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.
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)
Editorial Material
Plant Sciences
Rodrigo S. Reis
Summary: There is a significant gap in our understanding of thermomorphogenesis regulation, specifically in processes involving RNA. This gap presents opportunities for exciting new discoveries in post-transcriptional regulation, while also posing manageable challenges.
JOURNAL OF EXPERIMENTAL BOTANY
(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
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
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.
Article
Biochemical Research Methods
Yating Liu, Joseph D. Dougherty
Summary: Whole genome sequencing of patient populations is identifying thousands of new variants in untranslated regions (UTRs). While the consequences of UTR mutations are not as easily predicted from primary sequence as coding mutations are, there are known features that modulate their function. The utr.annotation R package can be used to annotate potential deleterious variants in UTR regions, providing detailed information on each variant.
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)
Review
Cell Biology
Suresh Kumar, Trilochan Mohapatra
Summary: Gene regulation depends on dynamic and reversibly modifiable biological and chemical information in the epigenome/epitranscriptome, especially in animal systems, with vital roles in developmental processes and stress responses, although some underlying mechanisms are not fully understood.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
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
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
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.
Article
Biochemistry & Molecular Biology
Wan-Jung C. Lai, Mingyi Zhu, Margarita Belinite, Gregory Ballard, David H. Mathews, Dmitri N. Ermolenko
Summary: Adding unstructured sequences to the 3'UTR of mRNA decreases translation, resulting in a weakened ability of the poly(A) tail.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
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
Alison C. Greenlaw, Kris G. Alavattam, Toshio Tsukiyama
Summary: To ensure cell survival during quiescence, cells modulate their gene expression and transcription. By studying the nascent transcriptome, researchers identified over a thousand noncoding RNAs in quiescent and G1 yeast cells, revealing that noncoding transcription plays a larger role in the quiescent state. Furthermore, post-transcriptional regulation is increased in quiescence, affecting both mRNA and ncRNA. The nuclear exosome-NNS pathway was found to regulate the abundance of mRNAs involved in various cellular processes during quiescent entry, highlighting its important biological role in mRNA regulation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Hye-Young Nam, Darshan S. Chandrashekar, Anirban Kundu, Sandeep Shelar, Eun-Young Kho, Guru Sonpavde, Gurudatta Naik, Pooja Ghatalia, Carolina B. Livi, Sooryanarayana Varambally, Sunil Sudarshan
MOLECULAR CANCER RESEARCH
(2019)
Article
Oncology
Robert S. Svatek, Niannian Ji, Essel de Leon, Neelam Z. Mukherjee, Aashish Kabra, Vincent Hurez, Marlo Nicolas, Joel E. Michalek, Martin Javors, Karen Wheeler, Z. Dave Sharp, Carolina B. Livi, Zhen-Ju Shu, David Henkes, Tyler J. Curiel
CANCER IMMUNOLOGY RESEARCH
(2019)
Article
Oncology
Adam Kosti, Liqin Du, Haridha Shivram, Mei Qiao, Suzanne Burns, Juan Gabriel Garcia, Alexander Pertsemlidis, Vishwanath R. Iyer, Erzsebet Kokovay, Luiz O. F. Penalva
MOLECULAR CANCER RESEARCH
(2020)
Article
Cell & Tissue Engineering
Zhe Zhu, Pinar Mesci, Jean A. Bernatchez, Ryan C. Gimple, Xiuxing Wang, Simon T. Schafer, Hiromi Wettersten, Sungjun Beck, Alex E. Clark, Qiulian Wu, Briana C. Prager, Leo J. Y. Kim, Rekha Dhanwani, Sonia Sharma, Alexandra Garancher, Sara M. Weis, Stephen C. Mack, Priscilla D. Negraes, Cleber A. Trujillo, Luiz O. Penalva, Jing Feng, Zhou Lan, Rong Zhang, Alex W. Wessel, Sanjay Dhawan, Michael S. Diamond, Clark C. Chen, Robert J. Wechsler-Reya, Fred H. Gage, Hongzhen Hu, Jair L. Siqueira-Neto, Alysson R. Muotri, David A. Cheresh, Jeremy N. Rich
Article
Genetics & Heredity
Gabriela D. A. Guardia, Bruna R. Correa, Patricia Rosa Araujo, Mei Qiao, Suzanne Burns, Luiz O. F. Penalva, Pedro A. F. Galante
NPJ GENOMIC MEDICINE
(2020)
Article
Immunology
Anirban Kundu, Hyeyoung Nam, Sandeep Shelar, Darshan S. Chandrashekar, Garrett Brinkley, Suman Karki, Tanecia Mitchell, Carolina B. Livi, Phillip Buckhaults, Richard Kirkman, Yawen Tang, Glenn C. Rowe, Shi Wei, Sooryanarayana Varambally, Sunil Sudarshan
JOURNAL OF EXPERIMENTAL MEDICINE
(2020)
Article
Multidisciplinary Sciences
Saket Choudhary, Suzanne C. Burns, Hoda Mirsafian, Wenzheng Li, Dat T. Vo, Mei Qiao, Xiufen Lei, Andrew D. Smith, Luiz O. Penalva
SCIENTIFIC REPORTS
(2020)
Correction
Multidisciplinary Sciences
Saket Choudhary, Suzanne C. Burns, Hoda Mirsafian, Wenzheng Li, Dat T. Vo, Mei Qiao, Xiufen Lei, Andrew D. Smith, Luiz O. Penalva
SCIENTIFIC REPORTS
(2020)
Article
Oncology
Rebecca Poetschke, Jacob Haase, Markus Glass, Sebastian Simmermacher, Claudia Misiak, Luiz O. F. Penalva, Caspar D. Kuehnoel, Stefan Huettelmaier
Article
Oncology
Adam Kosti, Rodrigo Barreiro, Gabriela D. A. Guardia, Shiva Ostadrahimi, Erzsebet Kokovay, Alexander Pertsemlidis, Pedro A. F. Galante, Luiz O. F. Penalva
Summary: miRNAs act as key regulators of gene expression, contributing to cancer phenotypes as oncogenes or tumor suppressors. Cooperative action of miRNAs regulates biological processes and pathways, suggesting that miRNA combinations could be more effective in targeting cancer stem cells. Using combinations of tumor suppressor miRNAs may offer new routes to disrupt cancer phenotypes and growth of cancer-initiating cell populations.
