DNA methylation in higher organisms has become an expanding field of study as it often involves the regulation of gene expression. Although Whole Genome Bisulfite Sequencing (WG-BS) based on next-generation sequencing (NGS) is the most versatile method, this is a costly technique that lacks in-depth analytic power. There are no conventional methods based on NGS that enable researchers to easily compare the level of DNA methylation from the practical number of samples handled in the laboratory. Although the targeted BS method based on Sanger sequencing is generally used in this case, it lacks in-depth analytic power. Therefore, we propose a new method that combines the high throughput analytic power of NGS and bioinformatics with the specificity and focus offered by PCR-amplification-based bisulfite sequencing methods. We use in silico size sieving of DNA-fragments and primer matchings instead of whole-fragment alignment in our bioinformatics analyses, and named our method SIMON (Simple Inference for Methylome based On NGS). The results of our targeted BS method based on NGS (SIMON method) show that small variations in DNA methylation patterns can be precisely and efficiently measured at a single nucleotide resolution. SIMON method combines pre-existing techniques to provide a cost-effective technique for in-depth studies that focus on pre-identified loci. It offers significant improvements with regard to workflow and the quality of the acquired DNA methylation information. Because of the high accuracy of the analysis, small variations of DNA methylation levels can be precisely determined even with large numbers of samples and loci.
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http://dx.doi.org/10.5511/plantbiotechnology.19.0822a | DOI Listing |
Virol J
December 2024
Department of Hepatology, Qilu Hospital of Shandong University, Wenhuaxi Road 107#, Jinan, 250012, China.
Background: Oxidative stress plays a crucial role in the pathogenesis of HBV. This study aimed to investigate the value of fibroblast growth factor 21 (FGF21) promoter methylation in the occurrence and development of chronic hepatitis B (CHB) oxidative stress.
Methods: A total of 241 participants including 221 patients with CHB and 20 healthy controls (HCs) were recruited.
Zhonghua Wei Chang Wai Ke Za Zhi
December 2024
Department of Gastrointestinal Endoscopy, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou510655, China Biomedical Innovation Center, the Sixth Affiliated Hospital, Sun Yat-sen University,Guangzhou510655, China.
To examine follow-up data of different subgroups in order to further evaluate the performance and practical value of community colorectal cancer screening by detection of stool methylation syndecan-2 gene (m) among residents of Shipai Town, Dongguan City. This was an observational study. From May 2021 to February 2022, the Shipai Town government of Dongguan City completed screening for colorectal cancer by detection of stool m in 10,708 residents from 18 villages who had met the initial screening criteria and been selected using whole population sampling.
View Article and Find Full Text PDFBiol Pharm Bull
December 2024
Department of Laboratory Medicine, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences.
The aim of this study was to analyze dihydrolipoyllysine-residue acetyltransferase (DLAT) expression and diagnostic ability in hepatocellular carcinoma (HCC), assess its role in HCC growth, and factors affecting it. We conducted bioinformatics analyses, examined DLAT expression and prognosis in pre-cancer, and performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment studies while investigating its correlation with immunity. We also predicted regulatory factors, and detected DLAT in HCC cells using quantitative PCR (qPCR) and Western blotting, and in patient serum via enzyme-linked immunosorbent assay (ELISA).
View Article and Find Full Text PDFEndocr J
December 2024
Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan.
Over 70 intragenic copy-number variations (CNVs) of PHEX have been identified in patients with X-linked hypophosphatemia (XLH). However, the underlying mechanism of these CNVs has been poorly investigated. Furthermore, although PHEX undergoes X chromosome inactivation (XCI), the association between XLH in women with heterozygous PHEX variants and skewed XCI remains unknown.
View Article and Find Full Text PDFJ Dairy Sci
December 2024
North Dakota State University, Fargo, ND, USA.
Recent evidence suggests that environmental factors experienced by sires can be transmitted through the ejaculate (seminal plasma + sperm) into the female reproductive tract, influencing fertilization, embryo development, and postnatal offspring outcomes. This concept is termed paternal programming. In rodents, sire nutrition was shown to directly alter offspring outcomes through sperm epigenetic signatures, DNA damage/oxidative stress, cytokine profiles, and/or the seminal microbiome.
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