Article
Multidisciplinary Sciences
Shengzhe Shang, Xia Li, Alexander Azzo, Tin Truong, Mikhail Dozmorov, Charles Lyons, Asit K. Manna, David C. Williams, Gordon D. Ginder
Summary: During human development, expression of fetal hemoglobin (HbF) is silenced in erythroid cells after birth. This silencing can be reversed to treat sickle cell anemia, and two potent factors involved are BCL11A and MBD2-NuRD. In this study, it is shown that MBD2-NuRD occupies the γ-globin gene promoter and forms a closed chromatin conformation, preventing activation by NF-Y. The isoform MBD2a is essential for the formation and stability of this repressor complex that includes BCL11A, MBD2a-NuRD, and the arginine methyltransferase, PRMT5.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Rodrigo O. de Castro, Agustin Carbajal, Luciana Previato de Almeida, Victor Goitea, Courtney T. Griffin, Roberto J. Pezza
Summary: Testis development and germ cell production rely on spermatogonia stem cells. The Chd4 chromatin remodeling complex is important for gene expression and maintenance of spermatogonia stem cells during gamete development.
EPIGENETICS & CHROMATIN
(2022)
Article
Multidisciplinary Sciences
Masayuki Kamei, Abigail J. Ameri, Aileen R. Ferraro, Yael Bar-Peled, Fangzhou Zhao, Christina L. Ethridge, Kathleen Lail, Mojgan Amirebrahimi, Anna Lipzen, Vivian Ng, Igor Grigoriev, Robert J. Schmitz, Yi Liu, Zachary A. Lewis
Summary: Polycomb Group (PcG) proteins are part of an epigenetic cell memory system that plays essential roles in multicellular development, stem cell biology, X chromosome inactivation, and cancer. Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to assemble transcriptionally repressed facultative heterochromatin in animals, plants, and many fungi. IMITATION SWITCH (ISW) is critical for normal transcriptional repression, nucleosome organization, and establishment of typical histone methylation patterns in facultative heterochromatin domains.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Kyle Brown, Pin Yu Chew, Steven Ingersoll, Jorge R. Espinosa, Anne Aguirre, Axel Espinoza, Joey Wen, Kalkidan Astatike, Tatiana G. Kutateladze, Rosana Collepardo-Guevara, Xiaojun Ren
Summary: This study reveals the assembly and regulation mechanism of Polycomb repressive complex 1 (PRC1). The findings demonstrate that the formation and dynamic properties of PRC1 condensates are sensitively regulated by their composition and stoichiometry.
Article
Biochemistry & Molecular Biology
Gang Wang, Yongyan Wang, Jiacheng Ni, Rongrong Li, Fengling Zhu, Ruyin Wang, Qiuzhen Tian, Qingwen Shen, Qinghua Yang, Jihua Tang, Monika W. Murcha, Guifeng Wang
Summary: The CRK1 gene in maize encodes a crucial assembly factor for mitochondrial complex I, which is essential for both the assembly of complex I and seed development in plants. The study also reveals the interaction between CRK1 and two other proteins, leading to their involvement in complex I assembly.
Article
Cell Biology
Shunpan Shu, Mingsheng Jiang, Xue Deng, Wenkai Yue, Xu Cao, Kai Zhang, Zeqing Wang, Hao He, Jihong Cui, Qiangqiang Wang, Kun Qu, Yanshan Fang
Summary: In this study, the downregulation of the Drosophila gene CG32529/GLAD in adult flies led to shortened lifespan and age-dependent brain degeneration. The regulation mainly affected the surface glia and cortex glia, disrupting the blood-brain barrier and glial meshwork. The upregulation of immune-related genes was found to be the most significant transcriptional change in response to RNAi-GLAD.
Article
Biochemistry & Molecular Biology
Jarod M. Waybright, Sarah E. Clinkscales, Kimberly D. Barnash, Gabrielle R. Budziszewski, Justin M. Rectenwald, Anna M. Chiarella, Jacqueline L. Norris-Drouin, Stephanie H. Cholensky, Kenneth H. Pearce, Laura E. Herring, Robert K. McGinty, Nathaniel A. Hathaway, Lindsey James
Summary: The study demonstrates how histone post-translational modifications are interpreted by reader proteins, affecting gene expression patterns. By targeting the chromodomain of MPP8, researchers identified a novel protein interaction and revealed its potential role in cancer metastasis.
