Article
Biology
Kevin H-C Wei, Carolus Chan, Doris Bachtrog
Summary: The study reveals that heterochromatin in Drosophila embryos is established through H3K9me3 enrichment over repetitive sequences, with initial nucleation sites appearing in specific retrotransposon families and gradually broadening into stable domains. Early nucleating transposable elements are associated with maternal piRNAs and early zygotic transcription, suggesting a model of piRNA-associated co-transcriptional silencing and additional mechanisms for site-restricted H3K9me3 nucleation at TEs in pre-cellular Drosophila embryos.
Article
Immunology
Rohit Chandwani, Terry C. Fang, Scott Dewell, Alexander Tarakhovsky
Summary: This study identifies the histone demethylase Kdm4d/JMJD2d as a positive regulator of type I interferon responses. It demonstrates that the demethylase affects both enhancer transcription and dynamic H3K9me2 modification at associated promoters, thereby modulating transcriptional responses.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Cell Biology
Baoyu Chen, Yuwen Zhu, Junliang Chen, Yifei Feng, Yong Xu
Summary: This study reveals that differential TCL expression in malignant colorectal cancer cells is associated with histone H3K9 methylation, and the lysine demethylase KDM4B is essential for TCL transcription. KDM4B interacts with the transcription factor ERG1 to activate TCL transcription by facilitating the assembly of pre-initiation complex on the TCL promoter, ultimately influencing migration and invasion of CRC cells. Additionally, upregulation of KDM4B in advanced stage CRC specimens suggests it may serve as a potential therapeutic target for CRC intervention.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Oncology
Qiao Li, Qingsan Zhu
Summary: The AlkB family has the ability to catalyze the demethylation of various substrates, regulating gene transcription and expression. Altered methylation of DNA, RNA, and histones is frequently observed in cancer. The AlkB homologs play important roles in cancer genesis, progression, metastasis, and invasion, and may serve as new targets for tumor diagnosis and treatment.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tianqi Wang, Yang Liu, Hailin Zhang, Zhen Fang, Rong Zhang, Wenqing Zhang, Yan Fan, Rong Xiang
Summary: Crystal complex structures of two KDM4D inhibitors, OWS and 10r, have been determined, offering new insights for rational design and optimization of KDM4D inhibitors.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Oncology
Pedro A. Lazo
Summary: Chromatin remodeling plays a crucial role in tumor biology. Targeting epigenetic enzymes and chromatin kinases can be a novel strategy for cancer treatment. Targeting these enzymes can enhance tumor cell sensitivity to treatment and improve treatment outcomes.
Article
Biochemistry & Molecular Biology
Jinpeng Du, Wenwei Liao, Haichuan Wang, Guimin Hou, Min Liao, Lin Xu, Jiwei Huang, Kefei Yuan, Xiangzheng Chen, Yong Zeng
Summary: This study demonstrates the essential role of MDIG in liver regeneration by regulating histone methylation to alter chromatin accessibility. MDIG deficiency results in impaired liver regeneration and delayed cell cycle progression, and it is found that MDIG regulates Myc by modifying chromatin accessibility.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)
Article
Biochemistry & Molecular Biology
Qian Li, Weiyue Sun, Chao Chen, Dingxiao Dong, Yaoliang Cao, Yanlong Dong, Lijie Yu, Zhonghui Yue, Xiaoxia Jin
Summary: This study identified the SlJMJ524 gene highly expressed in tomato, and found that its overexpression enhanced the tolerance of transgenic plants to cadmium by increasing the expression of genes involved in heavy metal uptake and flavonoid synthesis. This research advances our understanding of the functional role of JMJs and provides a potential approach for improving cadmium tolerance and breeding of crops and plants.
Article
Chemistry, Multidisciplinary
Zhipeng A. Wang, Jonathan W. Markert, Samuel D. Whedon, Maheeshi Yapa Abeywardana, Kwangwoon Lee, Hanjie Jiang, Carolay Suarez, Hening Lin, Lucas Farnung, Philip A. Cole
Summary: The reversible acetylation of histone lysine residues is controlled by the action of acetyltransferases and deacetylases (HDACs), which regulate chromatin structure and gene expression. One member of the HDAC family, Sirt6, efficiently deacetylates several histone H3 acetylation sites on nucleosomes. The structure of Sirt6 bound to a nucleosome reveals its extensive interactions with H2A/H2B acidic patch and nucleosomal DNA, providing insights into how HDACs target and regulate chromatin.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Engineering, Environmental
Ming-hao Liu, Qian Zhang, Wan-tong Yu, Jian-Ge Qiu, Hui-min Yuan, Chuan-rui Wang, Bing-Hua Jiang, Yan Zhang, Chun-yang Zhang
Summary: This study developed a single-molecule detection method for simultaneous quantification of RNA demethylases FTO and ALKBH3. The method exhibited high sensitivity and could measure enzyme kinetic parameters, screen inhibitors, and quantify cellular FTO and ALKBH3 activities with single-cell sensitivity. Furthermore, it could differentiate the levels of FTO and ALKBH3 in healthy human tissues and breast cancer patients, providing a robust platform for biomedical research and clinical diagnosis.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Cell Biology
Yuechao Sun, Weipeng Gong, Song Zhang
Summary: The study revealed the dual role of METTL3 in colorectal cancer as both an m6A writer and a transcription regulator, working together in the same signaling pathway to drive the malignancy of colorectal cancer.