Article
Oncology
Carla Frau, Catherine Jamard, Gaspard Delpouve, Gabriela D. A. Guardia, Christelle Machon, Camilla Pilati, Clementine Le Neve, Pierre Laurent-Puig, Jerome Guitton, Pedro A. F. Galante, Luiz O. Penalva, Jean-Noel Freund, Christelle de la Fouchardiere, Michelina Plateroti
Summary: The study reveals paradoxical roles of MSI1 in both facilitating intestinal regeneration after injury and promoting drug-resistant colorectal cancer stem cells. Increased levels of MSI1 contribute to the reprogramming of progenitor cells into drug-resistant phenotypes, highlighting its importance in chemotherapy resistance and tumor grading in colorectal cancer patients. These findings shed light on the biology and plasticity of normal and cancer cell populations, presenting potential new targets for improving chemotherapy outcomes.
Article
Oncology
Mirella Baroni, Caihong Yi, Saket Choudhary, Xiufen Lei, Adam Kosti, Denise Grieshober, Mitzli Velasco, Mei Qiao, Suzanne S. Burns, Patricia R. Araujo, Talia DeLambre, Mi Young Son, Michelina Plateroti, Marco A. R. Ferreira, E. Paul Hasty, Luiz O. F. Penalva
Summary: RNA binding protein Msi1 plays a crucial role in glioblastoma by regulating cell cycle and DNA replication genes, impacting tumor growth and response to therapy. High levels of Msi1 are associated with poor prognosis and tumor growth in multiple cancers.
Article
Neurosciences
Sajina Shakya, Anthony D. Gromovsky, James S. Hale, Arnon M. Knudsen, Briana Prager, Lisa C. Wallace, Luiz O. F. Penalva, H. Alex Brown, Bjarne W. Kristensen, Jeremy N. Rich, Justin D. Lathia, J. Mark Brown, Christopher G. Hubert
Summary: Glioblastoma displays significant cellular and metabolic heterogeneity, with striking differences in lipid metabolism across different microenvironments, and cancer stem cells (CSCs) also show altered lipid metabolism. The differences in lipid metabolism may not only be a product of the microenvironment, but also a reflection of cellular state, providing new insights into therapeutic targets for GBM.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Antoine Baudin, Alma K. Moreno-Romero, Xiaoping Xu, Emily E. Selig, Luiz O. F. Penalva, David S. Libich
Summary: RNA binding proteins (RBPs) such as SERBP1 play crucial roles in mRNA processing and translation regulation, with implications in diseases like cancer and neurodegeneration. Despite being initially identified as a hyaluronic acid binding protein, SERBP1 is now recognized for its central roles in brain function and development, including neurogenesis and synaptogenesis. Studies have shown that SERBP1 regulates One-carbon metabolism and epigenetic modification of histones, with increased expression in various cancers correlating with poor patient outcomes. Further research on SERBP1's structural and dynamic properties, as well as its interaction mechanisms with RNA, contribute to the understanding of its functions in physiological and pathological processes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Adam Kosti, Patricia Rosa de Araujo, Wei-Qing Li, Gabriela D. A. Guardia, Jennifer Chiou, Caihong Yi, Debashish Ray, Fabiana Meliso, Yi-Ming Li, Talia Delambre, Mei Qiao, Suzanne S. Burns, Franziska K. Lorbeer, Fanny Georgi, Markus Flosbach, Sarah Klinnert, Anne Jenseit, Xiufen Lei, Carolina Romero Sandoval, Kevin Ha, Hong Zheng, Renu Pandey, Aleksandra Gruslova, Yogesh K. Gupta, Andrew Brenner, Erzsebet Kokovay, Timothy R. Hughes, Quaid D. Morris, Pedro A. F. Galante, Stefano Tiziani, Luiz O. F. Penalva