Review
Biochemical Research Methods
Mattia Furlan, Stefano de Pretis, Mattia Pelizzola
Summary: Despite RNA abundance being commonly assumed as a proxy for transcriptional activity, it is now possible to calculate how synthesis, processing, and degradation rates collectively determine the abundance of each gene's RNA. Different transcriptional outputs can correspond to different combinations of kinetic rates, indicating the existence of markedly different modes of gene expression regulation and their profound effects on gene self-expression regulation.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Noof Aloufi, Aeshah Alluli, David H. Eidelman, Carolyn J. Baglole
Summary: Chronic obstructive pulmonary disease (COPD) is a respiratory disorder characterized by chronic inflammation and emphysema, primarily caused by cigarette smoke. Various cellular processes are altered by cigarette smoke, including post-transcriptional regulation of mRNAs. RNA-binding proteins, microRNAs, and long non-coding RNAs play key roles in regulating RNA biology and may contribute to the pathogenesis of COPD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Laura Piel, K. Shanmugha Rajan, Giovanni Bussotti, Hugo Varet, Rachel Legendre, Caroline Proux, Thibaut Douche, Quentin Giai-Gianetto, Thibault Chaze, Thomas Cokelaer, Barbora Vojtkova, Nadav Gordon-Bar, Tirza Doniger, Smadar Cohen-Chalamish, Praveenkumar Rengaraj, Celine Besse, Anne Boland, Jovana Sadlova, Jean-Francois Deleuze, Mariette Matondo, Ron Unger, Petr Volf, Shulamit Michaeli, Pascale Pescher, Gerald Spath
Summary: Genome instability plays a crucial role in the adaptation and regulation of the protozoan parasite Leishmania, utilizing post-transcriptional and epitranscriptomic regulation to adapt to its host environment.
Review
Biochemistry & Molecular Biology
Marcos Morgan, Lokesh Kumar, Yin Li, Marine Baptissart
Summary: Multiple RNA pathways are essential in producing functional sperm, with a particular focus on 3' end modifications. Studies have shown a correlation between RNA 3' end metabolism and male germ cell differentiation, as well as the importance of RNA pathways in maintaining genomic integrity.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Microbiology
Murat C. Kalem, Harini Subbiah, Jay Leipheimer, Virginia E. Glazier, John C. Panepinto
Summary: Research has shown that the lack of Puf4 in Cryptococcus neoformans results in increased resistance to caspofungin, while overexpression of Puf4 leads to increased sensitivity to the drug. Additionally, Puf4 regulates multiple cell wall biosynthesis genes and affects cell wall composition. These findings reveal a potential mechanism by which caspofungin resistance and cell wall biogenesis are post-transcriptionally regulated by Puf4.
Review
Biochemistry & Molecular Biology
Weijin Xu, Jeetayu Biswas, Robert H. Singer, Michael Rosbash
Summary: RNA binding proteins (RBPs) regulate post-transcriptional processes in cells, and it is crucial to identify their in vivo targets for understanding their function. Standard techniques for profiling RBP targets have limitations in certain situations, but new genetic approaches have been developed for such circumstances. These approaches, including TRIBE, RNA tagging, and STAMP, provide useful tools for studying post-transcriptional regulation and RBP identification, with potential therapeutic implications.
Review
Immunology
Anissa Guillemin, Anuj Kumar, Melanie Wencker, Emiliano P. Ricci
Summary: Innate immunity is the first line of defense against infections and tissue damage, and it relies on a dynamic and coordinated gene expression program. Transcriptional and post-transcriptional regulatory pathways, involving RNA-binding proteins and other effectors, play crucial roles in shaping the innate immune response. Recently, microRNAs and post-transcriptional modification of RNA bases have also emerged as essential players in this process.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ullas Valiya Chembazhi, Wesley S. Tung, Hyojeong Hwang, Yuexi Wang, Aryan Lalwani, Ka Lam Nguyen, Sushant Bangru, Danielle Yee, Kristy Chin, Jing Yang, Auinash Kalsotra, Wenyan Mei
Summary: Intestinal epithelial regeneration is driven by intestinal stem cells. Upon the loss of intestinal stem cells, differentiated intestinal epithelial cells, such as Paneth cells, are capable of acquiring multipotency and contributing to regeneration. Depletion of an RNA-binding protein named PTBP1 in mouse intestinal epithelial cells leads to intestinal stem cell death and epithelial regeneration failure.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Cell Biology
Nicolas Curdy, Olivia Lanvin, Sarah Cadot, Camille Laurent, Jean-Jacques Fournie, Don-Marc Franchini
Summary: Immune cell activation leads to transcriptional and translational programs, with stress granules playing a crucial role in controlling protein synthesis and ensuring accurate effector functions in immune cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Immunology
Takuya Uehata, Osamu Takeuchi
Summary: The regulation of mRNA decay is crucial in controlling gene expression, involving both canonical pathways and endoribonucleolytic cleavage. Regnase-1 plays a critical role in immune regulation by dampening mRNA, particularly cytokines and inflammatory mediators. A group of Regnase-1-related RNases are also involved in immune regulation and antiviral host defense.
