Article
Multidisciplinary Sciences
Zhi Duan, Linda B. Baughn, Xiaohua Wang, Yongwei Zhang, Varun Gupta, Thomas MacCarthy, Matthew D. Scharff, Guojun Yu
Summary: The study shows that H3K79me2/3 and Dot1L are more abundant on the V region of Ig genes compared to the C region, with their knockout significantly reducing V region mutation and H3K79me2/3 levels. Knockout of Dot1L also leads to decreased Pol II levels and S2 phosphorylation at the IgH locus, along with reduced abundance of BRD4 and CDK9 on the V region. Treatment with inhibitors of BRD4 or CDK9 also affects SHM and Pol II S2P levels at the IgH locus, highlighting the importance of chromatin context and transcription dynamics in SHM.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Abigail K. Huffines, Krysta L. Engel, Sarah L. French, Yinfeng Zhang, Olga V. Viktorovskaya, David A. Schneider
Summary: Transcription of ribosomal DNA by RNA polymerase I (Pol I) is one of the initial steps in ribosome biogenesis. In this study, a mutant form of Pol I, rpa190-F1205H, was used to investigate the link between transcription elongation and ribosome assembly. The mutant Pol I showed increased pause propensity during processive transcription elongation, both in vitro and in vivo. Additionally, alternative pause site preferences were observed in the mutant Pol I in vivo. These findings provide novel insights into Pol I elongation properties and its impact on rRNA processing and ribosome assembly.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Guojun Yu, Yongwei Zhang, Varun Gupta, Jinghang Zhang, Thomas MacCarthy, Zhi Duan, Matthew D. Scharff
Summary: The H3.3 histone variant and its chaperone HIRA play important roles in regulating somatic hypermutation (SHM) of immunoglobulin variable regions in human B cells by affecting the expression levels of active transcription factors, transcription at the IgH locus, and chromatin accessibility. Furthermore, the H3.3G34V mutant inhibits SHM in Ramos cells by reducing the recruitment of elongation factors and ZMYND11 at the IgH variable and downstream switching regions. This study extends our understanding of how transcription-associated chromatin structure and accessibility contribute to SHM in human B cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Anastasia Rastokina, Jorge Cebrian, Negin Mozafari, Nicholas H. Mandel, C. I. Edvard Smith, Massimo Lopes, Rula Zain, Sergei M. Mirkin
Summary: The article describes an experimental system to analyze large-scale repeat expansions in cultured human cells. The system uses a shuttle plasmid that can replicate in human cells or be stably maintained in S. cerevisiae, and it contains a selectable cassette to detect repeat expansions in human cells upon plasmid transformation into yeast. The study observed massive expansions of GAA•TTC repeats, making it the first genetically tractable experimental system for studying large-scale repeat expansions in human cells.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Supawat Thongthip, Annika Carlson, Magdalena P. Crossley, Bjoern Schwer
Summary: The study uncovers different classes of DNA double-strand breaks in neural stem/progenitor cells, as well as the distribution of R-loop structures under different conditions. The findings suggest that further investigation is needed to understand the relationship between R-loops and recurrent DSB cluster formation.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Valeria Savoca, Julieta Rivosecchi, Alice Gaiatto, Annalisa Rossi, Riccardo Mosca, Irene Gialdini, Lorena Zubovic, Toma Tebaldi, Paolo Macchi, Emilio Cusanelli
Summary: This study reveals that the stability of TERRA transcripts is regulated by the RNA-binding protein associated with lethal yellow mutation (RALY). Depletion of RALY leads to decreased levels of TERRA, impaired localization of TERRA at telomeres, and ultimately telomere damage. Furthermore, TERRA interacts with the poly(A)-binding protein nuclear 1 (PABPN1), suggesting an interplay between RALY and PABPN1 in regulating TERRA stability.
Article
Biochemistry & Molecular Biology
Amr Elghondakly, Chih Hao Wu, Steven Klupt, Jonathan Goodson, Wade C. Winkler
Summary: Bacterial NusG interacts with RNA polymerase through its N-terminal domain, and its C-terminal domain forms dynamic interactions with various factors to affect transcription elongation. LoaP binds to a small RNA hairpin in the 50 leader region of its target operons with high affinity and specificity, expanding the repertoire of macromolecular interactions exhibited by NusG.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemical Research Methods
Lea H. Gregersen, Richard Mitter, Jesper Q. Svejstrup
Summary: The transcription of protein-coding genes is regulated by the dynamic association of co-factors with RNA polymerase II (RNAPII). This study presents an approach called elongation-factor-specific mNET capture (ELCAP) for investigating the function of RNAPII regulatory proteins. By applying ELCAP to the proteins SCAF4 and SCAF8, it was found that they are part of RNAPII elongation complexes containing 3' end processing factors but lacking splicing components. The ELCAP sequencing (ELCAP-seq) profiles of SCAF4 and SCAF8-RNAPII complexes accurately reflect their function as mRNA-anti-terminators and their competing functions at the end of genes.
