Review
Immunology
Audrey Dauba, Ahmed Amine Khamlichi
Summary: CSR is a crucial mechanism in adaptive immune responses, triggered by both T-cell-dependent and T-cell-independent antigens. Transcription of switch sequences and regulation within dynamic chromatin domains play key roles in controlling CSR.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Jana Koers, Casper Marsman, Juulke Steuten, Simon Tol, Ninotska I. L. Derksen, Anja ten Brinke, S. Marieke van Ham, Theo Rispens
Summary: In this study, the researchers used optimized in vitro culture conditions and in-depth assessment of B cell characteristics and signaling pathways to investigate the role of oxygen in regulating human naive B cell differentiation and class switch recombination. They found that normoxia promotes differentiation into functional antibody secreting cells, while a unique population of CD27(++) B cells is generated under hypoxia. Additionally, time-dependent transitions between hypoxic and normoxic oxygen levels during culture can direct different trajectories of human B cell differentiation and IgG class switch recombination.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Leticia Laura Niborski, Paul Gueguen, Mengliang Ye, Allan Thiolat, Rodrigo Nalio Ramos, Pamela Caudana, Jordan Denizeau, Ludovic Colombeau, Raphael Rodriguez, Christel Goudot, Jean-Michel Luccarini, Anne Soude, Bruno Bournique, Pierre Broqua, Luigia Pace, Sylvain Baulande, Christine Sedlik, Jean-Pierre Quivy, Genevieve Almouzni, Jose L. Cohen, Elina Zueva, Joshua J. Waterfall, Sebastian Amigorena, Eliane Piaggio
Summary: This study reveals that the inhibition of histone lysine methyltransferase Suv39h1 can delay tumor growth and enhance the anti-tumor effect of anti-PD-1 therapy. In the absence of Suv39h1, alternative activation pathways induced by anti-PD-1 allow the survival and differentiation of effector cells, resulting in a biomarker of clinical response. The findings suggest that Suv39h1 acts as an epigenetic checkpoint for tumor immunity.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Michael Jonathan Lehrke, Michael Jeremy Shapiro, Matthew J. Rajcula, Madeleine M. Kennedy, Shaylene A. McCue, Kay L. Medina, Virginia Smith Shapiro
Summary: ABCB7 is essential for early B cell development, proliferation, and class switch recombination. Loss of ABCB7 results in replication-induced DNA damage and slowed DNA replication in pro-B cells.
Article
Biochemistry & Molecular Biology
Yuyin Yi, Hua Zhu, Christian Klausen, Peter C. K. Leung
Summary: The study identifies SOX4 as a direct target gene induced by BMP2 in trophoblasts during early placental development. SOX4 plays a pro-invasive role in human trophoblasts and contributes to BMP2-enhanced trophoblast invasion by regulating genes associated with cell migration and extracellular matrix organization. Furthermore, SOX4 mediates BMP2-induced trophoblast invasion through binding to regulatory elements like enhancers.
Article
Multidisciplinary Sciences
Liat Stoler-Barak, Ethan Harris, Ayelet Peres, Hadas Hezroni, Mirela Kuka, Pietro Di Lucia, Amalie Grenov, Neta Gurwicz, Meital Kupervaser, Bon Ham Yip, Matteo Iannacone, Gur Yaari, John D. Crispino, Ziv Shulman
Summary: The protein kinase DYRK1A is essential for B cell-mediated protection from viral infection and effective vaccination by regulating class switch recombination (CSR). It plays a crucial role in B cell immune responses, including attenuating B cell proliferation and promoting the production of pathogen-eliminating antibodies.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Yijang Xu, Hang Zhou, Ginell Post, Hong Zan, Paolo Casali
Summary: The study demonstrates that Rad52 mediates IgD CSR through a microhomology-based DNA repair pathway, leading to the expression of IgD in B cells.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Kylie C. Moe, Jack N. Maxwell, Jing Wang, Cheyenne A. Jones, Grace T. Csaki, Andrea C. Florian, Alexander S. Romer, Daniel L. Bryant, Anthony L. Farone, Qi Liu, William P. Tansey, April M. Weissmiller
Summary: This study reveals the connection between residual SWI/SNF complexes and oncogenic processes, providing insights into the function of SWI/SNF in maintaining tumor cells.
