Article
Oncology
Ruth Pidsley, Dilys Lam, Wenjia Qu, Timothy J. Peters, Phuc-Loi Luu, Darren Korbie, Clare Stirzaker, Roger J. Daly, Phillip Stricker, James G. Kench, Lisa G. Horvath, Susan J. Clark
Summary: This study used methylome sequencing to investigate the DNA methylation patterns in prostate cancer patients, and identified methylation patterns associated with prostate cancer-specific mortality, as well as prognostic biomarkers. The combination of DNA methylation biomarkers and clinicopathological measures improved the prognostic models for prostate cancer mortality.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Plant Sciences
Yan Shi, Xingtan Zhang, Xiaojun Chang, Maokai Yan, Heming Zhao, Yuan Qin, Haifeng Wang
Summary: The study investigated the role of DNA methylation in regulating CAM photosynthesis by analyzing the DNA methylome and transcriptome of pineapple leaves. Differences in DNA methylation patterns and gene expression levels were observed between non-photosynthetic and photosynthetic tissues, with thousands of genes related to the CAM pathway showing differential methylation and expression levels.
Article
Environmental Sciences
Meng -Die Cheng, Chang -Lei Li, Xiang -Yu Pei, Yi-Fei Zhang, Dong-Dong Jia, Ying-Bing Zuo, Shang -Lang Cai, Pei-Feng Li, Hui Xin, Yin-Feng Zhang
Summary: Cardiac hypertrophy can lead to heart dysfunction and failure, and bisphenols (BPs) such as BPA and its alternatives BPAF, BPF, and BPS, which are widely used in various products, may pose high cardiovascular risks for humans. This study aimed to investigate the effects of BPs on heart function and cardiomyocyte hypertrophy, as well as their role in DNA methylation and transcription dysregulation. The results showed that BPAF, BPF, and BPS exposure, similar to BPA, deteriorated heart function in mice and induced cardiomyocyte hypertrophy. These BPs also exhibited similar effects on transcription and methylation as BPA. Moreover, the study validated the upregulation of four candidate genes related to cardiomyocyte hypertrophy, Psmc1, Piptnm2, Maz, and Dusp18, which showed DNA hypomethylation. The findings suggest the potential detrimental risks of BPA analogues on heart function through cardiomyocyte hypertrophy and DNA methylation.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Biochemistry & Molecular Biology
Weilin Zhu, Chunling Yang, Qingyun Liu, Min Peng, Qiangyong Li, Huanling Wang, Xiuli Chen, Bin Zhang, Pengfei Feng, Tiancong Chen, Digang Zeng, Yongzhen Zhao
Summary: In this study, a comprehensive comparative analysis was conducted using whole genome bisulfite sequencing (WGBS) and transcriptome sequencing to investigate the DNA methylation profiles and differentially expressed genes in two strains of Litopenaeus vannamei with significantly different cold tolerance. The results revealed that differentially methylated regions (DMRs) were mainly located in gene exons and introns. The DMR-related genes (DMRGs) were significantly enriched in cell parts, catalytic activity, and metabolic processes, as revealed by Gene Ontology (GO) analysis. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed significant enrichment of these DMRGs in various metabolic pathways. These findings provide important insights into DNA methylation patterns and identification of cold tolerance genes in shrimp.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Hiroshi Tojo, Aki Nakamura, Ali Ferjani, Yusuke Kazama, Tomoko Abe, Hidetoshi Iida
Summary: This study reports a method for screening mutants of Arabidopsis thaliana with root penetration defects, isolating five mutants named creep1 to creep5 and observing their phenotypes. The mutants exhibited different behaviors in root skewing when growing along impenetrable surfaces, showing the potential of the method to isolate mutants for investigating root mechanical behavior regulation in various plant species.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Yan Shi, Yuan Qin, Fenglan Li, Haifeng Wang
Summary: The role of DNA methylation in regulating potato response to Fusarium toxin deoxynivalenol (DON) stress and potato disease resistance was investigated in this study. The results showed that different concentrations of DON treatment caused significant changes in global DNA methylation levels in potato tubers. Differentially methylated regions (DMRs)-associated differentially expressed genes (DEGs) were enriched in resistance-related metabolic pathways. In addition, DON stress potentially induced resistance in potato tubers, possibly related to epigenetic memory created after DNA methylation changes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Developmental Biology
D'Juan T. Farmer, Punam Patel, Rachelle Choi, Chih-Yu Liu, J. Gage Crump
Summary: Irx genes play crucial roles in vertebrate skeletal development, with conserved requirements for shoulder blade formation, anterior neural crest precursors, and gill cartilages. Loss of Irx gene clusters leads to joint loss and cartilage fusions through inappropriate chondrogenesis, revealing diverse roles in the formation and segmentation of the facial skeleton.
