Approaches for the study of epigenetic modifications in the inner ear and related tissues

Abstract

DNA methylation and histone modifications such as methylation, acetylation, and phosphorylation, are two types of epigenetic modifications that alter gene expression. These additions to DNA regulatory elements or to the tails of histones can be inherited or can also occur de novo. Since epigenetic modifications can have significant effects on various processes at both the cellular and organismal level, there has been a rapid increase in research on this topic throughout all fields of biology in recent years. However, epigenetic research is relativity new for the inner ear field, likely due to the limited number of cells present and their quiescent nature. Here, we provide an overview of methods used to detect DNA methylation and histone modifications with a focus on those that have been validated for use with limited cell numbers and a discussion of the strengths and limitations for each. We also provide examples for how these methods have been used to investigate the epigenetic landscape in the inner ear and related tissues.

Deciphering the complex interplay of risk factors in type 2 diabetes mellitus: A comprehensive review

“…Although these epigenetic modifications can be reversed, they can be inherited through both mitotic and meiotic cell divisions [ 18 ]. DNA methylation, histone modification, and RNA interference are examples of epigenetic alterations that can occur naturally in response to environmental cues or genetic mutations that alter the enzymes that catalyze these modifications [ [19] , [20] , [21] ]. Epigenetic modifications usually interact and regulate each other, collectively forming a distinct epigenetic profile that alters genome function, notably gene expression, by modifying chromatin structure.…”

Harnessing the Full Potential of Multi-Omic Analyses to Advance the Study and Treatment of Chronic Kidney Disease

“…Much like the SNP arrays harnessed for GWAS analysis, commercial arrays have been developed to facilitate the reproducible and high-throughput study of CpG sites across the human genome, for example, the Illumina MethylationEPIC BeadChip Infinium array investigates 853,307 CpG (850K) sites, with increased coverage of regulatory regions compared to previous methylation arrays ( 109 , 110 ). Alternative forms of epigenetic regulation, such as ncRNA or chromatin modifications, can be analysed via methods such as quantitative polymerase chain reaction (qPCR), RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) ( 111 , 112 ), recently reviewed by Walters and Cox ( 113 ). Interestingly, computational methods have facilitated the direct detection of epigenetic modifications during Oxford Nanopore genome sequencing ( 114 ), identifying a potential avenue for future kidney disease research to intricately integrate and streamline genetic and epigenetic analyses.…”

Dnmt1 is required for the development of auditory organs via cell cycle arrest and Fgf signalling

“…The formation of inner ear is a complex process, involving multiple factors and multistep actions 6 . In addition to the genetic mechanism, there are also epigenetic mechanisms in the development of inner ear 9,10 …”

“…6 In addition to the genetic mechanism, there are also epigenetic mechanisms in the development of inner ear. 9,10 Epigenetics is on the study of heritable and reversible changes in gene expression patterns rather than altering the intrinsic DNA sequence. DNA methylation is one of the major forms of epigenetic modifications, which is catalysed by DNA methyltransferases family (DNMTs) through adding a methyl group to CpG dinucleotides at the fifth carbon of cytosine residue.…”