Review
Developmental Biology
Alex Wei, Hao Wu
Summary: DNA methylation is a conserved epigenetic modification that is crucial for mammalian gene regulation, genome stability, and development. It can exhibit cell-type specificity and dynamic changes in gene regulatory elements during early embryonic development, stem cell differentiation, reprogramming, and tissue maturation. The interaction between DNA methylation and histone modifications plays a vital role in mammalian development and tissue maturation. Recent advances in technology have enabled high-resolution analysis of DNA methylome dynamics.
Article
Biochemistry & Molecular Biology
Chirada Dusadeemeelap, Thira Rojasawasthien, Takuma Matsubara, Shoichiro Kokabu, William N. Addison
Summary: This study investigates the role of TET-mediated DNA hydroxymethylation in bone formation using a novel selective TET enzyme inhibitor, BC339. The results show that inhibiting TET with BC339 suppresses osteoblast differentiation and functions through increasing the methylation level of the Sp7 promoter.
Article
Biochemistry & Molecular Biology
Cathia Rausch, Peng Zhang, Corella S. Casas-Delucchi, Julia L. Daiss, Christoph Engel, Gideon Coster, Florian D. Hastert, Patrick Weber, M. Cristina Cardoso
Summary: DNA base modifications, specifically cytosine methylation, have been shown to stabilize the DNA helix and influence genome metabolism. However, oxidation of methylated cytosine can reverse these effects, highlighting the importance of cytosine modifications in regulating DNA helix stability and fine-tuning DNA metabolism locally.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Elitsa Stoyanova, Michael Riad, Anjana Rao, Nathaniel Heintz
Summary: At birth, the mammalian brain contains billions of neurons, which develop into networks and learn adult brain tasks through chemical marks such as methylation and hydroxymethylation. Accumulation of 5hmC, possibly essential for neuronal maturation, highlights the role of Tet proteins in preparing and removing DNA marks. Problematic control of 5hmC levels could potentially contribute to brain disorders, while future studies may provide insights into cancerous cell development due to loss of 5hmC.
Article
Multidisciplinary Sciences
Evan J. Burke, Samuel S. Rodda, Sean R. Lund, Zhiyi Sun, Malcolm R. Zeroka, Katherine H. O'Toole, Mackenzie J. Parker, Dharit S. Doshi, Chudi Guan, Yan-Jiun Lee, Nan Dai, David M. Hough, Daria A. Shnider, Ivan R. Correa, Peter R. Weigele, Lana Saleh
Summary: TET/JBP enzymes are iron(II)-and 2-oxo-glutarate-dependent dioxygenases found across all kingdoms of life, playing roles in epigenetic regulation through oxidation of 5-methylpyrimidines. Phage-encoded TETs have been shown to favor Gp5mC dinucleotides and complex cytosine modifications important for DNA packaging and evasion of host restriction. The sequence specificity of phage TETs correlates with their genomically cooccurring cytosine C5-methyltransferases.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Medicinal
Nicholas A. Weirath, Alexander K. Hurben, Christopher Chao, Suresh S. Pujari, Tao Cheng, Shujun Liu, Natalia Y. Tretyakova
Summary: Ten eleven translocation (TET) dioxygenases are enzymes that play important roles in gene activation and epigenetic remodeling. Inhibitors of TET, such as alpha-ketoglutarate mimics, have been developed, but they may interfere with other enzymes. A recent study reported a new cytosine-based inhibitor called Bobcat339, but further research found that its inhibitory activity against TET enzymes is minimal and mainly comes from contaminating copper ions (Cu(II)).
ACS MEDICINAL CHEMISTRY LETTERS
(2022)
Article
Genetics & Heredity
Anna Schmuecker, Bingkun Lei, Zdravko J. Lorkovic, Matias Capella, Sigurd Braun, Pierre Bourguet, Olivier Mathieu, Karl Mechtler, Frederic Berger
Summary: The selection of C-terminal motifs contributes to the evolution of distinct histone H2A variants, with cell cycle dependent kinases playing a crucial role. Interference between the functions carried by these motifs led to their mutual exclusion and the evolution of different classes of H2A variants.
