Article
Cell Biology
Vincent Gaggioli, Calvin S. Y. Lo, Nazaret Reveron-Gomez, Zuzana Jasencakova, Heura Domenech, Hong Nguyen, Simone Sidoli, Andrey Tvardovskiy, Sidrit Uruci, Johan A. Slotman, Yi Chai, Joao G. S. C. Souto Goncalves, Eleni Maria Manolika, Ole N. Jensen, David Wheeler, Sriram Sridharan, Sanjiban Chakrabarty, Jeroen Demmers, Roland Kanaar, Anja Groth, Nitika Taneja
Summary: Chromatin signalling cascade, regulated by a checkpoint, activates the histone methyltransferase EHMT2/G9a to assemble heterochromatin at stressed replication forks. G9a, together with SUV39h1, induces chromatin compaction through accumulating repressive modifications, H3K9me1/me2/me3, at stressed replication forks. Untimely heterochromatin disassembly by demethylase KDM3A exposes forks to PRIMPOL-mediated genome instability, leading to chemotherapeutic drug sensitivity.
NATURE CELL BIOLOGY
(2023)
Article
Reproductive Biology
Jingjing Qian, Fan Guo
Summary: Both human and mouse oocytes have unique epigenomic landscapes. New measurement technologies allow us to study genome regulation at different levels, including DNA methylation, transcription, and chromatin accessibility. Recent studies have also explored the relationship between different histone modifications and DNA methylation, revealing the mechanisms behind oocyte DNA methylome formation.
BIOLOGY OF REPRODUCTION
(2022)
Article
Cell Biology
Fatma Dogan, Rakad M. Kh Aljumaily, Mark Kitchen, Nicholas R. Forsyth
Summary: Research has shown that physoxia affects the DNA methylation patterns and enzymatic activity in human mesenchymal stem cells, resulting in upregulation of SOX2, decreased levels of 5mC and 5hmC, and reduced transcription of DNA methyltransferase and Ten-eleven translocation enzyme. This suggests that oxygen sensitivity plays a role in epigenetic regulation within stem cells, potentially influencing their therapeutic development.
Article
Biochemistry & Molecular Biology
Boxun Zhao, Jill A. Madden, Jasmine Lin, Gerard T. Berry, Monica H. Wojcik, Xuefang Zhao, Harrison Brand, Michael Talkowski, Eunjung Alice Lee, Pankaj B. Agrawal
Summary: This study reports the discovery of a de novo transposon insertion in the SRCAP gene, which causes neurodevelopmental disorders in a 28-year-old female. The insertion is a full-length antisense-oriented SVA insertion and originates from an intron of a highly expressed long non-coding RNA in testis. The insertion results in significant depletion of SRCAP expression and exon skipping.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Cardiac & Cardiovascular Systems
Concetta Schiano, Carolina Balbi, Jacopo Burrello, Antonio Ruocco, Teresa Infante, Carmela Fiorito, Stefano Panella, Lucio Barile, Ciro Mauro, Giuseppe Vassalli, Claudio Napoli
Summary: DNA methylation is associated with cardiovascular diseases (CVDs). This study found that circulating extracellular vesicles (EVs) from acute coronary syndrome (ACS) patients showed increased levels of DNA methyltransferases (DNMTs) and reduced Ten-eleven translocation (TET) genes. By treating lymphocytes from healthy individuals with EVs, it was discovered that DNMTs carried by EVs play an important role in DNA methylation. Furthermore, ACS-EVs were found to regulate signaling pathways and gene expression in target cells.
Article
Biochemistry & Molecular Biology
Massimo Carraro, Ivo A. Hendriks, Colin M. Hammond, Victor Solis-Mezarino, Moritz Volker-Albert, Jonas D. Elsborg, Melanie B. Weisser, Christos Spanos, Guillermo Montoya, Juri Rappsilber, Axel Imhof, Michael L. Nielsen, Anja Groth
Summary: This study expands the role of ASF1 in histone dynamics by uncovering the interaction between ASF1 and SPT2 subunits. It also reveals the unique functionality of DAXX in the histone chaperone network, recruiting histone methyltransferases to catalyze H3K9me3 on newly synthesized histone H3.3-H4 prior to deposition onto DNA. Thus, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly.
Article
Genetics & Heredity
Ryuji Uehara, Wan Kin Au Yeung, Keisuke Toriyama, Hiroaki Ohishi, Naoki Kubo, Hidehiro Toh, Isao Suetake, Kenjiro Shirane, Hiroyuki Sasaki
Summary: This study investigates the role of histone-tail recognition by DNMT3A in mediating de novo DNA methylation in mammalian oocytes. It shows that disruption of the interaction between the ADD domain of DNMT3A and histone H3 tail leads to mosaic loss of DNA methylation, resulting in lethality of derived embryos during mid-to-late gestation and stochastic multi-locus imprinting defects. These findings highlight the importance of the ADD domain in efficient de novo DNA methylation and provide a model for studying the stochastic inheritance of epigenetic perturbations in germ cells.
