Article
Chemistry, Analytical
Zi-yue Wang, Huimin Yuan, Dong-ling Li, Juan Hu, Jian-Ge Qiu, Chun-yang Zhang
Summary: In this study, a ligation-mediated nanosensor was developed for sensitive quantification of 5hmC modification in cancer cells. The nanosensor showed excellent specificity and high amplification efficiency, and could detect as low as 0.001% 5hmC DNA in complex mixtures. It also had the ability to monitor cellular 5hmC level and distinguish cancer cells from normal cells.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Wei Cui, Zhijun Huang, Gerd P. Pfeifer
Summary: This study found that succinate, a competitive inhibitor of TET protein function, did not cause significant changes in DNA demethylation contrary to expectations. The significance of these findings and their implications for tumorigenesis require further investigation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Xiao-Yang Jin, Zu-Rui Huang, Li-Jun Xie, Li Liu, Da-Li Han, Liang Cheng
Summary: This study developed a sensitive antibody-free method for detecting and sequencing f(5)C in tRNA. The method uses chemical labeling and fluorescence signal, allowing high-resolution detection of f(5)C with high selectivity and sensitivity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biochemistry & Molecular Biology
Marion Turpin, Gilles Salbert
Summary: DNA methylation is a highly dynamic process regulated by the cooperative actions of DNMT and TET enzymes, influenced by factors such as chromatin environment and protein partners. Mathematical models can help explain variable methylation levels during development and reveal cell-type epigenetic heterogeneity. These discoveries hold significant implications for disease treatment and the development of epigenetic drugs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Analytical
Jing Tang, Guangrong Zou, Chen Chen, Jing Ren, Fang Wang, Zilin Chen
Summary: This study introduced a novel electrochemical method for the selective detection of formylpyrimidines in DNA, specifically targeting 5-formyluracil (5fU) in the presence of 5-formylcytosine (5fC) and apyrimidinic (AP) sites. By combining molecule-depended chemical recognition and electrochemical sensing, the approach showed promise in sensitive and accurate detection of 5fU, with potential applications in various fields.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Zi-yue Wang, Huimin Yuan, Dong-ling Li, Juan Hu, Jian-Ge Qiu, Chun-yang Zhang
Summary: This study develops a nanosensor for quantification of 5hmC modification in cancer cells, which shows high specificity and amplification efficiency.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Catalina Molina, Natalia Cristina Aguirre, Pablo Alfredo Vera, Carla Valeria Filippi, Andrea Fabiana Puebla, Susana Noemi Marcucci Poltri, Norma Beatriz Paniego, Alberto Acevedo
Summary: The study optimized the identification of SNPs in sugarcane and recommended the use of long read size and paired-end reads, medium sequencing coverage, and Illumina NovaSeq6000 platform. Functional analysis showed that most of the SNPs landed within regulatory regions. The protocol demonstrated robustness in analyzing replicated genotypes.
PLANT MOLECULAR BIOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Hao Lv, Fu-Ying Dao, Dan Zhang, Hui Yang, Hao Lin
Summary: DNA modification is crucial in regulating gene expression in cell development, with advances in DNA sequencing technology allowing for the resolution of different modifications at a genome-wide scale. This has led to the discovery of new insights into the complexity and functions of multiple methylations. The review discusses various mapping approaches and the development of future sequencing technologies for improving detection resolution.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Multidisciplinary Sciences
Bo He, Chao Zhang, Xiaoxue Zhang, Yu Fan, Hu Zeng, Jun'e Liu, Haowei Meng, Dongsheng Bai, Jinying Peng, Qian Zhang, Wei Tao, Chengqi Yi
Summary: 5hmC in human tissues shows tissue-specific patterns that may affect tissue-specific gene expression networks and are associated with specific single-nucleotide polymorphisms and diseases.
NATURE COMMUNICATIONS
(2021)
Article
Cell & Tissue Engineering
Yangchan Li, Meilin Xue, Xiaolan Deng, Lei Dong, Le Xuan Truong Nguyen, Lili Ren, Li Han, Chenying Li, Jianhuang Xue, Zhicong Zhao, Wei Li, Ying Qing, Chao Shen, Brandon Tan, Zhenhua Chen, Keith Leung, Kitty Wang, Srividya Swaminathan, Ling Li, Mark Wunderlich, James C. Mulloy, Xiaobo Li, Hao Chen, Bin Zhang, David Horne, Steven T. Rosen, Guido Marcucci, Mingjiang Xu, Zejuan Li, Minjie Wei, Jingyan Tian, Baiyong Shen, Rui Su, Jianjun Chen
Summary: TET2 deficiency promotes leukemogenesis by enhancing leukemia stem cell self-renewal and facilitating their migration into the bone marrow niche. TET2 deficiency increases the expression of TSPAN13, which activates the CXCR4/CXCL12 signaling pathway and promotes the homing and migration of leukemia stem cells. This study reveals the functional importance of TET2 as an mRNA m5C demethylase in leukemogenesis, leukemia cell migration/homing, and stem cell self-renewal.
