Article
Virology
Gary Z. Wang, Stephen P. Goff
Summary: This study reveals the essential role of p12 protein in tethering viral DNA to host chromatin to allow loading of histones onto the viral DNA. Mutants lacking tethering activity fail to acquire histones, retain capsid and nucleocapsid proteins, and are poorly transcribed, defining a new requirement for a viral protein in chromatinization of viral DNA.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xiaojun Ma, Ashwin Somasundaram, Zengbiao Qi, Douglas J. Hartman, Harinder Singh, Hatice Ulku Osmanbeyoglu
Summary: The study introduces a computational method called SPaRTAN that can link cell-surface receptors with transcription factors to predict the relationships between signaling and transcriptional regulators. Applied to immune cells and tumor infiltrating CD8(+) T cells, the method offers a new approach to developing cell-context-specific maps of the interface between signaling and transcriptional regulators.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Microbiology
Fanny Nazaret, Genevieve Alloing, Karine Mandon, Pierre Frendo
Summary: The relationship between plants and associated soil microorganisms plays a crucial role in ecosystem functioning. This review focuses on MarR-like transcriptional regulators and their mechanisms of plant-signal perception, including how they help bacteria cope with the rhizosphere and plant endosphere, regulate the beneficial functions of Plant-Growth-Promoting Bacteria, and regulate the virulence of phytopathogenic bacteria.
Article
Fisheries
Xiaobing Lu, Zhe Hu, Hao Huang, Meisheng Yi, Kuntong Jia
Summary: MOV10 is highly expressed in the blood of sea perch and its expression can be activated by IFNc, IFNh, and IFN & gamma;. VHSV infection upregulates MOV10 expression and enhances IFNh expression, showing strong antiviral activity. This study provides a basis to investigate the immune escape of VHSV.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Heankel Lyons, Reshma T. Veettil, Prashant Pradhan, Christy Fornero, Nancy De La Cruz, Keiichi Ito, Mikayla Eppert, Robert G. Roeder, Benjamin R. Sabari
Summary: Components of transcriptional machinery are selectively partitioned into specific condensates, often mediated by protein disorder, to regulate biochemical pathways. In this study, it was found that condensates composed of the intrinsically disordered region (IDR) of MED1 can selectively partition RNA polymerase II and its positive allosteric regulators, while excluding negative regulators. This selective compartmentalization is necessary for gene activation during a cell-state transition and is achieved through alternating blocks of charged amino acids in the IDRs of partitioned proteins.
Article
Biochemistry & Molecular Biology
Xufang Qiu, Liang Kong, Han Chen, Yachun Lin, Siqun Tu, Lei Wang, Zhiyuan Chen, Mengzhu Zeng, Junhua Xiao, Peiguo Yuan, Min Qiu, Yan Wang, Wenwu Ye, Kaixuan Duan, Suomeng Dong, Yuanchao Wang
Summary: This study reveals that the nuclear effector PsAvh110 from the pathogen Phytophthora sojae suppresses plant immunity by disrupting the formation of the GmLHP1-2/GmPHD6 complex, leading to reduced expression of immunity genes. PsAvh110 also represses the expression of immune-associated genes through binding to G-rich elements in gene promoters. The findings suggest a regulatory mechanism by which pathogen effectors target a transcriptional complex to manipulate plant immunity.
Review
Cell Biology
Angelos Yfantis, Ilias Mylonis, Georgia Chachami, Marios Nikolaidis, Grigorios D. Amoutzias, Efrosyni Paraskeva, George Simos
Summary: HIF-1 is a key regulator in cell survival under low oxygen conditions and its interaction with chromatin and transcriptional machinery is still being investigated. This review examines the co-regulators of HIF-1 and their impact on the expression of HIF-1 direct target genes in response to hypoxia, with the aim of identifying potential targets for anticancer therapy.
Article
Biochemistry & Molecular Biology
Kee-Pyo Kim, Jinmi Choi, Juyong Yoon, Jan M. Bruder, Borami Shin, Jonghun Kim, Marcos J. Arauzo-Bravo, Dong Han, Guangming Wu, Dong Wook Han, Johnny Kim, Patrick Cramer, Hans R. Schoeler
Summary: A chemical screen targeting major epigenetic pathways can identify permissive epigenetic states that enhance reprogramming competence of transcription factors. In this study, inhibiting specific epigenetic roadblocks simultaneously was found to dramatically improve the reprogramming ability of most OCT factors and enable dismantling species-dependent reprogramming competence of certain transcription factors such as OCT6.
NATURE CHEMICAL BIOLOGY
(2021)
Review
Microbiology
S. Mayo-Perez, Y. Gama-Martinez, S. Davila, N. Rivera, I. Hernandez-Lucas
Summary: This review focuses on the distribution, abundance, evolution, structural organization, transcriptional regulation, and fundamental roles of LysR-type transcriptional regulators (LTTRs) in bacteria, archaea, and algae. It also discusses their involvement in free life, pathogenesis, and bacteria-plant interaction, providing a current understanding of LTTR biology.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Microbiology
Ivan Nombela, Martine Michiels, Dominique Van Looveren, Lukas Marcelis, Sara El Ashkar, Siska Van Belle, Anne Bruggemans, Thomas Tousseyn, Jurg Schwaller, Frauke Christ, Rik Gijsbers, Jan De Rijck, Zeger Debyser
Summary: In this study, it was found that the replication of murine leukemia virus in vivo occurs independently of BET proteins, which are key host determinants in retroviral integration site selection. This discovery opens up a new research direction to discover alternative viral or host factors that may complement the dominant host factor. Additionally, the study showed that BET-independent murine leukemia virus decouples insertional mutagenesis from gene enhancers, although lymphomagenesis still occurs despite the lack of interaction with BET proteins. This finding has implications for the safety of BET-independent MLV-based vectors for gene therapy.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Philippe J. Batut, Xin Yang Bing, Zachary Sisco, Joao Raimundo, Michal Levo, Michael S. Levine
Summary: Past studies have provided contradictory claims about the role of genome organization in gene activity regulation. This study demonstrates that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. These two levels of genome organization operate independently to ensure precise transcriptional dynamics and reliable complex patterning processes.
