Article
Obstetrics & Gynecology
Delna Irani, Vandana Bansal, Deepti Tandon, Anushree Patil, Dipty Singh
Summary: The objective of this study was to investigate the genome-wide alterations in sperm DNA methylation in male partners of idiopathic recurrent pregnancy loss (iRPL) cases and identify potential diagnostic markers. A case-control study and methylome analysis of human sperm were conducted. The control group consisted of apparently healthy fertile men (n = 39), while the case group consisted of male partners of iRPL cases (n = 47). Whole genome bisulfite sequencing was performed to analyze differentially methylated CpG sites and genes in iRPL cases compared to fertile controls. Pathway analysis revealed enrichment of development-related signaling pathways. Specific hypomethylated CpGs within genes PPARG, KCNQ1, SETD2, and MAP3K4 were identified in the iRPL study population. In conclusion, this study provides insights into the altered methylation landscape of iRPL sperm and suggests the potential use of specific hypomethylated CpG sites as predictive biomarkers.
FERTILITY AND STERILITY
(2023)
Article
Plant Sciences
Ivan Simko
Summary: This study provides the first insight into DNA methylation in cultivated lettuce and suggests a potential role of heritable variation in cytosine methylation in lettuce morphology. Differences in methylation profiles between different horticultural types are already detectable in seeds.
Article
Biochemical Research Methods
Yingyu Chen, Chin Kiu Kwok, Hangjin Jiang, Xiaodan Fan
Summary: A novel Bayesian method called BSDMR was developed for detecting differentially methylated regions from paired bisulfite sequencing data, which provides a better modeling strategy for the spatial correlation between CpG sites and considers the relationship between methylation signals from normal and disease samples. Simulations showed that BSDMR performs well even under low read depth with smaller false discovery rates, and was validated in colon cancer data.
Article
Biochemical Research Methods
Heesun Kim, Mikang Sim, Nayoung Park, Kisang Kwon, Junyoung Kim, Jaebum Kim
Summary: msPIPE is an end-to-end pipeline for DNA methylation analyses, allowing seamless connection of all necessary tasks from data pre-processing to downstream DNA methylation analyses. It generates various methylation profiles for analyzing methylation patterns, including statistical summaries and methylation levels. The pipeline also computes methylation levels in functional regions of the genome with proper annotation. The results can be visualized in high-quality figures. msPIPE can be easily used with a Docker image that includes all required packages and software for DNA methylation analyses.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Timothy J. Peters, Michael J. Buckley, Yunshun Chen, Gordon K. Smyth, Christopher C. Goodnow, Susan J. Clark
Summary: Whole genome bisulphite sequencing (WGBS) allows for genome-wide study of single molecule methylation patterns. The study aims to locate differential methylation patterns across the genome using statistical methods, data simulation, and benchmarking. DMRcate is found to be the fastest and the best predictor of DMRs among the methods compared in the study.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Elizabeth M. Martin, Sara A. Grimm, Zongli Xu, Jack A. Taylor, Paul A. Wade
Summary: This study compared the DNA methylation assessment using Illumina Mouse Methylation BeadChip (MMB) technology with the gold-standard method of whole-genome bisulfite sequencing (WGBS). The results showed that MMB produced similar measurements of methylation as WGBS, and the differentially methylated cytosines and regions identified by both methods overlapped and enriched for similar biological functions, indicating that MMB faithfully recapitulates the findings of WGBS.
Article
Biology
Vahid Akbari, Jean-Michel Garant, Kieran O'Neill, Pawan Pandoh, Richard Moore, Marco A. Marra, Martin Hirst, Steven J. M. Jones
Summary: This study used nanopore sequencing data to map the imprinted intervals in the human genome. It successfully phased the human methylome and detected both known and novel imprinted DMRs. The study also found several conserved imprinted DMRs in mouse, rhesus monkey, and chimpanzee. These findings expand our understanding of imprinting and demonstrate the potential of nanopore sequencing in identifying imprinting regions.
