Article
Oncology
Avery C. Lee, Sai Ravi Pingali, Javier A. Pinilla-Ibarz, Michael L. Atchison, Constantinos Koumenis, Yair Argon, Andrei Thomas-Tikhonenko, Carl De Trez, Chih-Chi Andrew Hu, Chih-Hang Anthony Tang
Summary: In this study, we found that the loss of activation-induced cytidine deaminase (AID) leads to worsened B cell chronic lymphocytic leukemia (CLL). AID-deficient CLL cells exhibit increased endoplasmic reticulum stress response and support leukemic growth through the IRE1/XBP1s pathway. Additionally, AID deficiency alters the tumor suppressive SMAD1/S1PR2 pathway and CLL cell homing. Patients with IgHV-unmutated CLL express higher levels of XBP1s mRNA compared to those with IgHV-mutated CLL.
Article
Immunology
Justin H. M. Heltzel, Robert W. Maul, William Yang, Patricia J. Gearhart
Summary: This study demonstrates that the distance between the V region and J gene does not affect the extent of mutation. The majority of mutations occur within a 1 kb region downstream of the J gene, regardless of the specific J gene used. This suggests that mutations are targeted by AID interactions with RNA polymerase II.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Immunology
Artem Krantsevich, Catherine Tang, Thomas MacCarthy
Summary: Somatic hypermutation (SHM) of Immunoglobulin (Ig) genes is crucial for antibody affinity maturation in B cells, with the mutagenic enzyme activation induced deaminase (AID) and DNA polymerase eta (Pol eta) playing key roles in introducing mutations at specific hotspots. By studying correlations between mutation sites, it was found that short-range interactions are dominated by AID and/or Pol eta overlapping hotspots, particularly in highly mutating IGHV sub-regions like CDRs. The results suggest that the hotspot preferences for AID and Pol eta have evolved to allow for greater interactions between induced mutations, shedding light on the mechanisms behind antibody affinity maturation.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Melanie Rogier, Jacques Moritz, Isabelle Robert, Chloe Lescale, Vincent Heyer, Arthur Abello, Ophelie Martin, Katia Capitani, Morgane Thomas, Anne-Sophie Thomas-Claudepierre, Brice Laffleur, Florence Jouan, Eric Pinaud, Karin Tarte, Michel Cogne, Silvestro G. Conticello, Evi Soutoglou, Ludovic Deriano, Bernardo Reina-San-Martin
Summary: The study revealed that the interaction between FAM72A and UNG2 regulates class-switch recombination and somatic hypermutation in B cells. This finding suggests a new mechanism for controlling DNA repair processes and immune responses, providing insights into the balance between error-prone and error-free repair pathways.
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
Immunology
Amanda Bello, Antonia Mueller, Gianna Hirth, Liane N. Giebeler, Katrin Boettcher, Stefanie Voigt, Berit Jungnickel
Summary: Secondary Ig diversification in B cells requires the enzyme activation-induced cytidine deaminase (AID) to introduce DNA damage into Ig genes. The regulation of this process is important to prevent lymphomagenesis. This study investigated the cell cycle contribution to the regulation of somatic hypermutation, class switch recombination, and Ig gene conversion in B cells. The results show that AID activity in G1 phase is essential for efficient secondary Ig diversification mechanisms.
JOURNAL OF IMMUNOLOGY
(2023)
Article
Cell Biology
Lizhen Wu, Vipul Shukla, Anurupa Devi Yadavalli, Ravi K. Dinesh, Dijin Xu, Anjana Rao, David G. Schatz
Summary: The DNA repair factor HMCES can strongly suppress deletions, facilitating the production of antigen-specific antibodies. Their findings propose a novel model for protecting Ig gene integrity during SHM.
GENES & DEVELOPMENT
(2022)
Article
Multidisciplinary Sciences
Heather E. Machado, Emily Mitchell, Nina F. Obro, Kirsten Kubler, Megan Davies, Daniel Leongamornlert, Alyssa Cull, Francesco Maura, Mathijs A. Sanders, Alex T. J. Cagan, Craig McDonald, Miriam Belmonte, Mairi S. Shepherd, Felipe A. Vieira Braga, Robert J. Osborne, Krishnaa Mahbubani, Inigo Martincorena, Elisa Laurenti, Anthony R. Green, Gad Getz, Paz Polak, Kourosh Saeb-Parsy, Daniel J. Hodson, David G. Kent, Peter J. Campbell
Summary: The lymphocyte genome is prone to many threats, including programmed mutation during differentiation, antigen-driven proliferation, and residency in diverse microenvironments. This study found that lymphocyte subsets carry more mutations than hematopoietic stem cells, with memory cells having higher burdens than naive cells. T cells accumulate mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for half of the additional mutations in lymphocytes. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering and the consequences of differentiation, proliferation, and residency in diverse microenvironments.