Article
Immunology
Chloe Oudinet, Xuefei Zhang, Nadine Puget, Nia Kyritsis, Claire Leduc, Fatima-Zohra Braikia, Audrey Dauba, Frederick W. Alt, Ahmed Amine Khamlichi
Summary: Immunoglobulin class switch recombination plays a crucial role in humoral immune responses by altering the effector functions of antibodies. The A-NHEJ pathway in CSR shows a preference for longer junctional micro-homologies, and the molecular basis of S mu specificity remains unclear. Introducing the E mu enhancer into the S gamma 3 region confers the recombinational features of S mu to S gamma 3, indicating a bias for longer MH.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Cell Biology
Ahmed M. Refaat, Mikiyo Nakata, Afzal Husain, Hidetaka Kosako, Tasuku Honjo, Nasim A. Begum
Summary: B cells generate different classes of antibodies through class-switch recombination (CSR) mediated by classical non-homologous end joining (C-NHEJ). The RNA-binding protein HNRNPU promotes the joining of DNA breaks at the switch (S) regions through the 53BP1-shieldin DNA-repair complex. HNRNPU interacts with S region RNA/DNA G-quadruplexes and regulates R-loop and single-stranded DNA (ssDNA) accumulation. It facilitates CSR by forming and stabilizing the C-NHEJ ribonucleoprotein complex and preventing excessive R-loop accumulation, which can lead to genomic instability.
Article
Chemistry, Analytical
Jiekai Yin, Tianyu F. Qi, Lin Li, Yinsheng Wang
Summary: H3K36me3 modification is associated with various cellular processes and its aberrant expression is linked to cancer. This study used LC-PRM to analyze 154 RWE proteins and found that H3K36me3 regulates their chromatin occupancies. METTL14 and TRMT11 were identified as important in kidney cancer.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Rachel Bayley, Valerie Borel, Rhiannon J. Moss, Ellie Sweatman, Philip Ruis, Alice Ormrod, Amalia Goula, Rachel M. A. Mottram, Tyler Stanage, Graeme Hewitt, Marco Saponaro, Grant S. Stewart, Simon J. Boulton, Martin R. Higgs
Summary: The study suggests that methylation of histone H3 by SETD1A-BOD1L contributes to the recruitment of RIF1 to double-strand breaks, preventing excessive degradation of DNA ends and maintaining genome stability. This mechanism plays a crucial role in preserving telomere function and class switch recombination, and may be associated with the treatment and resistance of certain cancers.
Article
Biochemistry & Molecular Biology
Fritz Nagae, Giovanni B. Brandani, Shoji Takada, Tsuyoshi Terakawa
Summary: Translocases involved in eukaryotic DNA transcription, replication, and repair encounter nucleosomes formed by histone octamers wrapped around genomic DNA, triggering downstream repositioning of nucleosomes. This study identified a lane-switch mechanism for downstream repositioning, where wrapped DNA switches binding lanes after unwrapping, providing insights into transcription through nucleosomes and histone recycling.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Hongchang Zhao, Stella R. Hartono, Kirtney Mae Flores de Vera, Zheyuan Yu, Krishni Satchi, Tracy Zhao, Roger Sciammas, Lionel Sanz, Frederic Chedin, Jacqueline Barlow, Michela Di Virgilio
Summary: Class switch recombination is a crucial process for generating distinct antibody isotypes, and defects in this process are associated with autoimmune disorders and lymphoma genesis. In this study, we found that cells lacking two enzymes involved in removing R loops exhibited increased R loop formation and genome instability at the immunoglobulin heavy chain locus. However, this did not affect transcriptional activity, AID recruitment, or class switch recombination efficiency. Our findings suggest that senataxin and RNase H2 act together in removing R loops, promoting efficient repair and suppressing AID-dependent genome instability and insertional mutagenesis.