Article
Biotechnology & Applied Microbiology
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie M. Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Karim Karimi, Guoyu Hu, Shafagh Valipour, Younes Miar
Summary: This study presents the first genome-wide CNV analysis of American mink, using whole-genome sequence data from 100 individuals. The results suggest potential links between CNVs and mink behavior, fur quality, and immune response.
Article
Chemistry, Multidisciplinary
Yang Feng, Juan-Juan Chen, Neng-Bin Xie, Jiang-Hui Ding, Xue-Jiao You, Wan-Bing Tao, Xiaoxue Zhang, Chengqi Yi, Xiang Zhou, Bi-Feng Yuan, Yu-Qi Feng
Summary: DNA cytosine methylation, specifically 5mC, is a crucial epigenetic process in higher eukaryotes, regulated by DNMTs, TET, and TDG. Active demethylation of 5mC can occur through the TET-TDG-BER pathway or direct decarboxylation of 5caC, both of which may impact genome integrity.
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
Medicine, General & Internal
Wan-Yu Sung, Yuan-Zhao Lin, Daw-Yang Hwang, Chia-Hui Lin, Ruei-Nian Li, Chia-Chun Tseng, Cheng-Chin Wu, Tsan-Teng Ou, Jeng-Hsien Yen
Summary: This study found that 5-methylcytosine and 5-hydroxymethylcytosine were decreased in SLE patients, while the mRNA expression of TET2 was significantly high and correlated with SLE disease activity biomarkers. Methylation rates in the TET2 promoter region were also found to differ significantly in SLE patients.
Article
Microbiology
Yingshan Li, Kai Peng, Yi Yin, Xinran Sun, Wenhui Zhang, Ruichao Li, Zhiqiang Wang
Summary: The study identified widespread dissemination of different tet(X) variants in the chicken farming environment, with tet(X4) being the dominant variant. It is recommended to limit antibiotic usage to control the emergence and transmission of novel tet(X) variants in the poultry industry.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Abhishek Aditham, Hailing Shi, Jianting Guo, Hu Zeng, Yiming Zhou, Sarah Dunn Wade, Jiahao Huang, Jia Liu, Xiao Wang
Summary: mRNA has limitations in terms of translational capacity and RNA stability. This study introduces messenger-oligonucleotide conjugated RNAs (mocRNAs) as a method to enhance protein expression by incorporating chemical modifications. The results show significant increases in protein production using this approach. The mocRNA design opens up new possibilities for RNA-based vectors in research and therapeutics.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Pan Zhang, Lin Zhang, Zhaoyuan Hou, Houwen Lin, Hai Gao, Liang Zhang
Summary: This study reported the structures of the ATP-sulfurylase domain of PAPSS2 and its complex with APS, revealing the unique mechanism ATPS2 uses for substrate recognition and binding. This discovery provides important information for a better understanding of the biological function of PAPSS2 in tumorigenesis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Senhao Xiao, Siqi Guo, Jie Han, Yanli Sun, Mingchen Wang, Yantao Chen, Xueyu Fang, Feng Yang, Yajuan Mu, Liang Zhang, Yiluan Ding, Naixia Zhang, Hualiang Jiang, Kaixian Chen, Kehao Zhao, Cheng Luo, Shijie Chen
Summary: This study developed a fluorescence polarization-based assay for high-throughput screening and evaluation of enzymatic activity of DNA/RNA methyltransferases and demethylases. The assay is simple, sensitive, and quick.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Organic
Ru-Yi Shang, Jie Cui, Jia-Xin Li, Xian-Xian Miao, Lu Zhang, Dong-Dong Xie, Liang Zhang, Hou-Wen Lin, Wei-Hua Jiao
Summary: Four new sesquiterpenoids were isolated from a marine sponge collected from the South China Sea. One of the compounds, nigerin, has a unique carbon skeleton and showed potent biological activity.
