Article
Multidisciplinary Sciences
Paula Metselaar, Lucero Mendoza-Maldonado, Andrew Yung Fong Li Yim, Ilias Abarkan, Peter Henneman, Anje A. te Velde, Alexander Schoenhuth, Jos A. Bosch, Aletta D. Kraneveld, Alejandro Lopez-Rincon
Summary: The study combined mRNA expression and DNA methylation data to identify a gene signature that distinguishes ME/CFS patients from healthy controls. The results suggest that these genes are related to the dysregulated immune system in ME/CFS patients.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Teresa Improda, Valentina Morgera, Maria Vitale, Lorenzo Chiariotti, Fabiana Passaro, Antonia Feola, Antonio Porcellini, Mariella Cuomo, Antonio Pezone
Summary: Cell identity is determined by chromatin structure and gene expression profiles, which rely on chromatin accessibility and DNA methylation. These epigenetic modifications are crucial for mammalian development and cellular identity. Dynamic DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. By analyzing the methylation configurations of gene promoters during murine brain differentiation, we found significant methyl-CpG profiles associated with gene silencing or activation. Interestingly, these methylation patterns mark different brain areas and cell types during differentiation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Ayala Tovy, Jaime M. Reyes, Linda Zhang, Yung-Hsin Huang, Carina Rosas, Alexes C. Daquinag, Anna Guzman, Raghav Ramabadran, Chun-Wei Chen, Tianpeng Gu, Sinjini Gupta, Laura Ortinau, Dongsu Park, Aaron R. Cox, Rachel E. Rau, Sean M. Hartig, Mikhail G. Kolonin, Margaret A. Goodell
Summary: DNMT3A plays a crucial role in the differentiation of embryonic and hematopoietic stem cells. Heterozygous mutations in DNMT3A lead to Tatton-Brown-Rahman syndrome, characterized by obesity and excessive height. This study shows that DNMT3A affects feeding behavior and adipocyte progenitor differentiation, contributing to the development of inflammatory obesity.
Article
Cell Biology
Zoltan Kraboth, Bela Kajtar, Bence Galik, Attila Gyenesei, Attila Miseta, Bernadette Kalman
Summary: Glioblastoma (GBM) is the most aggressive tumor of the central nervous system (CNS) and current treatments have limited effectiveness, prompting the exploration of new therapeutic targets. Certain neurotransmitter pathway markers may play a role in the development and growth of GBM.
Article
Endocrinology & Metabolism
Leona Kovac, Thomas Goj, Meriem Ouni, Martin Irmler, Markus Jaehnert, Johannes Beckers, Martin Hrabe De Angelis, Andreas Peter, Anja Moller, Andreas L. Birkenfeld, Cora Weigert, Annette Schuermann
Summary: Exercise training can improve glucose tolerance in obese individuals, but some may not respond positively. This study analyzed gene expression and DNA methylation in skeletal muscle of low and high responders to endurance training, identifying differences in gene expression and potential novel markers for intervention success.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2023)
Article
Oncology
Xiaoqing Yu, Ling Cen, Y. Ann Chen, Joseph Markowitz, Timothy Shaw, Kenneth Y. Tsai, Jose R. Conejo-Garcia, Xuefeng Wang
Summary: DNA methylation signatures can be used as reliable biomarkers to predict patient prognosis and immune status in tumors. This study introduces the concept of tumor-based expression quantitative trait methylation (eQTM) for the identification of predictive biomarkers. eQTM CpGs and genes represent new and efficient candidate targets for prognosis and immune status monitoring.
Article
Biochemical Research Methods
Manqi Cai, Molin Yue, Tianmeng Chen, Jinling Liu, Erick Forno, Xinghua Lu, Timothy Billiar, Juan Celedon, Chris McKennan, Wei Chen, Jiebiao Wang
Summary: This study focuses on using cellular deconvolution methods to extract cell-type-specific signals from tissue-level omics data. However, different methods produce different results under various real data settings. The study proposes EnsDeconv, an ensemble deconvolution method that synthesizes the results from multiple single deconvolution methods to achieve robust and accurate estimation of cellular fractions.