Article
Biochemistry & Molecular Biology
Bingyu Ye, Wenlong Shen, Yanchang Li, Dong Wang, Yan Zhang, Ping Li, Man Yin, Yahao Wang, Dejian Xie, Shu Shi, Tao Yao, Juncai Chen, Ping Xu, Zhihu Zhao
Summary: Certain transcription factors remain associated with chromosomes during mitosis and play a role in maintaining gene expression patterns upon mitotic exit. By using FAIRE-MS, researchers identified 189 regulatory factors that are maintained during interphase and mitosis, with intrinsically disordered proteins and regions being highly enriched. These proteins are involved in liquid-liquid phase separation and chromatin organization during the cell cycle, and some of them are partially bound to mitotic chromosomes.
Article
Medicine, Research & Experimental
Laura M. Tsujikawa, Olesya A. Kharenko, Stephanie C. Stotz, Brooke D. Rakai, Christopher D. Sarsons, Dean Gilham, Sylwia Wasiak, Li Fu, Michael Sweeney, Jan O. Johansson, Norman C. W. Wong, Ewelina Kulikowski
Summary: The study reveals a new role for BET protein BRD4 in maintaining higher order chromatin structure at TADBs, highlighting the differential impact of BET inhibitors on TADB stability.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Multidisciplinary Sciences
Tulsi Patel, Jennifer Hammelman, Siaresh Aziz, Sumin Jang, Michael Closser, Theodore L. Michaels, Jacob A. Blum, David K. Gifford, Hynek Wichterle
Summary: In this study, the researchers found that mouse motor neurons undergo widespread changes in gene expression and associated regulatory regions during development. Stem cell-derived neurons can recapitulate a portion of the maturation expression program in vitro, with neural activity playing a modest role in the late-stage regulation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Haley M. Amemiya, Thomas J. Goss, Taylor M. Nye, Rebecca L. Hurto, Lyle A. Simmons, Peter L. Freddolino
Summary: The study found that prokaryotes maintain chromosome structure similar to eukaryotic heterochromatin, with transcriptionally silent regions called extended protein occupancy domains (EPODs) containing metabolic pathway genes and parasitic elements. Deletion of specific nucleoid-associated proteins (NAPs) in E. coli and B. subtilis opens up chromosomal regions for RNA polymerase binding and further transcriptional regulation, preparing cells for exposure to different metabolic environments. Additionally, novel xenogeneic silencing roles were identified for the NAPs Fis and Hfq, essential for cell viability in the presence of domesticated prophages.
Article
Microbiology
Gary Z. Wang, Ying Wang, Stephen P. Goff
CELL HOST & MICROBE
(2016)
Article
Virology
Roger Valle-Tenney, Tatiana Opazo, Jorge Cancino, Stephen P. Goff, Gloria Arriagada
JOURNAL OF VIROLOGY
(2016)
Article
Virology
Gary Z. Wang, Stephen P. Goff
JOURNAL OF VIROLOGY
(2017)
Article
Multidisciplinary Sciences
Michael J. Metzger, Antonio Villalba, Maria J. Carballal, David Iglesias, James Sherry, Carol Reinisch, Annette F. Muttray, Susan A. Baldwin, Stephen P. Goff
Article
Virology
Daniel O. Griffin, Stephen P. Goff
Editorial Material
Multidisciplinary Sciences
Stephen P. Goff
Article
Multidisciplinary Sciences
Cheng Wang, Stephen P. Goff
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Virology
Franziska K. Geis, Melanie Galla, Dirk Hoffmann, Johannes Kuehle, Daniela Zychlinski, Tobias Maetzig, Juliane W. Schott, Adrian Schwarzer, Christine Goffinet, Stephen P. Goff, Axel Schambach
Article
Multidisciplinary Sciences
Oya Cingoz, Stephen P. Goff
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Multidisciplinary Sciences
Michael J. Metzger, Ashley N. Paynter, Mark E. Siddall, Stephen P. Goff
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Virology
Andreia Lee, Oya CingOz, Yosef Sabo, Stephen P. Goff
Article
Multidisciplinary Sciences
Yiping Zhu, Gary Z. Wang, Oya Cingoz, Stephen P. Goff
Article
Biochemistry & Molecular Biology
Xinlu Wang, Yifang Xuan, Yuling Han, Xiang Ding, Kai Ye, Fuquan Yang, Pu Gao, Stephen P. Goff, Guangxia Gao
Article
Microbiology
Oya Cingoz, Stephen P. Goff
Article
Microbiology
Yiping Zhu, Shukun Luo, Yosef Sabo, Cheng Wang, Liang Tong, Stephen P. Goff
CELL HOST & MICROBE
(2017)