Epigenetic Regulations in Mammalian Cells: Roles and Profiling Techniques

Abstract

The genome is almost identical in all the cells of the body. However, the functions and morphologies of each cell are different, and the factors that determine them are the genes and proteins expressed in the cells. Over the past decades, studies on epigenetic information, such as DNA methylation, histone modifications, chromatin accessibility, and chromatin conformation have shown that these properties play a fundamental role in gene regulation. Furthermore, various diseases such as cancer have been found to be associated with epigenetic mechanisms. In this study, we summarized the biological properties of epigenetics and single-cell epigenomic profiling techniques, and discussed future challenges in the field of epigenetics.

Brief guide to RNA sequencing analysis for nonexperts in bioinformatics

“…Although detailed protocols, workflows, parameters, and versions for each tool need to be modified depending on the aims of experiments ( Hao et al, 2023 , Hong and Jeong, 2023 , Jang et al, 2022 , Ju et al, 2023 , Park et al, 2023 ), our guideline will be valuable for biologists who are not bioinformaticians to analyze their own and publicly available RNA-seq data. Users will need to refer to other papers for assessing microarray, scRNA sequencing data ( Ryu et al, 2023 , Hwang, 2023 , Kim, 2023 , Kim and Lee, 2023 ), and hardware requirements for transcriptome analysis, which we did not include in this guideline. In addition, users will need to investigate additional publications to understand how to combine RNA-seq data with other types of datasets at various biological levels, including proteins (proteomics), metabolites (metabolomics), transcription factor-binding regions (Chromatin ImmunoPrecipitation sequencing: ChIP-seq), DNA-protein interaction (Assay for Transposase-Accessible Chromatin using sequencing: ATAC-seq), and expression/splicing variations in quantitative trait loci (eQTL/sQTL).…”

The continuing challenges facing gene‐targeted therapies

“…In addition, the modification status of individual and networks of genes changes over time. 2 For this reason, understanding the impact of errors in or modifications of the DNA sequence requires an anatomical and temporo-physiological map of each of these biochemical processes. The ability to do single-cell transcriptomics, methylomic and acetylomic analyses, and cryo-electron microscopy should aid this basic science enterprise and its translation to an understanding of genetic and metabolic disease cell by cell, organ by organ, and system by system.…”

“…Histone and DNA methylation, histone acetylation, transcription factor activation and binding, and the presence of enhancers and suppressors of transcription all play roles in gating production of proteins from DNA and mRNA. In addition, the modification status of individual and networks of genes changes over time 2 …”

Antitumor Effect and Gut Microbiota Modulation by Quercetin, Luteolin, and Xanthohumol in a Rat Model for Colorectal Cancer Prevention

“…The initiation of CRC involves genetic (such as loss of APC , TP53 , or KRAS genes or in the mismatch repair genes MLH1 , MSH2 , MSH6 , or PMS2 , due to direct mutations, or the BRAF gene due to microsatellite instability-associated point mutations), and epigenetic alterations (such as silencing of MLH1 gene by promoter hypermethylation, CpG islands hypermethylation silencing at promoter regions in several genes, or miRNA methylation) in the stem cells located at the base of the colon crypts, which globally generate different subtypes of CRC cases (based on chromosomal instability, microsatellite instability, or CpG-island methylator phenotype) as those following the adenoma/carcinoma pathway or the serrated pathway [ 9 , 10 ]. These modifications affect tumor suppressor genes and oncogenes, leading to the transformation of normal stem cells into neoplastic stem cells [ 11 ].…”