Article
Biochemistry & Molecular Biology
Yajuan Mu, Lin Zhang, Jingyan Hu, Jiashen Zhou, Hou-Wen Lin, Chuan He, Hong-Zhuan Chen, Liang Zhang
Summary: The research uncovered a 6mA demethylase CcTet that works on dsDNA in the fungus Coprinopsis cinerea, revealing potential 6mA demethylation and the catalytic mechanism of CcTet in fungi. The CcTet D337F mutant protein also serves as a chemical biology tool for manipulating DNA 6mA in vivo.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jinfeng Chen, Jingfei Cheng, Xiufei Chen, Masato Inoue, Yibin Liu, Chun-Xiao Song
Summary: Long-read sequencing provides valuable information on difficult-to-map genomic regions and can improve genome assembly when combined with short-read sequencing. This study presents a method called whole-genome long-read TAPS (wglrTAPS), which combines TET-assisted pyridine borane sequencing with PacBio single-molecule real-time sequencing. Application of wglrTAPS to mouse embryonic stem cells showed the ability to detect previously uncovered CpG sites in problematic genomic regions. This method enhances the use of third-generation sequencing technologies for DNA epigenetics.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Biochemistry & Molecular Biology
Yibin Liu, Chun-Xiao Song
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Emily L. Sylwestrak, YoungJu Jo, Sam Vesuna, Xiao Wang, Blake Holcomb, Rebecca H. Tien, Doo Kyung Kim, Lief Fenno, Charu Ramakrishnan, William E. Allen, Ritchie Chen, Krishna Shenoy, David Sussillo, Karl Deisseroth
Summary: The integration of computational analysis of cellular activity and modern transcriptomic cell typology is crucial for understanding the cellular-level mechanisms underlying brain function and dysfunction. By applying this approach to the study of the habenula, researchers discovered how reward-predictive cues and reward outcomes are encoded in distinct genetically defined neural populations. They used genetically targeted recordings to train a nonlinear dynamical systems model, which revealed activity dynamics consistent with a line attractor. High-density, cell-type-specific electrophysiological recordings and optogenetic perturbation provided further evidence for this model. Reverse-engineering techniques predicted how Tac1(+) cells integrate reward history, and in vivo experimentation confirmed these predictions. This integrated approach allows for data-driven computational models to generate actionable hypotheses for cell-type-specific investigation in biological systems.
Article
Neurosciences
Hu Zeng, Jiahao Huang, Haowen Zhou, William J. Meilandt, Borislav Dejanovic, Yiming Zhou, Christopher J. Bohlen, Seung-Hye Lee, Jingyi Ren, Albert Liu, Zefang Tang, Hao Sheng, Jia Liu, Morgan Sheng, Xiao Wang
Summary: The STARmap PLUS method combines high-resolution spatial transcriptomics with protein detection, providing comprehensive insights into the spatiotemporal dynamics of complex diseases. By analyzing brain tissues of a mouse model of Alzheimer's disease, the authors uncover the cellular structure and molecular changes underlying disease progression.
NATURE NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
Xinyi Zhang, Xiao Wang, G. V. Shivashankar, Caroline Uhler
Summary: This study presents a computational framework, STACI, for integrating different spatial data modalities to identify molecular and functional alterations in tissues. STACI can predict spatial transcriptomic data and perform batch correction of gene expression and tissue morphology. The application of STACI in analyzing the progression of Alzheimer's disease has identified relevant nuclear morphometric and coupled gene expression features.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Chanan D. Sessler, Yiming Zhou, Wenbo Wang, Nolan D. Hartley, Zhanyan Fu, David Graykowski, Morgan Sheng, Xiao Wang, Jia Liu
Summary: This study demonstrates the successful assembly of electrically functional polymers in neurons using genetically targetable photosensitizer proteins, allowing for precise modulation of neuron membrane capacitance and intrinsic excitability.
Article
Chemistry, Multidisciplinary
Haiqi Xu, Jinfeng Chen, Jingfei Cheng, Linzhen Kong, Xiufei Chen, Masato Inoue, Yibin Liu, Skirmantas Kriaucionis, Meiping Zhao, Chun-Xiao Song
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Lin Zhang, Wenyan Song, Tingting Li, Yajuan Mu, Pan Zhang, Jingyan Hu, Houwen Lin, Jian Zhang, Hai Gao, Liang Zhang
Summary: APSK2 enhances excess PAPS production and promotes cancer development through its dynamic substrate recognition mechanism.
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)
Article
Cell Biology
Naoko Irie, Sun-Min Lee, Valentina Lorenzi, Haiqi Xu, Jinfeng Chen, Masato Inoue, Toshihiro Kobayashi, Carmen Sancho-Serra, Elena Drousioti, Sabine Dietmann, Roser Vento-Tormo, Chun-Xiao Song, M. Azim Surani
Summary: The commitment of germline during early human development is crucial for the subsequent gametogenesis. A study on PGC-like cells derived from human embryonic stem cells reveals that the induction of DMRT1 and SOX17 promotes epigenetic resetting and the expression of DNA methylation-sensitive genes, indicating the initiation of the germline commitment programme.
NATURE CELL BIOLOGY
(2023)