Article
Cell Biology
Junnan Liang, Tongtong Liu, Jingyu Liao, Lu Zhang, Mi Zhou, Weiqi Xu, Yi He, Guangzhen Cai, Guannan Jin, Jia Song, Ganxun Li, Huifang Liang, Zeyang Ding, Bixiang Zhang
Summary: The study identified a CIMP-related methylation signature specific for CCA (CMSC) that can classify patients into different risk groups and predict patient outcomes. Additionally, a subset of patients with an unfavorable prognosis correlated with CIMP-H was identified. Gene enrichment analysis suggested a potential mechanism of CIMP as a promoter of carcinogenesis by regulating proliferation.
JOURNAL OF CELLULAR PHYSIOLOGY
(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
Biochemistry & Molecular Biology
Heejoo Kim, Hwee Won Ji, Hyeon Woo Kim, Sung Hwan Yun, Jae Eun Park, Sun Jung Kim
Summary: The research revealed that Rg3 regulates the expression of lncRNA ATXN8OS and miR-424-5p in MCF-7 cancer cells, impacting cell proliferation and apoptosis, and subsequently affecting the expression of oncogenic target genes.
Article
Plant Sciences
Jiayu Liang, Xiaodan Li, Ya Wen, Xinyi Wu, Hui Wang, Dayong Li, Fengming Song
Summary: The present study characterized the MBD families in watermelon and other cucurbit plants and revealed their roles in plant immunity.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Ayano Goto, Wataru Yoshida
Summary: A hybridization-based CpG methylation level detection method using methyl-CpG-binding domain-fused firefly luciferase (MBD-Fluc) was developed to quantify the CpG methylation levels of SEPT9, BRCA1, and LINE-1 oligonucleotides. It was demonstrated that methylated CpG of the target region could be accurately detected.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Taiko Kim To, Chikae Yamasaki, Shoko Oda, Sayaka Tominaga, Akie Kobayashi, Yoshiaki Tarutani, Tetsuji Kakutani
Summary: In plant genomes, both mCG and H3K9me2/mCH play important roles in silencing TEs. The establishment of mCH is dependent on the presence of mCG, and the efficiency of mCH targeting depends on the relative levels of mCG in the genome. The study also proposes a model where local positive feedback and global negative feedback regulate DNA methylation patterning.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Jing Zhang, Yan Zhang, Qinglong You, Chang Huang, Tiantian Zhang, Mingzhu Wang, Tianwei Zhang, Xiaocheng Yang, Jun Xiong, Yingfeng Li, Chao-Pei Liu, Zhuqiang Zhang, Rui-Ming Xu, Bing Zhu
Summary: BEND3 is a CpG island-binding protein that is enriched at regulatory elements. It binds to DNA in a methylation-sensitive manner. Mice embryos lacking Bend3 die at the pregastrulation stage, while Bend3 null embryonic stem cells exhibit severe defects in differentiation, leading to premature activation of hundreds of CpG island-containing bivalent genes. BEND3 is required for maintaining high levels of H3K27me3 at these bivalent genes in order to prevent their premature activation in upcoming developmental stages.
