Cytosine methylation in DNA constitutes an important epigenetic layer of transcriptional and regulatory control in many eukaryotes. Profiling DNA methylation across the genome is critical to understanding the influence of epigenetics in normal biology and disease, such as cancer. Genome-wide analyses such as arrays and next-generation sequencing (NGS) technologies have been used to assess large fractions of the methylome at a single-base-pair resolution. However, the range of DNA methylation profiling techniques can make selecting the appropriate protocol a challenge. This chapter discusses the advantages and disadvantages of various methylome detection approaches to assess which is appropriate for the question at hand. Here, we focus on four prominent genome-wide approaches: whole-genome bisulfite sequencing (WGBS); methyl-binding domain capture sequencing (MBDCap-Seq); reduced-representation-bisulfite-sequencing (RRBS); and Infinium Methylation450 BeadChips (450 K, Illumina). We discuss some of the requirements, merits, and challenges that should be considered when choosing a methylome technology to ensure that it will be informative. In addition, we show how genome-wide methylation detection arrays and high-throughput sequencing have provided immense insight into ovarian cancer-specific methylation signatures that may serve as diagnostic biomarkers or predict patient response to epigenetic therapy.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1007/978-1-4939-1804-1_34 | DOI Listing |
Biol Psychiatry Glob Open Sci
March 2025
Department of Psychology, Arizona State University, Tempe, Arizona.
Background: Hippocampal volume increases throughout early development and is an important indicator of cognitive abilities and mental health. However, hippocampal development is highly vulnerable to exposures during development, as seen by smaller hippocampal volume and differential epigenetic programming in genes implicated in mental health. However, few studies have investigated hippocampal volume in relation to the peripheral epigenome across development, and even less is known about potential genetic moderators.
View Article and Find Full Text PDFBioinform Adv
January 2025
Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, D-69120 Heidelberg, Germany.
Motivation: Since their introduction about 10 years ago, methylation clocks have provided broad insights into the biological age of different species, tissues, and in the context of several diseases or aging. However, their application to single-cell methylation data remains a major challenge, because of the inherent sparsity of such data, as many CpG sites are not covered. A methylation clock applicable on single-cell level could help to further disentangle the processes that drive the ticking of epigenetic clocks.
View Article and Find Full Text PDFCharacterization of tumor epigenetic aberrations is integral to understanding the mechanisms of tumorigenesis and provide diagnostic, prognostic, and predictive information of high clinical relevance. Among the different tumor-associated epigenetic signatures, 5 methyl-cytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the two most well-characterized DNA methylation alterations linked to cancer pathogenesis. 5hmC has a tissue-specific distribution and its abundance is subjected to changes in tumor DNA, making it a promising biomarker.
View Article and Find Full Text PDFHortic Res
January 2025
College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China.
DNA methylation is a stable epigenetic mark that plays a crucial role in plant life processes. However, the specific functions of DNA methylation in grape berry development remain largely unknown. In this study, we performed whole-genome bisulfite sequencing on 'Kyoho' grape and its early-ripening bud mutant 'Fengzao' at different developmental stages.
View Article and Find Full Text PDFHeliyon
January 2025
Department of Cardiothoracic Surgery, Affiliated Hospital 6 of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China.
Research has demonstrated that POU3F4 is integral to various cancers, in addition to its significance in inner ear development, pancreatic differentiation, as well as neural stem cell differentiation. Nevertheless, comprehensive pan-cancer analyses focusing on POU3F4 remain limited. This study aims to assess the prognostic value of POU3F4 in thirty-three cancers and explore its immune-related functions.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!