Objective: To establish and improve the method of bisulfite sequencing for methylation status of imprinted genes in single human oocytes.
Methods: Single superovulated immature human oocyte was embedded into low melting point agarose, followed by bisulfite treatment and polymerase chain reaction (PCR) amplification of the H19 and MEST genes. The PCR products were then subjected to TA cloning and sequencing to determine the methylation status.
Results: With the modified methods of embedding and bisulfite treatment, we achieved a high PCR success rate of 82.46%, with the somatic cell contamination rate as low as 7.14%. The sequencing results showed no non-CpG cytosine and exact conformity to the theoretical sequences.
Conclusion: The bisulfite sequencing method we used to determine the methylation status of imprinted genes at the single-cell level was highly efficient and reliable, which can serve as a foundation for the further study of the influences of human assisted reproductive technology on genomic imprinting.
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Clin Chim Acta
January 2025
Department of Urology, The People's Hospital of Qingyang City/Qingyang Hospital of the Second Hospital of Lanzhou University, Qingyang 745000 China. Electronic address:
Background: Urothelial carcinoma (UC) is a common malignancy worldwide. Aberrant DNA methylation is implicated in UC carcinogenesis. This study sought to delineate the DNA methylation landscape in UC and identify DNA methylation-based biomarkers for early detection of UC.
View Article and Find Full Text PDFAnal Chem
January 2025
School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China.
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are crucial epigenetic modifications in eukaryotic genomic DNA that regulate gene expression and are associated with the occurrence of various cancers. Here, we combined bisulfite conversion with 4-acetamido-2,2,6,6-tetramethyl-1-oxopiperridinium tetrafluoroborate (ACTBF, TCI) oxidation to develop a label-free and sequence-independent isothermal amplification (BTIA) assay for a genome-wide 5mC and 5hmC analysis. The BTIA strategy can distinguish 5mC and 5hmC signatures from other bases with high sensitivity and good specificity, avoiding sophisticated chemical modifications and expensive protein labeling.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Genome graphs, including the recently released draft human pangenome graph, can represent the breadth of genetic diversity and thus transcend the limits of traditional linear reference genomes. However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored for accurate DNA methylation analysis by mapping WGBS data to a genome graph.
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 PDFEndocrinology
January 2025
Neuroendocrinology Department, ICMR-National Institute for Research in Reproductive and Child Health, J. M. Street, Parel, Mumbai 400012, India.
Estrogen through its receptors, ERα and ERβ, regulate various aspects of spermatogenesis and male fertility. Since the sperm epigenome is an important contributing factor to male fertility, we evaluated the effects of estrogen signaling activation through the ERs on sperm DNA methylome in adult rats. Whole genome-bisulfite sequencing (WGBS) in caudal sperm DNA was performed.
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