Article
Oncology
Jingjin Li, Xiaoping Zhang, Mengxi Yang, Hang Yang, Ning Xu, Xueqiang Fan, Gang Liu, Xintong Jiang, Jiasai Fan, Lifang Zhang, Hu Zhang, Ying Zhou, Rui Li, Si Gao, Jiangli Jin, Zening Jin, Jingang Zheng, Qiang Tu, Jingyi Ren
Summary: Through genome-wide analysis of DNA methylation, it was found that hypomethylation in vulnerable atherosclerotic plaques is associated with genes involved in inflammation, indicating a potential role in driving the progression and destabilization of atherosclerotic cardiovascular disease.
CLINICAL EPIGENETICS
(2021)
Article
Cell Biology
Xinran Yang, Jianfang Wang, Xinhao Ma, Jiawei Du, Chugang Mei, Linsen Zan
Summary: The research identified the important role of m(6)A methylation in transcriptional regulation and RNA metabolism during bovine skeletal myogenesis. Analysis on differentially methylated genes revealed that m(6)A modification may affect myoblast differentiation by mediating the expression of specific genes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Plant Sciences
Daniel Lunn, Gracen A. Smith, James G. Wallis, John Browse
Summary: The overexpression of MPD1 protein in low temperature conditions leads to the accumulation of reactive oxygen species (ROS) and causes chilling damage, indicating the importance of Mpv17_PMP22 proteins in oxidative stress in plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Microbiology
Jeffrey S. Bourgeois, Caroline E. Anderson, Liuyang Wang, Jennifer L. Modliszewski, Wei Chen, Benjamin H. Schott, Nicolas Devos, Dennis C. Ko
Summary: This study found that most DNA methylation in Salmonella enterica serovar Typhimurium remains unchanged, even under different growth conditions that cause significant changes in the transcriptome. Furthermore, even when individual bases undergo methylation changes, these changes are generally not correlated with changes in gene expression. Finally, the study demonstrates a method to identify coupled changes in methylation and gene expression through data stratification.
Article
Microbiology
Kusum Rana, Junhu Yuan, Hongmei Liao, Surinder S. Banga, Rahul Kumar, Wei Qian, Yijuan Ding
Summary: This study successfully silenced the Ssoah1 gene in the Sclerotinia sclerotiorum fungus using host-induced gene silencing (HIGS) technology. Pathogenicity assays and oxalic acid estimation in transgenic Arabidopsis thaliana lines with silenced Ssoah1 gene showed higher resistance and reduced oxalic acid accumulation compared to non-transgenic controls. These results indicate the possibility of using HIGS to enhance resistance against Sclerotinia sclerotiorum.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Plant Sciences
Jiakai Liao, Ban Deng, Xinyu Cai, Qixin Yang, Bangping Hu, Jiajing Cong, Yuxiang Zhang, Gang Wang, Guiliang Xin, Yuting Li, Li Yang, Daizhen Zhang, Jin Zhang, Bobin Liu
Summary: Seed dormancy and germination are crucial for plant survival and population expansion, but the molecular mechanisms underlying their control are still unclear. This study identified WOX11 as a hub transcription factor regulating seed dormancy in Arabidopsis. WOX11 and its homolog WOX12 are highly expressed during seed dormancy induction and release stages, and are activated by red-light signaling mediated by phytochrome B. These findings provide insights into the regulation and evolutionary adaptation of plants to changes in the light environment.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Naoyuki Sotta, Yukako Chiba, Kyoko Miwa, Seidai Takamatsu, Mayuki Tanaka, Yui Yamashita, Satoshi Naito, Toru Fujiwara
Summary: The study revealed the translation regulation mechanism in response to boron conditions in Arabidopsis thaliana shoots, with uORFs and AUG-stops playing important roles in this process.
Article
Plant Sciences
Sung-Aeong Oh, Hyo-Jin Park, Myung-Hee Kim, Soon-Ki Park
Summary: The SGC gene suppresses callose deposition in pollen, aiding in the proper internalization and localization of generative cells during development. Additionally, the GCTLP1 protein, which may interact with SGC, was identified as a potential player in regulating pollen development in Arabidopsis.
