Review
Immunology
Taishin Akiyama, Tadashi Yamamoto
Summary: Lymphocyte development is precisely regulated by various mechanisms, including the CCR4-NOT complex which controls mRNA longevity by catalyzing mRNA deadenylation. This process is crucial for differentiation of lymphocytes and selection of thymocytes, as it inhibits abnormal apoptosis and induces cell quiescence.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Hannah M. Burgess, Rebecca Grande, Sofia Riccio, Ikshitaa Dinesh, Gerlof Sebastiaan Winkler, Daniel P. Depledge, Ian Mohr
Summary: Human cytomegalovirus (HCMV) extensively remodels host translatome without mRNA decay enzyme. CNOT1 and CNOT3, members of host CCR4-NOT complex, are identified as unexpected pro-viral factors that selectively regulate HCMV reproduction. Poly(A)-tails of viral mRNAs are longer and less sensitive to CCR4-NOT disruption compared to cellular mRNAs. This study reveals a new mechanism of how herpesvirus infection remodels gene expression landscape and identifies a potential therapeutic target against HCMV.
Article
Biochemistry & Molecular Biology
Jing Tong, Hongwanyu Li, Cong Zhang
Summary: In this study, the authors investigated the characteristics and roles of m(5)C modification and mRNA expression profiles in the decidua of pre-eclampsia (PE). Through comprehensive analysis, they identified 50 candidate genes linked to PE and validated their expression changes. The findings suggest that m(5)C modification and relevant mRNA expression changes may influence the pathogenesis of PE.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Anil Kumar Vijjamarri, Neha Gupta, Chisom Onu, Xiao Niu, Fan Zhang, Rakesh Kumar, Zhenguo Lin, Miriam L. Greenberg, Alan G. Hinnebusch
Summary: We investigated the roles of Pat1 and Dhh1 in regulating mRNA translation and abundance in yeast cells under nutrient-replete conditions. Our findings suggest that Pat1 and Dhh1 cooperatively repress the expression of numerous non-ESR transcripts by reducing decapping and transcription in wild-type cells. Furthermore, we observed impaired mRNA turnover in mutants lacking Dhh1 or Pat1, leading to derepression of these transcripts. Pat1 and Dhh1 also contribute to translational repression and decreased protein production for multiple pathways involved in cell adhesion, nitrogen metabolism, respiration, and autophagy. These findings highlight the post-transcriptional regulatory functions of Pat1 and Dhh1 during nutrient limitation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Shivani Chhabra, Zachary F. Mandell, Bo Liu, Paul Babitzke, David H. Bechhofer
Summary: This study mapped the 3' ends of mRNA decay intermediates in strains lacking the major 3' exoribonuclease PNPase or the RNA helicase CshA, confirming the primary role of PNPase in mRNA turnover and suggesting the involvement of one or more unknown RNases.
Article
Environmental Sciences
Min Zhang, Jun Shi, Huiping Deng
Summary: This study found that microplastics caused inflammatory damage and histological changes in the heart tissue of mice. It also discovered the role of m6A modification in gene expression in microplastic-induced cardiotoxicity, providing new insights into the chronic toxicity of microplastic exposure on the heart.
Review
Cell Biology
Lorenzo Pavanello, Michael Hall, Gerlof Sebastiaan Winkler
Summary: Accurate and precise regulation of gene expression in eukaryotes involves the coordinated control of transcription, mRNA stability, and translation. Recent progress has been made in understanding the role of sequence elements in the 3' untranslated region in mRNA degradation regulation. The recruitment of the Ccr4-Not complex to target mRNA is a critical step in mRNA decay regulation. This article reviews the role of the human Ccr4-Not complex in cytoplasmic deadenylation of mRNA, focusing on its recruitment mechanisms and general mechanisms involving the poly(A) tail.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Fabian Poetz, Joshua Corbo, Yevgen Levdansky, Alexander Spiegelhalter, Doris Lindner, Vera Magg, Svetlana Lebedeva, Jorg Schweiggert, Johanna Schott, Eugene Valkov, Georg Stoecklin
Summary: The study identified RNF219 as an acetylation-regulated cofactor of the CCR4-NOT complex, which inhibits mRNA degradation mediated by the complex through interaction with NOT9. RNF219 attenuates global mRNA turnover in cells with a differential requirement of its RING domain.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Owais R. Hakiem, Syed M. A. Rizvi, Cuper Ramirez, Ming Tan
Summary: In this study, we used DNA immunoprecipitation-seq and RNA-seq analyses to investigate the role of the transcription factor Euo in Chlamydia trachomatis. We found that Euo represses late chlamydial genes and activates a subset of midcycle genes, as well as regulating its own expression. Our findings highlight the important role of Euo as a developmental regulator in C. trachomatis and demonstrate a correlative approach that can be used to study transcription factors in other pathogenic bacteria.