Review
Chemistry, Medicinal
Shoghag Panjarian, Jean-Pierre J. Issa
Summary: Triple-negative breast cancers (TNBCs) are highly heterogeneous and molecularly diverse, with a distinct DNA methylation profile characterized by hypomethylation and lower gains of methylations compared to other subtypes. The balance between DNA methylases (DNMTs) and DNA demethylases (TETs) plays a crucial role in regulating DNA methylation in TNBCs.
Article
Infectious Diseases
Yu-Chia Hsieh, Jia-Wen Wu, Yi-Yin Chen, Tran Lam Tu Quyen, Wei-Chao Liao, Shiao-Wen Li, Yin-Cheng Chen, Yi-Jiun Pan
Summary: The study found that seven strains of tigecycline-non-susceptible Acinetobacter baumannii isolates in Taiwan carried tet(X)-like genes, which were considered outbreak strains. The co-harboring of tet(X6) and bla(OXA-72) genes in these strains highlights the potential risk of spreading tigecycline- and carbapenem-resistant A. baumannii in healthcare settings.
Review
Biochemistry & Molecular Biology
Xiufei Chen, Haiqi Xu, Xiao Shu, Chun-Xiao Song
Summary: The concept of epigenetics was first proposed in 1942. Chemical modifications on histones, DNA, and RNA have been identified as three key components of epigenetic modifications. These modifications play a crucial role in various biological processes and diseases, including cancer. With the advancement of sequencing technologies, scientists are now able to accurately map and quantify different types of epigenetic modifications in histones, DNA, and RNA, providing insights into gene regulation.
CELL DEATH AND DIFFERENTIATION
(2023)
Review
Chemistry, Multidisciplinary
Wenlong Ding, Hongxia Zhao, Yulin Chen, Shixian Lin
Summary: Protein post-translational modification (PTM) is a mechanism for functional diversification of the human genome, and the dysregulation of the PTM network is associated with human diseases. The genetic code expansion (GCE) strategy allows for gain-of-function studies of PTMs. Mass spectrometry can be used to discover and identify new PTMs.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Biology
Joao C. Sabino, Madalena R. de Almeida, Patricia L. Abreu, Ana M. Ferreira, Paulo Caldas, Marco M. Domingues, Nuno C. Santos, Claus M. Azzalin, Ana Rita Grosso, Sergio Fernandes de Almeida
Summary: The activity of TET enzymes promotes the formation of R-loops, revealing new mechanisms of gene expression regulation.
Article
Environmental Sciences
Ling Luo, Jinlu Feng, Rui Xue, Jianhua Ma, Liping Lou, Jinsong He, Yan Liu, Hong Xiao, Ouping Deng, Liyuan Xie
Summary: Successive DNA extraction of swine manures increased the abundance of ARGs, intI1, and 16S rRNA, leading to shifts in bacterial phylum and genus, emphasizing the need to pay more attention to the possible hosts carrying these genes.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Review
Biochemistry & Molecular Biology
Wenxia Zhan, Yi Li, Jie Yuan, Na Zhi, Yiyuan Huang, Yingqi Liu, Ming Zhang, Shengxi Wu, Xianghui Zhao
Summary: This article reviews the progress of studies on the roles of TET proteins and 5hmC patterns in neurobiology and psychiatric disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Tuvshintugs Baljinnyam, Mark L. Sowers, Chia Wei Hsu, James W. Conrad, Jason L. Herring, Linda C. Hackfeld, Lawrence C. Sowers
Summary: DNA damage caused by internal reactions can lead to tumor development, and enzymatic modification of DNA bases can modulate epigenetic control of gene transcription. This study reveals the role of human glycosylases in DNA repair and epigenetic reprogramming, introducing new observations and raising new questions.