Article
Cell Biology
Xubin Zheng, Qiong Wu, Haonan Wu, Kwong-Sak Leung, Man-Hon Wong, Xueyan Liu, Lixin Cheng
Summary: This study introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Differential methylated genes measured by various bisulfite sequencing assays and 450 k beadchip were consistently hypo-methylated in liver cancer with high functional similarity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Veterinary Sciences
Caijuan Yue, Jiakang Wang, Yifei Shen, Junli Zhang, Jian Liu, Aiping Xiao, Yisha Liu, Hehua Eer, Qiao-e Zhang
Summary: In this study, whole-genome bisulfite sequencing and bioinformatics analysis were used to compare the DNA methylation patterns between Tan sheep and Hu sheep. It was found that six genes - ACTA1, MYH11, WAS, VAV1, FN1, and ROCK2 - showed significant differences in methylation levels between Tan sheep and Hu sheep, and these genes are involved in muscle cell differentiation and development. This study highlights the importance of gene methylation in the formation of muscle-related traits.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Qian Yan, Ying Tang, Fan He, Jiao Xue, Ruisheng Zhou, Xiaoying Zhang, Huiyan Luo, Daihan Zhou, Xiongwen Wang
Summary: This study investigated alterations in DNA methylation patterns in hepatocellular carcinoma (HCC) using whole-genome bisulfite sequencing technology. The research identified a genome-wide hypomethylation pattern in HCC, with hyper-DMGs mainly involved in metabolism pathways and hypo-DMGs mainly involved in cell adhesion. By constructing a prognostic model based on aberrantly methylated genes, the study provided insights into the epigenetic mechanisms of HCC development.
Article
Agronomy
Jazba Anum, Charlotte O'Shea, Karen Skriver, Muhammad Saeed, Muhammad Zeeshan Hyder, Sumaira Farrakh, Tayyaba Yasmin
Summary: This study analyzed the epigenetic effects of drought and salinity on DNA methylation of stress responsive genes in rice. The results showed differential methylation status at cytosine residues depending on cultivar, tissue, and stress conditions. The promoter region of OsGLP8-12 gene was heavily methylated and showed significant differential methylation depending on variety, tissue, or stress conditions. This suggests a possible association between promoter methylation and regulation of OsGLP genes under abiotic stresses.
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Article
Environmental Sciences
Julia S. Mouat, Xueshu Li, Kari Neier, Yihui Zhu, Charles E. Mordaunt, Michele A. La Merrill, Hans -Joachim Lehmler, Michael P. Jones, Pamela J. Lein, Rebecca J. Schmidt, Janine M. LaSalle
Summary: This study aimed to explore the impact of gestational exposure to polychlorinated biphenyls (PCBs) on placental epigenetics and its correlation with child neurodevelopmental outcomes. The results suggested that placental DNA co-methylation modules were associated with maternal PCB levels and child neurodevelopment, particularly the methylation of CSMD1 and AUTS2, which could be potential markers of altered placental function and/or increased risk of autism spectrum disorder (ASD) following maternal PCB exposure.
ENVIRONMENTAL RESEARCH
(2023)
Article
Genetics & Heredity
Jacob Morrison, Julie M. Koeman, Benjamin K. Johnson, Kelly K. Foy, Ian Beddows, Wanding Zhou, David W. Chesla, Larissa L. Rossell, Emily J. Siegwald, Marie Adams, Hui Shen
Summary: This study extensively benchmarked common library preparation protocols for whole-genome DNA methylation sequencing, with NEBNext Enzymatic Methyl-seq and Swift Accel-NGS Methyl-Seq kits showing superior performance quantitatively. The NEBNext Enzymatic Methyl-seq kit is recommended for high-quality DNA samples, while the Swift kit is more suitable for degraded samples.