Article
Biotechnology & Applied Microbiology
Jiwon Lim, Yerim Heo, Sun Shim Choi
Summary: DNAm is important for regulating cellular activities, and this study investigated its alterations in obesity. Using methylome and transcriptome data, differentially methylated probes (DMPs) were identified between adipocytes and preadipocytes, as well as between obese and lean adipocytes. The study also examined the impact of hyper and hypomethylation on gene expression changes. Interestingly, greater DNAm alterations were observed during adipocyte differentiation under lean conditions compared to obese conditions. Overall, complex methylation changes affected adipogenesis-related genes, leading to differences in gene expression between lean and obese adipocytes.
Article
Multidisciplinary Sciences
Zhaoying Li, Weijing Wang, Xiaocao Tian, Haiping Duan, Chunsheng Xu, Dongfeng Zhang
Summary: In a bivariate twin study focused on genetic variants associated with BMI-SBP, BMI-DBP, and SBP-DBP, new single nucleotides and expression quantitative trait loci were identified. Furthermore, gene-based and pathway analyses revealed nominally associated genes and pathways related to BMI and BP traits, providing important insights for future research on the pathogenesis of hypertension and obesity in the northern Chinese population.
Article
Biochemistry & Molecular Biology
Kangli Wang, Rujia Dai, Yan Xia, Jianghua Tian, Chuan Jiao, Tatiana Mikhailova, Chunling Zhang, Chao Chen, Chunyu Liu
Summary: The study showed that DNA methylation and gene expression are coordinated across different human tissues and developmental stages, with correlations being tissue- and development-specific. These correlations are important for cellular functions, complex traits, and human diseases, highlighting the diverse roles of genetic and epigenetic factors in regulating gene expression.
Article
Oncology
Pinpin Long, Qiuhong Wang, Yizhi Zhang, Xiaoyan Zhu, Kuai Yu, Haijing Jiang, Xuezhen Liu, Min Zhou, Yu Yuan, Kang Liu, Jing Jiang, Xiaomin Zhang, Meian He, Huan Guo, Weihong Chen, Jing Yuan, Longxian Cheng, Liming Liang, Tangchun Wu
Summary: This study identified four novel DNA methylation alterations associated with plasma copper in Chinese populations, with one specific methylation site showing an increased risk of ACS. These findings provide new insights into the role of copper-related DNA methylation in regulating gene expression and suggest a potential link between DNA methylation and the risk of acute coronary syndrome.
CLINICAL EPIGENETICS
(2021)
Article
Genetics & Heredity
Li Yang, Lili Liu, Jinhua Cheng, Zhengchang Wu, Wenbin Bao, Shenglong Wu
Summary: The expression of FUT3 in the duodenal tissues of Meishan pigs was found to decrease with increasing age. Bisulfite sequencing identified nine methylated CpG sites in the FUT3 core promoter region, and methylation at the mC-9 site showed a significantly negative association with mRNA expression. The study also revealed that DNA methylation may regulate the developmental expression of the FUT3 gene by inhibiting the binding of the transcription factor Spl.
Article
Cell Biology
Chu Chu, Wenhao Zhang, Yu Kang, Chenyang Si, Weizhi Ji, Yuyu Niu, Yi Zhang
Summary: This study analyzes imprinting dynamics in primates by profiling transcriptomes, DNA methylomes, and H3K27me3 in uniparental monkey embryos. The research establishes SNP-free germline DMR identification methods, defines developmental imprinting dynamics in primates, and demonstrates imprinting defects in cloned monkey placenta, providing valuable insights for improving primate cloning techniques.
DEVELOPMENTAL CELL
(2021)
Article
Cardiac & Cardiovascular Systems
Runqi Tu, Xiaotian Liu, Xiaokang Dong, Ruiying Li, Wei Liao, Jian Hou, Zhenxing Mao, Wenqian Huo, Chongjian Wang, Yuqian Li
Summary: This study using Mendelian randomization analysis found a causal relationship between JAK2 methylation levels and obesity, indicating that the relationship between methylation levels and obesity may be related to the region of methylation.
NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Muhammad Azhar, Caoling Xu, Xue Jiang, Wenqing Li, Yuzhu Cao, Xiaoli Zhu, Xuemei Xing, Limin Wu, Jiaqi Zou, Lan Meng, Yu Cheng, Wenjie Han, Jianqiang Bao
Summary: This study reveals the crucial role of Prmt1 in the establishment and maintenance of spermatogonia, and its regulation of transcriptional homeostasis. The enrichment of Prmt1-deposited H4R3me2a mark in mouse spermatogonia has a significant impact on the transcriptomic landscape and alternative splicing pattern.
NUCLEIC ACIDS RESEARCH
(2023)