Article
Biochemistry & Molecular Biology
Maria Basanta-Sanchez, Rui Wang, Zhenzhen Liu, Xiaohan Ye, Minyong Li, Xiaodong Shi, Paul F. Agris, Yubin Zhou, Yun Huang, Jia Sheng
Article
Peripheral Vascular Disease
Aji Huang, Hongyu Wu, Takayuki Iriyama, Yujin Zhang, Kaiqi Sun, Anren Song, Hong Liu, Zhangzhe Peng, Lili Tang, Minjung Lee, Yun Huang, Xin Ni, Rodney E. Kellems, Yang Xia
Article
Medicine, Research & Experimental
Shengbing Zang, Jia Li, Haiyan Yang, Hongxiang Zeng, Wei Han, Jixiang Zhang, Minjung Lee, Margie Moczygemba, Sevinj Isgandarova, Yaling Yang, Yubin Zhou, Anjana Rao, M. James You, Deqiang Sun, Yun Huang
JOURNAL OF CLINICAL INVESTIGATION
(2017)
Article
Chemistry, Multidisciplinary
Minjung Lee, Jia Li, Yi Liang, Guolin Ma, Jixiang Zhang, Lian He, Yuliang Liu, Qian Li, Minyong Li, Deqiang Sun, Yubin Zhou, Yun Huang
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Chemistry, Multidisciplinary
Lian He, Ji Jing, Lei Zhu, Peng Tan, Guolin Ma, Qian Zhang, Nhung T. Nguyen, Junfeng Wang, Yubin Zhou, Yun Huang
Article
Chemistry, Multidisciplinary
Guolin Ma, Qian Zhang, Lian He, Nhung T. Nguyen, Shuzhong Liu, Zuojiong Gong, Yun Huang, Yubin Zhou
Article
Biochemistry & Molecular Biology
Jie Yang, John R. Horton, Dongxue Wang, Ren Ren, Jia Li, Deqiang Sun, Yun Huang, Xing Zhang, Robert M. Blumenthal, Xiaodong Cheng
NUCLEIC ACIDS RESEARCH
(2019)
Article
Neurosciences
Ji Jing, Gan Liu, Yun Huang, Yubin Zhou
JOURNAL OF PHYSIOLOGY-LONDON
(2020)
Article
Biochemistry & Molecular Biology
Jie Yang, John R. Horton, Jia Li, Yun Huang, Xing Zhang, Robert M. Blumenthal, Xiaodong Cheng
NUCLEIC ACIDS RESEARCH
(2019)
Review
Biochemistry & Molecular Biology
Phensinee Haruehanroengra, Ya Ying Zheng, Yubin Zhou, Yun Huang, Jia Sheng
Article
Biochemistry & Molecular Biology
Jie Yang, John R. Horton, Kadir C. Akdemir, Jia Li, Yun Huang, Janani Kumar, Robert M. Blumenthal, Xing Zhang, Xiaodong Cheng
Summary: DNA cytosine methylation in mammals can affect gene expression, chromatin accessibility, and mutation rates. A study found that C-to-T mutations are enriched in the binding sites of CCAAT/enhancer binding proteins (CEBP). The presence of a T:G mismatch in a CEBP site can significantly increase CEBP beta binding affinity and inhibit repair mechanisms, leading to the accumulation of C-to-T human somatic mutations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Jianfang Li, Xinwei Wu, Jie Ke, Minjung Lee, Qingping Lan, Jia Li, Jianxiu Yu, Yun Huang, De-Qiang Sun, Ruiyu Xie
Summary: In this study, the authors demonstrate that TET1 plays a crucial role in the generation of functional insulin-producing cells. They find that FOXA2 physically interacts with TET1 and contributes to the specific recruitment of TET1 to the regulatory elements of pancreatic lineage determinants, mediating chromatin opening.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Yaling Dou, Rui Chen, Siyao Liu, Yi-Tsang Lee, Ji Jing, Xiaoxuan Liu, Yuepeng Ke, Rui Wang, Yubin Zhou, Yun Huang
Summary: The study introduces a light-sensitive optogenetic device, LiSmore, to remotely modulate the cGAS/STING signaling pathway and enhance immune response. The authors demonstrate that LiSmore can boost antitumor immunity and improve the efficacy of immune checkpoint blockade in mice.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Janani Kumar, Gundeep Kaur, Ren Ren, Yue Lu, Kevin Lin, Jia Li, Yun Huang, Anamika Patel, Michelle C. Barton, Todd Macfarlan, Xing Zhang, Xiaodong Cheng
Article
Cell Biology
Guolin Ma, Shufan Wen, Lian He, Yun Huang, Youjun Wang, Yubin Zhou