ACS CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Thomas D. Jackson, Jordan J. Crameri, Linden Muellner-Wong, Ann E. Frazier, Catherine S. Palmer, Luke E. Formosa, Daniella H. Hock, Kenji M. Fujihara, Tegan Stait, Alice J. Sharpe, David R. Thorburn, Michael T. Ryan, David A. Stroud, Diana Stojanovski
Summary: Sideroflexins (SFXNs) are a family of proteins that have different functions in mitochondrial biology. Loss of SFXN4 leads to complex I assembly defect and it interacts with the core components of the mitochondrial complex I intermediate assembly complex.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Shantanu S. Iyer, Yidan Sun, Janine Seyfferth, Vinitha Manjunath, Maria Samata, Anastasios Alexiadis, Tanvi Kulkarni, Noel Gutierrez, Plamen Georgiev, Maria Shvedunova, Asifa Akhtar
Summary: The NSL complex is a transcriptional activator that plays a role in piRNA production and transposon repression in the Drosophila female germline. Knockdown of NSL complex subunits NSL1, NSL2, and NSL3 leads to reduced piRNA production from select piRNA clusters and derepression of transposons. NSL2 specifically binds to telomeric transposon promoters and its depletion also affects the levels of histone modifications and chromatin proteins associated with piRNA clusters.
LIFE SCIENCE ALLIANCE
(2023)
Article
Multidisciplinary Sciences
Charlotte Hodson, Jason K. K. Low, Sylvie van Twest, Samuel E. Jones, Paolo Swuec, Vincent Murphy, Kaima Tsukada, Matthew Fawkes, Rohan Bythell-Douglas, Adelina Davies, Jessica K. Holien, Julienne J. O'Rourke, Benjamin L. Parker, Astrid Glaser, Michael W. Parker, Joel P. Mackay, Andrew N. Blackford, Alessandro Costa, Andrew J. Deans
Summary: The RecQ-like helicase BLM cooperates with topoisomerase IIIa to dissolve double Holliday junctions in homologous recombination. Mutations in the Bloom syndrome complex can cause genome instability and cancer susceptibility, including breast cancer.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Qinglin Wang, Hao Wu, Jian Hu, Haijuan Fu, Yanghui Qu, Yijun Yang, Kathy Q. Cai, Andrey Efimov, Minghua Wu, Tim Yen, Yuan Wang, Zeng-Jie Yang
Summary: Nestin is significantly upregulated in human GBM compared to other types of glioma and its deficiency leads to apoptosis in tumor cells, interacts with beta II-tubulin, and sensitizes GBM cells to microtubule-destabilizing drugs.
MOLECULAR CANCER RESEARCH
(2021)
Article
Plant Sciences
Yasuyo Yamaoka, Seungjun Shin, Yuree Lee, Masaki Ito, Youngsook Lee, Ikuo Nishida
Summary: Phosphatidylserine (PS) plays a crucial role in root cytokinesis in Arabidopsis by mediating cargo vesicular trafficking required for cell plate formation, as the lack of PS leads to a delay in telophase progression during cell division.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Biology
Annemarie Kralt, Matthias Wojtynek, Jonas S. Fischer, Arantxa Agote-Aran, Roberta Mancini, Elisa Dultz, Elad Noor, Federico Uliana, Marianna Tatarek-Nossol, Wolfram Antonin, Evgeny Onischenko, Ohad Medalia, Karsten Weis
Summary: The nuclear pore complex (NPC) plays a central role in macromolecular exchange between the nucleus and cytoplasm, and the transmembrane protein Brl1 has been identified as an important factor in NPC assembly and fusion of the inner and outer nuclear membranes in budding yeast.