Article
Biology
Judith M. Hollander, Lingyun Li, Miraj Rawal, Si Kun Wang, Yue Shu, Ming Zhang, Heber C. Nielsen, Clifford J. Rosen, Li Zeng
Summary: Our study reveals the unique glucose metabolism signatures of chondrocytes and their transition from glycolysis to oxidative phosphorylation as they mature. We also highlight the critical role of IGF2 in maintaining a balanced glucose metabolism and preventing excessive oxidative phosphorylation.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Wenjun Hu, Nasim A. Begum, Samiran Mondal, Andre Stanlie, Tasuku Honjo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Multidisciplinary Sciences
Samiran Mondal, Nasim A. Begum, Wenjun Hu, Tasuku Honjo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Multidisciplinary Sciences
Afzal Husain, Nasim A. Begum, Takako Taniguchi, Hisaaki Taniguchi, Maki Kobayashi, Tasuku Honjo
NATURE COMMUNICATIONS
(2016)
Article
Immunology
Azza Al Ismail, Afzal Husain, Maki Kobayashi, Tasuku Honjo, Nasim A. Begum
INTERNATIONAL IMMUNOLOGY
(2017)
Article
Immunology
Makoto Matsumoto, Yuki Sasaki, Koubun Yasuda, Toshiyuki Takai, Masamichi Muramatsu, Tomohiro Yoshimoto, Kenji Nakanishi
INFECTION AND IMMUNITY
(2013)
Article
Immunology
Akikazu Murakami, Hayato Moriyama, Mina Osako-Kabasawa, Kanako Endo, Miyuki Nishimura, Keiko Udaka, Masamichi Muramatsu, Tasuku Honjo, Takachika Azuma, Takeyuki Shimizu
INTERNATIONAL IMMUNOLOGY
(2014)
Article
Immunology
Ashraf S. Yousif, Andre Stanlie, Nasim A. Begum, Tasuku Honjo
INTERNATIONAL IMMUNOLOGY
(2014)
Article
Virology
Zhe Wang, Kousho Wakae, Kouichi Kitamura, Satoru Aoyama, Guangyan Liu, Miki Koura, Ahasan M. Monjurul, Iwao Kukimoto, Masamichi Muramatsu
JOURNAL OF VIROLOGY
(2014)
Article
Biochemistry & Molecular Biology
Andre Stanlie, Ashraf S. Yousif, Hideo Akiyama, Tasuku Honjo, Nasim A. Begum
Article
Multidisciplinary Sciences
Ashraf S. Yousif, Andre Stanlie, Samiran Mondal, Tasuku Honjo, Nasim A. Begum
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Article
Multidisciplinary Sciences
Somayeh Sabouri, Maki Kobayashi, Nasim A. Begum, Jianliang Xu, Kouji Hirota, Tasuku Honjo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Article
Multidisciplinary Sciences
Ziwei Yin, Maki Kobayashi, Wenjun Hu, Koichi Higashi, Nasim A. Begum, Ken Kurokawa, Tasuku Honjo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Afzal Husain, Jianliang Xu, Hodaka Fujii, Mikiyo Nakata, Maki Kobayashi, Ji-Yang Wang, Jan Rehwinkel, Tasuku Honjo, Nasim A. Begum
Article
Biochemistry & Molecular Biology
Nasim A. Begum, Farazul Hague, Andre Stanlie, Afzal Husain, Samiran Mondal, Mikiyo Nakata, Takako Taniguchi, Hisaaki Taniguchi, Tasuku Honjo
Summary: Antibody class switch recombination (CSR) is a locus-specific genomic rearrangement that involves multiple factors, with Phf5a identified as a novel regulator of DNA repair in this process. Through maintaining chromatin integrity, Phf5a facilitates NHEJ-dependent DNA repair during CSR.
Article
Biology
Afzal Husain, Nasim A. Begum, Maki Kobayashi, Tasuku Honjo