Article
Genetics & Heredity
Yin Shen, Ling-Ling Chen, Junxiang Gao
Summary: Chromatin accessibility, a key structural feature for understanding gene transcription regulation, is dynamic during stress and developmental transitions. CharPlant, a bioinformatics tool, is developed for de novo prediction of OCRs in plant genomes, showing promise in prediction power and computational efficiency. This tool fills the gap of identifying potential OCRs in whole genomes.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Vivekanandan Ramalingam, Xinyang Yu, Brian D. Slaughter, Jay R. Unruh, Kaelan J. Brennan, Anastasiia Onyshchenko, Jeffrey J. Lange, Malini Natarajan, Michael Buck, Julia Zeitlinger
Summary: Lola-I, a Drosophila zinc finger transcription factor, can regulate the promoter state independently of gene activation. It makes the target promoters accessible and acquire paused RNA polymerase II throughout the embryo. This promoter transition is crucial for tissue-specific target gene activation. Lola-I mediates this function by depleting promoter nucleosomes.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Xionghui Zhou, Haizi Zheng, Hailu Fu, Kelsey L. Dillehay McKillip, Susan M. Pinney, Yaping Liu
Summary: A new method has been developed to characterize the hotspots of cell-free DNA fragmentation and it has been found that hotspots in early-stage liver cancer show global hypo-fragmentation and are associated with the development of hepatocellular carcinoma and cancer stem cells. These hotspots vary across different early-stage cancers and demonstrate high performance in the diagnosis and tissue-of-origin identification of early-stage cancers.
Article
Plant Sciences
Koichiro Otake, Kazuto Kugou, Jekson Robertlee, Jun-ichirou Ohzeki, Koei Okazaki, Shigeru Hanano, Seiji Takahashi, Daisuke Shibata, Hiroshi Masumoto
Summary: Genetic modifications in plants are essential for research, and transgene expression is influenced by the chromatin structure of the insertion site. This study demonstrates a strategy for manipulating chromatin in plant cells by tethering epigenetic effectors to a synthetic DNA platform. The results highlight the intrinsic interplay between DNA and histone methylation mechanisms in plants and suggest that the induced epigenetic modification states can be maintained even when the effector tethering is inhibited. This system provides a tool to study diverse epigenetic effectors and chromatin assembly mechanisms in plant cells.
Article
Multidisciplinary Sciences
Jonathan Markert, Keda Zhou, Karolin Luger
Summary: The study demonstrates that SMARCAD1 is capable of transferring the entire histone octamer from one DNA segment to another in an ATP-dependent manner, as well as de novo nucleosome assembly from histone octamer due to its ability to simultaneously bind all histones. The low-resolution cryo-electron microscopy structure of SMARCAD1 in complex with a nucleosome reveals a unique engagement of its adenosine triphosphatase domains with the substrate, providing mechanistic insights into nucleosome disassembly and reassembly induced by SMARCAD1.
Article
Cell Biology
Nan Wang, Tianzi Li, Wanyu Liu, Jinhua Lin, Ke Zhang, Zhenhao Li, Yanfei Huang, Yufei Shi, Meilan Xu, Xuekui Liu
Summary: PRMT5-mediated G3BP2-R468me2 enhances the binding to deubiquitinase USP7, ensuring the deubiquitination and stabilization of G3BP2. PRMT5-dependent methylation of G3BP2 is required for its deubiquitination and stabilization by USP7. The PRMT5-USP7-G3BP2 regulatory axis serves as a lipid metabolism reprogramming mechanism in tumorigenesis and could be a potential therapeutic target for head and neck squamous carcinoma.
CELL DEATH & DISEASE
(2023)
Review
Chemistry, Multidisciplinary
Dan Qiao, Yuang Chen, Haojing Tan, Ruhong Zhou, Jiandong Feng
Summary: This review discusses the crucial relationship between design and structure of transmembrane nanopores, compares different building blocks of bottom-up built nanopores in terms of construction methods, structures and applications, and describes important advances in de novo designed proteins from the perspective of theoretical simulations. An outlook for artificial intelligence-assisted nanopore design is also provided.
SCIENCE CHINA-CHEMISTRY
(2022)
Article
Biology
Shuangying Jiang, Yuanwei Tang, Liang Xiang, Xinlu Zhu, Zelin Cai, Ling Li, Yingxi Chen, Peishuang Chen, Yuge Feng, Xin Lin, Guoqiang Li, Jafar Sharif, Junbiao Dai
Summary: Synthetic genomics has opened new avenues for the functional study of viral and microbial genomes, as well as providing a method for constructing larger genomes of higher organisms. The study introduces an efficient pipeline for constructing large DNA fragments and describes a scar-free engineering method for assembling sequences. This method offers a standard framework for producing long DNA molecules crucial for synthetic genomics and metabolic engineering.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
GuoQing Ying, FangFang Zhu, Yu Yi, JianShu Chen, JianFeng Mei, YanLu Zhang, ShuQing Chen
BIOTECHNOLOGY LETTERS
(2015)
Review
Cell Biology
Guoqing Ying, Yanlu Zhang, Guoqiang Tang, Shuqing Chen
CELLULAR IMMUNOLOGY
(2015)
Article
Immunology
Yanlu Zhang, Xueping Zhou, Baohua Zhou
EUROPEAN JOURNAL OF IMMUNOLOGY
(2012)
Article
Immunology
Weiguo Yao, Yanlu Zhang, Rukhsana Jabeen, Evelyn T. Nguyen, David S. Wilkes, Robert S. Tepper, Mark H. Kaplan, Baohua Zhou
Article
Immunology
Yanlu Zhang, Baohua Zhou
IMMUNOLOGIC RESEARCH
(2012)
Article
Immunology
Liying Lei, Yanlu Zhang, Weiguo Yao, Mark H. Kaplan, Baohua Zhou
JOURNAL OF IMMUNOLOGY
(2011)