Article
Plant Sciences
Tracie N. N. Draeger, Maria-Dolores Rey, Sadiye Hayta, Mark Smedley, Abdul Kader Alabdullah, Graham Moore, Azahara C. C. Martin
Summary: Tetraploid and hexaploid wheat have multiple sets of similar chromosomes, with meiosis and fertility relying on synapsis and crossover formation only between homologous chromosomes. The major meiotic gene TaZIP4-B2 promotes crossover formation between homologous chromosomes and suppresses crossovers between related chromosomes in hexaploid wheat. Disruption of ZIP4 genes in tetraploid wheat results in a reduction in crossovers and delayed synapsis, confirming the importance of ZIP4 for efficient synapsis in wheat.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Luisa F. Bustamante-Jaramillo, Celia Ramos, Cristina Martin-Castellanos
Summary: Cyclins and CDKs play key roles in eukaryotic cell biology, coordinating physiological conditions with cell cycle progression. Meiosis is a specialized developmental program ensuring proper genetic propagation to the next generation, with meiosis-specific cyclins being widespread in evolution. Studies have shown that the meiosis-specific Crs1 cyclin in fission yeast exhibits diversified CDK functions, with roles in meiotic S-phase progression, chromosome architecture maintenance, and other key meiosis-specific events.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Correction
Genetics & Heredity
Karin Weiss, Hayley P. Lazar, Alina Kurolap, Ariel F. Martinez, Tamar Paperna, Lior Cohen, Marie F. Smeland, Sandra Whalen, Solveig Heide, Boris Keren, Pauline Terhal, Melita Irving, Motoki Takaku, John D. Roberts, Robert M. Petrovich, Samantha A. Schrier Vergano, Amy Kenney, Hanne Hove, Elizabeth DeChene, Shane C. Quinonez, Estelle Colin, Alban Ziegler, Melissa Rumple, Mahim Jain, Danielle Monteil, Elizabeth R. Roeder, Kimberly Nugent, Arie van Haeringen, Michael Gambello, Avni Santani, Livija Medne, Bryan Krock, Cara M. Skraban, Elaine H. Zackai, Holly A. Dubbs, Thomas Smol, Jamal Ghoumid, Michael J. Parker, Michael Wright, Peter Turnpenny, Jill Clayton-Smith, Kay Metcalfe, Hitoshi Kurumizaka, Bruce D. Gelb, Hagit Baris Feldman, Philippe M. Campeau, Maximilian Muenke, Paul A. Wade, Katherine Lachlan
GENETICS IN MEDICINE
(2020)
Article
Multidisciplinary Sciences
Yufeng Qin, Sara A. Grimm, John D. Roberts, Kaliopi Chrysovergis, Paul A. Wade
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Motoki Takaku, Sara A. Grimm, Bony De Kumar, Brian D. Bennett, Paul A. Wade
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Wendan Ren, Huitao Fan, Sara A. Grimm, Yiran Guo, Jae Jin Kim, Jiekai Yin, Linhui Li, Christopher J. Petell, Xiao-Feng Tan, Zhi-Min Zhang, John P. Coan, Linfeng Gao, Ling Cai, Brittany Detrick, Burak Cetin, Qiang Cui, Brian D. Strahl, Or Gozani, Yinsheng Wang, Kyle M. Miller, Sean E. O'Leary, Paul A. Wade, Dinshaw J. Patel, Gang Greg Wang, Jikui Song
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Linfeng Gao, Max Emperle, Yiran Guo, Sara A. Grimm, Wendan Ren, Sabrina Adam, Hidetaka Uryu, Zhi-Min Zhang, Dongliang Chen, Jiekai Yin, Michael Dukatz, Hiwot Anteneh, Renata Z. Jurkowska, Jiuwei Lu, Yinsheng Wang, Pavel Bashtrykov, Paul A. Wade, Gang Greg Wang, Albert Jeltsch, Jikui Song
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Hiroki Tanaka, Yoshimasa Takizawa, Motoki Takaku, Daiki Kato, Yusuke Kumagawa, Sara A. Grimm, Paul A. Wade, Hitoshi Kurumizaka
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Wendan Ren, Huitao Fan, Sara A. Grimm, Jae Jin Kim, Linhui Li, Yiran Guo, Christopher James Petell, Xiao-Feng Tan, Zhi-Min Zhang, John P. Coan, Jiekai Yin, Dae In Kim, Linfeng Gao, Ling Cai, Nelli Khudaverdyan, Burak Cetin, Dinshaw J. Patel, Yinsheng Wang, Qiang Cui, Brian D. Strahl, Or Gozani, Kyle M. Miller, Sean E. O'Leary, Paul A. Wade, Gang Greg Wang, Jikui Song
Summary: The study reveals that DNA methyltransferase DNMT1 acts as a reader for histone H4K20 trimethylation through its BAH1 domain, ensuring optimal maintenance of DNA methylation at repetitive LINE-1 elements.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Elizabeth M. Martin, Krystal A. Orlando, Kosuke Yokobori, Paul A. Wade
Summary: The identity and physiological function of mammary epithelial cells and breast cancers are influenced by a network of key transcriptional regulators, including estrogen receptor alpha, GATA3, and FOXA1. Recent large sequencing projects focusing on breast cancer have provided new insights into the role of mutation in transcription factors in altering tumor biology and transcriptional programs. The study of mutations in cancer and experimental exploration based on these findings are revealing more information on how estrogen receptor alpha, GATA3, and FOXA1 regulate gene transcription and contribute to shaping cell function.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Editorial Material
Cell Biology
Krystal A. Orlando, Paul A. Wade
Summary: FGFR-altered triple negative breast cancer develops adaptive resistance to FGFR inhibitor therapy, but a new study shows that dual inhibition of YAP or mTORC1 and FGFR has a synergistic effect on tumor growth. This indicates a potential new approach for treating this type of cancer.