EPIGENETICS & CHROMATIN
(2021)
Review
Chemistry, Physical
Ting Gong, Heather Borgard, Zao Zhang, Shaoqiu Chen, Zitong Gao, Youping Deng
Summary: DNA methylation is a phenomenon associated with transcriptional repression, genomic imprinting, stem cell differentiation, embryonic development, and inflammation. Aberrant DNA methylation can indicate disease states, making the understanding of the prevalence and location of DNA methylation in the human genome important. Whole-genome bisulfite sequencing (WGBS) is a high-throughput method for analyzing DNA methylation, and this review compares and introduces the detailed experimental methodology of WGBS.
Article
Peripheral Vascular Disease
Francesca Gaccioli, Ulla Sovio, Sungsam Gong, Emma Cook, D. Stephen Charnock-Jones, Gordon C. S. Smith
Summary: This study aimed to investigate the relationship between protein levels of sFLT1 and PlGF in maternal serum and placental tissue lysates. The findings showed that the sFLT1:PlGF ratio is increased in both preeclampsia and FGR, but in preeclampsia, it is primarily driven by increased placental sFLT1 levels, while in FGR, it is primarily driven by decreased placental PlGF levels.
Article
Cell Biology
Giulia Avellino, Ruhi Deshmukh, Stephanie N. Rogers, D. Stephen Charnock-Jones, Gordon C. S. Smith, Saverio Tardito, Irving L. M. H. Aye
Summary: Human trophoblast cultures are important for studying placental development. However, current in vitro studies using commercial media with nonphysiological nutrient levels have unknown effects on trophoblast metabolism and function. This study shows that a physiological medium called Plasmax, which mimics human plasma, improves the proliferation and differentiation of human trophoblast stem cells (hTSCs) compared to standard medium (DMEM-F12). hTSCs cultured in Plasmax-based medium also exhibit altered metabolism and reduced S-adenosylmethionine/S-adenosyl-homocysteine ratio. These findings highlight the importance of the nutritional environment for phenotyping cultured human trophoblasts.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2023)
Article
Medicine, General & Internal
Laurentya Olga, Ulla Sovio, Hilary Wong, Gordon Smith, Catherine Aiken
Summary: This study aimed to determine the relationship between antenatal FGR and mid-childhood educational outcomes. The researchers found that children with antenatally diagnosed FGR had poorer educational achievement in mid-childhood compared to children with normal fetal growth and no placental dysfunction markers.
Article
Obstetrics & Gynecology
Ulla Sovio, Francesca Gaccioli, Emma Cook, D. Stephen Charnock-Jones, Gordon C. S. Smith
Summary: This study aimed to determine the inter-relationships between five first-trimester biomarkers and a range of adverse pregnancy outcomes. The results showed that these biomarkers were associated with fetal growth restriction, preterm birth, and preeclampsia, indicating heterogeneity in the underlying pathophysiological pathways for different types of adverse pregnancy outcomes.
BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Roshan J. Selvaratnam, Ulla Sovio, Emma Cook, Francesca Gaccioli, D. Stephen Charnock-Jones, Gordon C. S. Smith
Summary: Consistent exposure to smoking throughout pregnancy is strongly associated with spontaneous preterm birth and fetal growth restriction. High levels of paraxanthine are not independently associated with any of the studied outcomes and are confounded by smoking.
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
(2023)
Correction
Immunology
G. C. Smith A, R. Kempker R, L. Wassie
OPEN FORUM INFECTIOUS DISEASES
(2023)
Article
Obstetrics & Gynecology
Yasmina Al Ghadban, Yuheng Du, D. Stephen Charnock-Jones, Lana X. Garmire, Gordon C. S. Smith, Ulla Sovio
Summary: This study identified and internally validated metabolites predictive of spontaneous preterm birth using multiple machine learning methods and sequential maternal serum samples. A lysolipid was found to be a novel predictor of preterm birth and early term birth.
BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY
(2023)