INTERNATIONAL IMMUNOLOGY
(2021)
Review
Neurosciences
Iva Salamon, Mladen-Roko Rasin
Summary: The evolution and development of the human neocortex rely on the abundance, diversity, and temporal molecular regulation of progenitor cells. RNA-binding proteins play important roles in different stages of early neurogenesis, particularly in the cell fate transition of transcriptionally primed cortical progenitors.
FRONTIERS IN NEUROSCIENCE
(2022)
Review
Cell Biology
Qiuqin Ma, Shihui Long, Zhending Gan, Gianluca Tettamanti, Kang Li, Ling Tian
Summary: Autophagy, a widely conserved process in eukaryotes, is regulated by nutrient deprivation, energy stress, and other unfavorable conditions through multiple pathways. It is primarily governed at the RNA and protein levels in a synergistic manner.
Article
Cell Biology
Michael J. McFadden, Alexa B. R. McIntyre, Haralambos Mourelatos, Nathan S. Abell, Nandan S. Gokhale, Helene Ipas, Blerta Xhemalce, Christopher E. Mason, Stacy M. Horner
Summary: The RNA base modification N6-methyladenosine (m(6)A) plays a role in post-transcriptional control of ISG translation during type I IFN response for antiviral restriction. m(6)A and m(6)A methyltransferase proteins METTL3, METTL14, along with m(6)A reader YTHDF1, significantly affect the expression of IFITM1. The m(6)A methyltransferase complex promotes the antiviral activity of type I IFN.
Article
Biochemistry & Molecular Biology
Geysson Javier Fernandez, Julieta M. Ramirez-Mejia, Silvio Urcuqui-Inchima
Summary: This study reveals that ZIKV-infected macrophages activate a genetic program involving inflammatory and antiviral responses, with changes in various signaling pathways. Key transcription factors, long non-coding RNAs, and miRNAs play regulatory roles in controlling gene expression and post-transcriptional control. Additionally, RNA binding proteins are involved in this regulatory mechanism.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2022)
Review
Immunology
Anouk P. Jurgens, Branka Popovic, Monika C. Wolkers
Summary: T cells play a central role in the adaptive immune system, protecting us from infections. Activation prompts T cells to change gene expression and produce effector molecules rapidly to combat threats. Dormant T cells regulate protein production to survive and prepare for potential re-infections.
EUROPEAN JOURNAL OF IMMUNOLOGY
(2021)
Review
Developmental Biology
Ashley L. Lennox, Hanqian Mao, Debra L. Silver
WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Ilaria Vitali, Sabine Fievre, Ludovic Telley, Polina Oberst, Sebastiano Bariselli, Laura Frangeul, Natalia Baumann, John J. McMahon, Esther Klingler, Riccardo Bocchi, Jozsef Z. Kiss, Camilla Bellone, Debra L. Silver, Denis Jabaudon
Editorial Material
Neurosciences
Fernando C. Alsina, Debra L. Silver
TRENDS IN NEUROSCIENCES
(2019)
Article
Developmental Biology
Charles J. Sheehan, John J. McMahon, Lucas D. Serdar, Debra L. Silver
Article
Neurosciences
Ashley L. Lennox, Mariah L. Hoye, Ruiji Jiang, Bethany L. Johnson-Kerner, Lindsey A. Suit, Srivats Venkataramanan, Charles J. Sheehan, Fernando C. Alsina, Brieana Fregeau, Kimberly A. Aldinger, Ching Moey, Iryna Lobach, Alexandra Afenjar, Dusica Babovic-Vuksanovic, Stephane Bezieau, Patrick R. Blackburn, Jens Bunt, Lydie Burglen, Philippe M. Campeau, Perrine Charles, Brian H. Y. Chung, Benjamin Cogne, Cynthia Curry, Maria Daniela D'Agostino, Nataliya Di Donato, Laurence Faivre, Delphine Heron, A. Micheil Innes, Bertrand Isidor, Boris Keren, Amy Kimball, Eric W. Klee, Paul Kuentz, Sebastien Kury, Dominique Martin-Coignard, Ghayda Mirzaa, Cyril Mignot, Noriko Miyake, Naomichi Matsumoto, Atsushi Fujita, Caroline Nava, Mathilde Nizon, Diana Rodriguez, Lot Snijders Blok, Christel Thauvin-Robinet, Julien Thevenon, Marie Vincent, Alban Ziegler, William Dobyns, Linda J. Richards, A. James Barkovich, Stephen N. Floor, Debra L. Silver, Elliott H. Sherr