CELL DEATH & DISEASE
(2023)
Article
Biochemistry & Molecular Biology
Wen Shao, Xianju Bi, Yixuan Pan, Boyang Gao, Jun Wu, Yafei Yin, Zhimin Liu, Mengyuan Peng, Wenhao Zhang, Xu Jiang, Wenlin Ren, Yanhui Xu, Zhongyang Wu, Kaili Wang, Ge Zhan, J. Yuyang Lu, Xue Han, Tong Li, Jianlong Wang, Guohong Li, Haiteng Deng, Bing Li, Xiaohua Shen
Summary: A new study suggests that RNA-binding proteins constitute half of the chromatin proteome in embryonic stem cells, with some colocalizing with RNA polymerase II at promoters and enhancers. These RNA-binding proteins inhibit premature release of Pol II and enhance the formation of transcription condensates using RNA as multivalent molecules, ultimately promoting polymerase engagement and activity. The study proposes a synergistic interplay between promoter-associated RNAs and their binding proteins to facilitate active transcription through phase separation of polymerase condensates.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Baohui Yuan, He Liu, Xiaohua Pan, Xiaoliang Dong, Le-Feng Qu, Jia Sun, Li-Long Pan
Summary: LSD1 plays a crucial role in neointima formation, and its overexpression is associated with neointima formation. Knockdown of LSD1 significantly reduces neointima formation and inhibits platelet-derived growth factor-induced VSMC proliferation. Moreover, LSD1 overexpression exhibits opposite effects in vivo and in vitro.
BIOCHEMICAL PHARMACOLOGY
(2022)
Article
Cell Biology
Jun-Cheng Guo, Zhuo Liu, Yi-Jun Yang, Min Guo, Jian-Quan Zhang, Jin-Fang Zheng
Summary: The study revealed that KDM5B regulates the YTHDF3/ITGA6 axis by inhibiting the expression of miR-448 to promote the occurrence of HCC.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2021)
Article
Cell & Tissue Engineering
Ruimin Xu, Sen Li, Qiu Wu, Chong Li, Manxi Jiang, Lei Guo, Mo Chen, Lingyue Yang, Xin Dong, Hong Wang, Chenfei Wang, Xiaoyu Liu, Xianghong Ou, Shaorong Gao
Summary: The deposition of H3K9me3 in human oocytes and early embryos has been found to be stage-specific, with enhancer-like regions being temporarily established during the 8-cell stage and greater stability during the blastocyst stage. The genes DUX and KRAB-ZNFs have been identified as potential factors involved in the establishment of stage-specific H3K9me3. Furthermore, the presence of bivalent chromatin domains in human blastocysts suggests priming for lineage differentiation.
Article
Biochemistry & Molecular Biology
Lital Lahav-Ariel, Michal Caspi, Prathamesh T. Nadar-Ponniah, Natalie Zelikson, Ilse Hofmann, Kirsten K. Hanson, Werner W. Franke, Ella H. Sklan, Karen B. Avraham, Rina Rosin-Arbesfeld
Review
Genetics & Heredity
Feras E. Machour, Nabieh Ayoub
TRENDS IN GENETICS
(2020)
Article
Immunology
Idan Yelin, Noga Aharony, Einat Shaer Tamar, Amir Argoetti, Esther Messer, Dina Berenbaum, Einat Shafran, Areen Kuzli, Nagham Gandali, Omer Shkedi, Tamar Hashimshony, Yael Mandel-Gutfreund, Michael Halberthal, Yuval Geffen, Moran Szwarcwort-Cohen, Roy Kishony
CLINICAL INFECTIOUS DISEASES
(2020)
Article
Cell Biology
Prathamesh T. Nadar-Ponniah, Shahar Taiber, Michal Caspi, Tal Koffler-Brill, Amiel A. Dror, Ronen Siman-Tov, Moran Rubinstein, Krishnanand Padmanabhan, Chen Luxenburg, Richard A. Lang, Karen B. Avraham, Rina Rosin-Arbesfeld
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Nada Danial-Farran, Elena Chervinsky, Prathamesh T. Nadar-Ponniah, Eran Cohen Barak, Shahar Taiber, Morad Khayat, Karen B. Avraham, Stavit A. Shalev
Summary: A new variant of the COCH gene was found to have a loss-of-function effect, resulting in a significant decrease in cochlin translation, which has a dramatic impact on the accuracy of genetic counseling for carriers of LOF variants in COCH.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Multidisciplinary Sciences
Ariel Afek, Honglue Shi, Atul Rangadurai, Harshit Sahay, Alon Senitzki, Suela Xhani, Mimi Fang, Raul Salinas, Zachery Mielko, Miles A. Pufall, Gregory M. K. Poon, Tali E. Haran, Maria A. Schumacher, Hashim M. Al-Hashimi, Raluca Gordan
Article
Genetics & Heredity
Laila A. Bishara, Feras E. Machour, Samah W. Awwad, Nabieh Ayoub
Summary: Studies have shown that NELF-E interacts with BRCA1, facilitating the formation of BRCA1 IRIF in HCC cells and reducing RAD51 IRIF. NELF-E deficiency in Hep3B cells results in impaired HDR of DSBs induced by the CRISPR-Cas9 system.