Article
Biochemical Research Methods
Hannah Spitzer, Scott Berry, Mark Donoghoe, Lucas Pelkmans, Fabian J. Theis
Summary: CAMPA is a deep learning framework that learns representations of molecular pixel profiles from multiplexed images. It clusters these representations to quantify subcellular landmarks and captures interpretable cellular phenotypes. Using this framework, the study reveals the changes in subcellular organization upon perturbation of RNA synthesis, RNA processing, or cell size, and uncovers the links between the molecular composition of membraneless organelles and cell-to-cell variability in bulk RNA synthesis rates.
Article
Multidisciplinary Sciences
Trevor van Eeuwen, Tao Li, Hee Jong Kim, Jose J. Gorbea Colon, Mitchell Parker, Roland L. Dunbrack, Benjamin A. Garcia, Kuang-Lei Tsai, Kenji Murakami
Summary: During transcription initiation, TFIIH marks RNA polymerase II by phosphorylating Ser5 of Rpb1's CTD, followed by modifications related to transcription elongation, mRNA processing, and histone dynamics. The structure of TFIIK helps extend the proposed model of the CTD path to TFIIH's active site.
Article
Biology
Shu-Hao Liou, Sameer K. Singh, Robert H. Singer, Robert A. Coleman, Wei-Li Liu
Summary: Liou et al. report a 4.6 angstrom resolution structure of the human p53/RNA polymerase II assembly, using single particle cryoelectron microscopy. This study suggests that p53's functional domains regulate the DNA binding activity of RNA polymerase II, providing insights into p53-regulated gene expression.
COMMUNICATIONS BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Kefei Yu
Summary: This mini review discusses recent advances in understanding the function and regulation of AID in B cells, including its molecular structure, advances in high throughput techniques, and the mechanism of AID-mediated class switch recombination. These studies have provided insights into the biochemical properties and function of AID.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2022)
Article
Multidisciplinary Sciences
Lara Djakovic, Thomas Hennig, Katharina Reinisch, Andrea Milic, Adam W. Whisnant, Katharina Wolf, Elena Weiss, Tobias Haas, Arnhild Grothey, Christopher S. Juerges, Michael Kluge, Elmar Wolf, Florian Erhard, Caroline C. Friedel, Lars Doelken
Summary: HSV-1 infection disrupts transcription termination by RNA Polymerase II and leads to increased chromatin accessibility downstream of genes. The immediate-early protein ICP22 of HSV-1 is found to induce open chromatin downstream of genes when transcription termination is disrupted, accompanied by histone loss downstream of affected genes.
NATURE COMMUNICATIONS
(2023)
Article
Hematology
Pablo Elias Morande, Xiao-Jie Yan, Julieta Sepulveda, Noe Seija, Maria Elena Marquez, Natalia Sotelo, Cecilia Abreu, Martina Crispo, Gabriel Fernandez-Grana, Natalia Rego, Therence Bois, Stephen P. Methot, Florencia Palacios, Victoria Remedi, Kanti R. Rai, Alejandro Buschiazzo, Javier M. Di Noia, Marcelo A. Navarrete, Nicholas Chiorazzi, Pablo Oppezzo
Summary: The study used chronic lymphocytic leukemia as a model and found a direct link between aberrant AID activity and cancer progression, whereby AID promotes aggressiveness in CLL and other B-cell neoplasms by selecting for CLL driver mutations with their oncogenic effects.
Article
Multidisciplinary Sciences
Yanfeng He, Shigeo Sato, Chieri Tomomori-Sato, Shiyuan Chen, Zach H. Goode, Joan W. Conaway, Ronald C. Conaway
Summary: The bZIP transcription factor ATF6 alpha is a master regulator of ER stress response genes, with the multifunctional RNA polymerase II transcription factor Elongin identified as a cofactor for ATF6 alpha-dependent transcription activation. Studies show that Elongin facilitates ATF6 alpha-dependent loading of Mediator at the promoters and enhancers of ER stress response genes, and depletion of Elongin leads to impaired transcription and recruitment of Mediator and its CDK8 kinase subunit during the ER stress response. Overall, these findings reveal a crucial role for Elongin as a loading factor for Mediator in the context of ER stress response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)