CELL REPORTS METHODS
(2022)
Article
Biochemistry & Molecular Biology
Xueqing Wang, Quanlong Jiang, Yuanyuan Song, Zhidong He, Hongdao Zhang, Mengjiao Song, Xiaona Zhang, Yumin Dai, Oezlem Karalay, Christoph Dieterich, Adam Antebi, Ligang Wu, Jing-Dong J. Han, Yidong Shen
Summary: Ageing is a complex process with different features in different tissues. This study isolated cells from different tissues in worms and analyzed the transcriptomic changes during ageing, revealing the diversity of ageing across tissues and identifying tissue-specific longevity regulators. Additionally, novel factors controlling intestinal barrier integrity and sarcomere structure during ageing were discovered.
Article
Biochemistry & Molecular Biology
Gunhyoung Lim, Seungha Hwang, Kilwon Yu, Jin Young Kang, Changwon Kang, Sungchul Hohng
Summary: In this single-molecule study, researchers discovered that actively transcribing RNA polymerase can act as an efficient sensor for DNA double-strand breaks (DSBs), resulting in the formation of R-loops. The efficiency of R-loop formation is influenced by DNA end structures and can interfere with transcription and prevent subsequent rounds of transcription. These findings provide valuable insights into the initiation of DSB repair on transcription templates across different organisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Kang Wang, Honghong Wang, Conghui Li, Zhinang Yin, Ruijing Xiao, Qiuzi Li, Ying Xiang, Wen Wang, Jian Huang, Liang Chen, Pingping Fang, Kaiwei Liang
Summary: The study establishes an independent R loop CUT&Tag method that enables high-resolution mapping of native R loops, demonstrating the significant role of capture strategies in the discrepancies between different methods.
Article
Agronomy
Ruiting Zhang, Chao Shen, De Zhu, Yu Le, Nian Wang, Yuanxue Li, Xianlong Zhang, Zhongxu Lin
Summary: In this study, a QTL controlling cotton fiber length was fine-mapped to a 96.5-kb region containing an uncharacterized gene. The identified gene, GhFL10, is speculated to interact with NF-YA transcription factors to negatively regulate fiber elongation.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Multidisciplinary Sciences
Rafael Alcala-Vida, Jonathan Seguin, Caroline Lotz, Anne M. Molitor, Ibai Irastorza-Azcarate, Ali Awada, Nezih Karasu, Aurelie Bombardier, Brigitte Cosquer, Jose Luis Gomez Skarmeta, Jean-Christophe Cassel, Anne-Laurence Boutillier, Thomas Sexton, Karine Merienne
Summary: This study utilizes a Huntington's mouse model to analyze the chromatin landscape in the striatum, revealing that the Huntington's mutation accelerates age-related epigenetic and transcriptional changes, and affects 3D chromatin organization locally.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kai Zhou, Songkuan Zhuang, Fulong Liu, Yanheng Chen, You Li, Shihui Wang, Yuxuan Li, Huixin Wen, Xiaohua Lin, Jie Wang, Yue Huang, Cailing He, Nan Xu, Zongshu Li, Lang Xu, Zixuan Zhang, Lin-Feng Chen, Ruichuan Chen, Min Liu
Summary: P-TEFb modulates RNA polymerase II elongation through interaction with Brd4 and SEC. This study uncovers a novel mechanism for the reassembly of Cdk9 and CycT1 monomers on chromatin to form active P-TEFb.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Physical
Congmin Yuan, Eshani C. Goonetilleke, Ilona Christy Unarta, Xuhui Huang
Summary: The ongoing pandemic caused by SARS-CoV-2 highlights the need for effective therapeutics. Inhibition of SARS-CoV-2 RdRp by nucleotide analogs offers a promising antiviral strategy. Research on 2'-modified nucleotides shows varying inhibitory effects on SARS-CoV-2 RdRp, which could potentially aid in the rational design of antiviral agents.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Neurosciences
Alice Karam, Lars Tebbe, Chantal Weber, Nadia Messaddeq, Laurette Morle, Pascal Kessler, Uwe Wolfrum, Yvon Trottier
NEUROBIOLOGY OF DISEASE
(2015)
Article
Biochemistry & Molecular Biology
Marina G. Yefimova, Emile Bere, Anne Cantereau-Becq, Thomas Harnois, Annie-Claire Meunier, Nadia Messaddeq, Frederic Becq, Yvon Trottier, Nicolas Bourmeyster
HUMAN MOLECULAR GENETICS
(2016)
Review
Neurosciences
Laetitia Francelle, Caroline Lotz, Tiago Outeiro, Emmanuel Brouillet, Karine Merienne
FRONTIERS IN HUMAN NEUROSCIENCE
(2017)
Article
Clinical Neurology