Article
Biochemistry & Molecular Biology
Yanling Li, Jiawei Qin, Menglu Chen, Nan Sun, Fangmei Tan, Hua Zhang, Yongdong Zou, Vladimir N. Uversky, Yun Liu
Summary: This paper investigates the structure and function of soybean GmMBD10c protein. Through bioinformatic prediction, circular dichroism, and nuclear magnetic resonance spectral analysis, it is found that part of the GmMBD10c protein is disordered. Experimental evidence shows that GmMBD10c protein can protect lactate dehydrogenase and other proteins from misfolding and aggregation induced by freeze-thaw process and heat stress. Moreover, overexpression of GmMBD10c enhances the salt tolerance of Escherichia coli. Overall, this research reveals the multifunctionality of GmMBD10c protein.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Gordana Supic, Debora Stefik, Nemanja Ivkovic, Ahmad Sami, Katarina Zeljic, Sasa Jovic, Ruzica Kozomara, Danilo Vojvodic, Srboljub Stosic
Summary: miR-34b/c hypermethylation and low miR-34b expression may promote the progression of HPV-negative OSCC and predict a poor prognosis, providing evidence for miR-34b/c as a promising biomarker and therapeutic target for OSCC in the future.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Zhen Wang, Jing Liu, Xing Qiu, Dingpeng Zhang, Hiroyuki Inuzuka, Li Chen, He Chen, Ling Xie, H. Umit Kaniskan, Xian Chen, Jian Jin, Wenyi Wei
Summary: This study presents a novel strategy, methyl-proteolysis-targeting chimera (methyl-PROTAC), for manipulating epigenetic factors by designing a modified nucleotide-based degradation approach. It has the potential to degrade undruggable epigenetic regulatory proteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Genetics & Heredity
Fernanda Silva Coelho, Sara Sangi, Juliana Lopes Moraes, Walaci da Silva Santos, Eduardo Alves Gamosa, Katia Valevski Sales Fernandes, Clicia Grativol
Summary: This study analyzed the evolution and conservation of MBD proteins in plants, finding subfunctionalization of MBD in soybean and similarity in MBDs' binding affinity between plants and humans.
Article
Physics, Fluids & Plasmas
Takeru Kameda, Miho M. Suzuki, Akinori Awazu, Yuichi Togashi
Summary: DNA methylation is associated with biological phenomena and epigenetic regulation, and can alter the mechanical properties of DNA molecules. This study used molecular dynamics simulations to show that methylation patterns affect the local flexibility of DNA, ultimately impacting its overall geometry and stiffness. These findings provide insights into methylation-dependent DNA dynamics in physiological conditions.
Article
Multidisciplinary Sciences
Ksenia Skvortsova, Stephanie Bertrand, Danila Voronov, Paul E. Duckett, Samuel E. Ross, Marta Silvia Magri, Ignacio Maeso, Robert J. Weatheritt, Jose Luis Gomez Skarmeta, Maria Ina Arnone, Hector Escriva, Ozren Bogdanovic
Summary: The study shows that invertebrate deuterostomes use TET enzymes for targeted demethylation of regulatory regions associated with developmental genes, indicating a conservation of this major gene-regulatory module in vertebrates.
Article
Cell Biology
Si-Si Xie, Yi-Zhe Zhang, Li Peng, Ding-Tian Yu, Guohui Zhu, Qingzhen Zhao, Chun-Han Wang, Qi Xie, Cheng-Guo Duan
Summary: In this study, researchers report that JMJ28 protein in Arabidopsis plays a crucial role in the recruitment and targeting of ATX1/2-containing COMPASS-like complex by recognizing specific DNA motifs through a plant-specific WRC domain. They also found that JMJ28 associates with COMPASS-like complex via direct interaction with RBL and its DNA-binding activity is essential for the targeting specificity and deposition of H3K4me at specific loci. Additionally, JMJ28 is identified as a negative regulator of plant immunity.
Article
Behavioral Sciences
Anastasia N. Freedman, Jeliyah Clark, Lauren A. Eaves, Kyle Roell, Ali Oran, Lauren Koval, Julia Rager, Hudson P. Santos Jr, Karl Kuban, Robert M. Joseph, Jean Frazier, Carmen J. Marsit, Amber A. Burt, T. Michael O'Shea, Rebecca C. Fry
Summary: Children born preterm have a higher risk of neurodevelopmental impairments, including Autism Spectrum Disorder (ASD). This study used a multi-omic approach to identify placental transcriptomic and epigenetic modifications related to ASD diagnosis at age 10 in preterm children. The study found 111 genes associated with ASD, including key genes that predicted the ASD case status. The findings highlight the relationship between functional epimutations in the placenta and the development of ASD in preterm children, providing new avenues for intervention.