Article
Multidisciplinary Sciences
Qiang Huang, Malkiel A. Cohen, Fernando C. Alsina, Garth Devlin, Aliesha Garrett, Jennifer McKey, Patrick Havlik, Nikolai Rakhilin, Ergang Wang, Kun Xiang, Parker Mathews, Lihua Wang, Cheryl Bock, Victor Ruthig, Yi Wang, Marcos Negrete, Chi Wut Wong, Preetish K. L. Murthy, Shupei Zhang, Andrea R. Daniel, David G. Kirsch, Yubin Kang, Blanche Capel, Aravind Asokan, Debra L. Silver, Rudolf Jaenisch, Xiling Shen
Review
Cell Biology
Brooke R. D'Arcy, Debra L. Silver
Article
Neurosciences
Mariah L. Hoye, Debra L. Silver
Summary: Regulation of stem cell fate decisions is crucial for development, homeostasis, and organismal fitness. Transcriptional priming of neural progenitors and dynamic post-transcriptional regulation, particularly in radial glial progenitors, play a vital role in defining cell fates and are implicated in neurodevelopmental disease. Post-transcriptional mechanisms, including subcellular mRNA localization, RNA decay, and translation, are highlighted in governing cortical development and translational control of neuronal fates.
CURRENT OPINION IN NEUROBIOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Jing Liu, Debra L. Silver
Summary: The study reveals the critical role of neuroepithelial progenitor shape transitions in human cortical expansion, using cerebral organoids derived across great apes.
Editorial Material
Multidisciplinary Sciences
Katherine T. Baldwin, Debra L. Silver
Article
Neurosciences
Jing Liu, Federica Mosti, Debra L. Silver
Summary: Humans differ from other primates in terms of neuroanatomy and cognitive functions, with human-specific features being particularly prominent in the cerebral cortex due to an expansion in size and unique cellular composition and circuitry. It is postulated that human-specific gene expression may explain neocortical anatomical differences across evolution, particularly in relation to noncoding regulatory loci linked to human traits. The review also highlights emerging noncoding elements in human cortical evolution and their associations with neurodevelopmental diseases.
CURRENT OPINION IN NEUROBIOLOGY
(2021)
Editorial Material
Neurosciences
Federica Mosti, Debra L. Silver
Summary: The article reviews the extensive genomic changes acquired by humans during evolution, defining unique features of our species, as well as discovering enhancer activity in human-specific cortical development within human accelerated regions (HARs).
Article
Biology
Mariah L. Hoye, Lorenzo Calviello, Abigail J. Poff, Nna-Emeka Ejimogu, Carly R. Newman, Maya D. Montgomery, Jianhong Ou, Stephen N. Floor, Debra L. Silver
Summary: Mutations in the DDX3X gene play a crucial role in cortical development and are associated with DDX3X syndrome. The study shows that DDX3X controls translational and cell cycle control of neural progenitors, influencing neurogenesis and cortical development.
Article
Developmental Biology
Bianca M. Lupan, Rachel A. Solecki, Camila M. Musso, Fernando C. Alsina, Debra L. Silver
Summary: This study demonstrates that EIF4A3 promotes cortical development by controlling progenitor mitosis, cell fate, and survival. The lack of EIF4A3 leads to cell death and impaired neurogenesis. The research also reveals new mechanisms of neurogenesis mediated by the exon junction complex (EJC).
Article
Biochemistry & Molecular Biology
Brooke D'Arcy, Ashley Lennox, Camila Manso Musso, Annalise L. Bracher, Carla Escobar-Tomlienovich, Stephany Perez-Sanchez, Debra Silver
Summary: Radial glial cells (RGCs) play a critical role in the generation and organization of neurons in the cerebral cortex. The subcellular compartmentalization of RGCs, particularly their basal and apical endfeet, is poorly understood in relation to cortical development.