Laurie Galvan, Laetitia Francelle, Marie-Claude Gaillard, Lucie de Longprez, Maria-Angeles Carrillo-de Sauvage, Geraldine Liot, Karine Cambon, Lev Stimmer, Sophie Luccantoni, Julien Flament, Julien Valette, Michel de Chaldee, Gwenaelle Auregan, Martine Guillermier, Charlene Josephine, Fanny Petit, Caroline Jan, Margot Jarrige, Noelle Dufour, Gilles Bonvento, Sandrine Humbert, Frederic Saudou, Philippe Hantraye, Karine Merienne, Alexis-Pierre Bemelmans, Anselme L. Perrier, Nicole Deglon, Emmanuel Brouillet
Article
Biochemistry & Molecular Biology
Hubert Aviolat, Yves Nomine, Sophie Gloria, Anna Bonhoure, David Hoffmann, Christine Ruhlmann, Helene Nierengarten, Frank Ruffenach, Pascal Villa, Yvon Trottier, Fabrice A. C. Klein
JOURNAL OF MOLECULAR BIOLOGY
(2018)
Review
Behavioral Sciences
David De Sa Nogueira, Karine Merienne, Katia Befort
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2019)
Article
Multidisciplinary Sciences
Stephanie Le Gras, Celine Keime, Anne Anthony, Caroline Lotz, Lucie De Longprez, Emmanuel Brouillet, Jean-Christophe Cassel, Anne-Laurence Boutillier, Karine Merienne
SCIENTIFIC REPORTS
(2017)
Article
Medicine, Research & Experimental
Snehajyoti Chatterjee, Raphaelle Cassel, Anne Schneider-Anthony, Karine Merienne, Brigitte Cosquer, Laura Tzeplaeff, Sarmistha Halder Sinha, Manoj Kumar, Piyush Chaturbedy, Muthusamy Eswaramoorthy, Stephanie Le Gras, Celine Keime, Olivier Bousiges, Patrick Dutar, Petnoi Petsophonsakul, Claire Rampon, Jean-Christophe Cassel, Luc Buee, David Blum, Tapas K. Kundu, Anne-Laurence Boutillier
EMBO MOLECULAR MEDICINE
(2018)
Article
Biochemistry & Molecular Biology
Samantha Carrillo-Rosas, Chantal Weber, Lorraine Fievet, Nadia Messaddeq, Alice Karam, Yvon Trottier
HUMAN MOLECULAR GENETICS
(2019)
Article
Cell Biology
Nicolas Merienne, Cecile Meunier, Anne Schneider, Jonathan Seguin, Satish S. Nair, Anne B. Rocher, Stephanie Le Gras, Celine Keime, Richard Faull, Luc Pellerin, Jean-Yves Chatton, Christian Neri, Karine Merienne, Nicole Deglon
Review
Clinical Neurology
Anna Niewiadomska-Cimicka, Yvon Trottier
Review
Neurosciences
Anna Niewiadomska-Cimicka, Antoine Hache, Yvon Trottier
FRONTIERS IN NEUROSCIENCE
(2020)
Article
Neurosciences
Anna Niewiadomska-Cimicka, Frederic Doussau, Jean-Baptiste Perot, Michel J. Roux, Celine Keime, Antoine Hache, Francoise Piguet, Ariana Novati, Chantal Weber, Binnaz Yalcin, Hamid Meziane, Marie-France Champy, Erwan Grandgirard, Alice Karam, Nadia Messaddeq, Aurelie Eisenmann, Emmanuel Brouillet, Hoa Huu Phuc Nguyen, Julien Flament, Philippe Isope, Yvon Trottier
Summary: SCA7 is a neurodegenerative disease characterized by motor incoordination, caused by polyglutamine expansion in ATXN7. Gene deregulation affects all cerebellar cell types, with Purkinje cells being the most affected, showing similar pathomechanisms as other types of ataxia.
JOURNAL OF NEUROSCIENCE
(2021)
Article
Neurosciences
Magdalena Surdyka, Ewelina Jesion, Anna Niewiadomska-Cimicka, Yvon Trottier, Zaneta Kalinowska-Poska, Maciej Figiel
Summary: This study investigates the targeted delivery of AAV to cerebellar cell populations using specific AAV serotypes, targeted injections, and transduction modes. The findings suggest that AAVrh10 is suitable for transducing neurons in a mode highly dependent on axonal terminals, while AAV-PHP.eB can selectively transduce Purkinje cells at axonal terminals in the deep cerebellar nuclei. These findings provide valuable insights for the development of gene delivery protocols for granule and Purkinje cells in the cerebellum using AAVrh10 and AAV-PHPeB.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Cell Biology
Anna Niewiadomska-Cimicka, Antoine Hache, Stephanie Le Gras, Celine Keime, Tao Ye, Aurelie Eisenmann, Imen Harichane, Michel J. J. Roux, Nadia Messaddeq, Emmanuelle Clerin, Thierry Leveillard, Yvon Trottier
Summary: SCA7 leads to reduced active transcription marks at gene promoters in the retina, with a preferential downregulation of highly expressed photoreceptor genes. The affected photoreceptor genes show altered histone acetylation, enhancer-related non-coding RNA expression, and increased RNA polymerase II pausing, suggesting impaired superenhancer-related features in SCA7.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)