Article
Biochemistry & Molecular Biology
Sven Giese, Theresia Reindl, Patrick Y. A. Reinke, Lilach Zattelman, Roman Fedorov, Arnon Henn, Manuel H. Taft, Dietmar J. Manstein
Summary: Myosin-1C is a single-headed, short-tailed member of the myosin class I subfamily. Alternative splicing of the MYO1C gene in vertebrates produces three isoforms with different N-terminal extensions. These extensions affect the chemomechanical coupling of the myosin-1C isoforms, leading to differences in power output, velocity, and resistive force. The N-terminal extensions reduce the length of the working stroke and the rate of ADP release, especially in myosin-1C35. The functional differences between isoforms are further amplified by the presence of external loads.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Alon Senitzki, Jessy Safieh, Vasundhara Sharma, Dmitrij Golovenko, Yael Danin-Poleg, Alberto Inga, Tali E. Haran
Summary: Research reveals that p53 exhibits hemi-specific binding and that sequences flanking the response elements can modulate p53 binding and activity. The arrangement of p53 half-sites within its response elements has been fine-tuned to optimize response levels, with directionality in the arrangement partly encoded in the structural properties of the elements. The orientation of half-sites in certain response elements minimizes the effects of flanking sequences, indicating a mechanism for optimizing p53 response levels.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Feras E. Machour, Enas R. Abu-Zhayia, Samah W. Awwad, Tirza Bidany-Mizrahi, Stefan Meinke, Laila A. Bishara, Florian Heyd, Rami Aqeilan, Nabieh Ayoub
Summary: The RNA-binding protein RBM6 has been identified as a novel regulator of DNA double-strand break repair and its deficiency can lead to increased sensitivity of cancer cells, particularly in breast tumors, to certain treatments. The loss of RBM6 in metastatic breast tumors compared to primary tumors suggests it may serve as a potential therapeutic target for advanced breast cancer.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Qiang Zhang, Dimitrios-Ilias Balourdas, Bruno Baron, Alon Senitzki, Tali E. Haran, Klas G. Wiman, Thierry Soussi, Andreas C. Joerger
Summary: The extremophile Alvinella pompejana, an annelid worm living near hydrothermal vents in the Pacific Ocean, has a p53 family gene with a highly thermostable DNA-binding domain, which may play a crucial role in maintaining genome integrity.
CELL DEATH & DISEASE
(2022)
Article
Multidisciplinary Sciences
Rani Zananiri, Sivasubramanyan Mangapuram Venkata, Vera Gaydar, Dan Yahalom, Omri Malik, Sergei Rudnizky, Oded Kleifeld, Ariel Kaplan, Arnon Henn
Summary: RecBCD helicase has additional non-catalytic ATP binding sites that enhance ATP flux to catalytic sites and enable fast unwinding even when ATP is scarce. The importance and functionality of these auxiliary binding sites are demonstrated by their impact on E.coli survival after exposure to damage-inducing radiation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Xiao-Jun Li, Charles Morgan, Prathamesh T. Nadar-Ponniah, Waldemar Kolanus, Angelika Doetzlhofer
Summary: Reactivation of LIN28B and TRIM71 enhances the regenerative potential of P5 cochlear supporting cells, allowing them to dedifferentiate and form progenitor-like cells, which leads to increased hair cell formation.
Meeting Abstract
Biophysics
Sivasubramanyan Mangapuram Venkata, Rani Zananiri, Vera Gaydar, Oded Kleifeld, Ariel Kaplan, Arnon Henn
BIOPHYSICAL JOURNAL
(2020)
Letter
Cell Biology
Enas R. Abu-Zhayia, Feras E. Machour, Nabieh Ayoub
JOURNAL OF MOLECULAR CELL BIOLOGY
(2019)