NATURE CELL BIOLOGY
(2021)
Article
Immunology
Holly A. Morrison, Yang Liu, Kristin Eden, Margaret A. Nagai-Singer, Paul A. Wade, Irving C. Allen
Summary: Patients with gluten sensitivities may experience dysbiosis of the gut microbiome due to genetic factors and innate immune system signaling. The gene expression of multiple NLR family members, including upregulation of NLRX1 in active CeD patients, suggests a potential role of NLRs in maintaining gut microbiome composition. Loss of NLRX1 in mice alters microbiome composition, particularly after adherence to a GFD.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tanner B. Jefferson, Tianyuan Wang, Wendy N. Jefferson, Yin Li, Katherine J. Hamilton, Paul A. Wade, Carmen J. Williams, Kenneth S. Korach
Summary: Developmental exposure to DES causes long-term infertility and abnormal reproductive tract phenotypes. DES exposure alters mRNA and lncRNA expression in adult seminal vesicles, and affects histone modification patterns and DNA methylation. These findings suggest that DES exposure reprograms reproductive tract tissue differentiation through multiple epigenetic mechanisms.
Article
Genetics & Heredity
Elizabeth M. Martin, Sara A. Grimm, Zongli Xu, Jack A. Taylor, Paul A. Wade
Summary: This study compared the DNA methylation assessment using Illumina Mouse Methylation BeadChip (MMB) technology with the gold-standard method of whole-genome bisulfite sequencing (WGBS). The results showed that MMB produced similar measurements of methylation as WGBS, and the differentially methylated cytosines and regions identified by both methods overlapped and enriched for similar biological functions, indicating that MMB faithfully recapitulates the findings of WGBS.
Article
Biochemistry & Molecular Biology
Hisashi Ishida, Atsushi Matsumoto, Hiroki Tanaka, Aya Okuda, Ken Morishima, Paul A. Wade, Hitoshi Kurumizaka, Masaaki Sugiyama, Hidetoshi Kono
Summary: This study investigates the binding of the pioneer factor GATA3 to nucleosomal DNA and its impact on the conformation and dynamics of nucleosomes. The results show that GATA3's N-finger and C-finger bindings enhance DNA dissociation at one of the two DNA ends, triggering a conformational change in chromatin.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Ruifang Li, Sara A. Grimm, Paul A. Wade
Summary: This study developed an efficient and low-cost method for simultaneously profiling histone modification and DNA methylation status from the same cells, demonstrating its validity and potential for studying the genomic relationship between these epigenetic factors in low-input scenarios.
CELL REPORTS METHODS
(2021)
Article
Biochemical Research Methods
Ruifang Li, Sara A. Grimm, Paul A. Wade
Summary: This study developed a low-input ATAC&mRNA-seq method for simultaneous analysis of chromatin structure and gene regulation in thousands of cells, providing high-quality data. Integrative data analysis showed that this dual-omics approach can accurately and reliably generate two types of data, analyzing the association between promoter accessibility and gene expression.
CELL REPORTS METHODS
(2021)