Article
Cell Biology
Zhangyuan Yin, Zhihai Zhang, Yuchen Lei, Daniel J. Klionsky
Summary: This study reveals that the Ccr4-Not complex in Saccharomyces cerevisiae has bidirectional roles in regulating autophagy before and after nutrient deprivation. Under nutrient-rich conditions, Ccr4-Not promotes the degradation of certain ATG genes to maintain basal autophagy. However, upon starvation, Ccr4-Not switches its role to promote the expression of a different subset of ATG genes, which is required for sufficient autophagy induction and activity.
Review
Biochemistry & Molecular Biology
Laura Monaghan, Dasa Longman, Javier F. Caceres
Summary: mRNA surveillance pathways play a crucial role in maintaining accurate gene expression and translation homeostasis. Studying these pathways can help us understand how cellular mRNA levels are regulated, how defective mRNAs are eliminated, and how dysregulation can contribute to human disease.
Article
Biotechnology & Applied Microbiology
Weiwei Luo, Junru Wang, Ying Zhou, Meixia Pang, Xiaomu Yu, Jingou Tong
Summary: This study used RNA sequencing and small RNA sequencing technologies to investigate the molecular mechanism of head development in bighead carp at different stages of development. Six key pathways and 114 candidate genes related to head development were identified. Additionally, 19 key miRNAs that play a role in the development of various tissues and mineralization of the head bone system were also discovered.
Article
Cardiac & Cardiovascular Systems
Tongbin Wu, Zhengyu Liang, Zengming Zhang, Canzhao Liu, Lunfeng Zhang, Yusu Gu, Kirk L. Peterson, Sylvia M. Evans, Xiang-Dong Fu, Ju Chen
Summary: Disruption of cardiomyocyte specification plays a key role in the pathogenesis of LVNC. The study sheds light on the underlying mechanisms of LV-specific transcriptional program governing LV chamber growth and maturation.
Article
Multidisciplinary Sciences
Hye Kyung Lee, Ludwig Knabl, Mary Walter, Priscilla A. Furth, Lothar Hennighausen
Summary: The study suggests that prior infection status significantly impacts the immune response following BA.2 infection, with significantly increased neutralizing antibody levels in patients with a previous history of COVID-19.
Article
Immunology
Jia Shu, Guannan Su, Jun Zhang, Zhangluxi Liu, Rui Chang, Qingfeng Wang, Peizeng Yang
Summary: Recent studies have uncovered the importance of circRNAs in various biological processes and autoimmune diseases, with a focus on their potential role in the classical autoimmune disease Vogt-Koyanagi-Harada (VKH) disease. Through RNA-seq analysis of VKH patients and healthy controls, differentially expressed circRNAs, miRNAs, and mRNAs were identified, suggesting a potential immunomodulatory function of circRNAs in the pathophysiology of VKH disease. Functional enrichment analyses indicated involvement of inflammatory response, adaptive immune response, and various signaling pathways in VKH disease pathogenesis.
FRONTIERS IN IMMUNOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Magdalena Boguta, Joseph C. Reese
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2018)
Review
Biochemistry & Molecular Biology
Joseph C. Reese
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2013)
Article
Cell Biology
Haoyang Jiang, Marley Wolgast, Laura M. Beebe, Joseph C. Reese
GENES & DEVELOPMENT
(2019)
Editorial Material
Biochemical Research Methods
Joseph C. Reese
Article
Genetics & Heredity
Oluwasegun T. Akinniyi, Joseph C. Reese
Summary: Degradation Factor 1, discovered 20 years ago as a yeast protein copurifying with Rad26, controls the ubiquitylation and destruction of the large subunit of DNA damage-arrested RNA Polymerase II. In addition to regulating RNA Polymerase II, Def1 is involved in maintaining chromosome and genomic integrity, and may serve as a central coordinator of ubiquitin signaling pathways in cells.
Review
Cell Biology
JC Reese
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2003)
Article
Biochemistry & Molecular Biology
JC Reese, MR Green
Article
Biochemistry & Molecular Biology
JC Reese, Z Zhang, H Kurpad
JOURNAL OF BIOLOGICAL CHEMISTRY
(2000)
Review
Biochemical Research Methods
JC Reese, MA Green
RNA POLYMERASES AND ASSOCIATED FACTORS, PT C
(2003)