced expression of a specific gene. In contrast, histone acetylation weakens the interaction between the histone complex and DNA, allowing transcription factors to bind to the promoter and increase gene expression. Non-coding RNAs also play a crucial role in the regulation of gene expression

Fig. 3

Perspectives of epigenome research. Epigenome researches in the past and in progress

Fig. 4

Common risk factors approach in the oral and general diseases. Periodontal disease and non-communicable diseases such as cardiovascular disease, diabetes, and respiratory disease share common risk factors including smoking, alcohol consumption, and poor dietary habits