Review
Biochemistry & Molecular Biology
Francisco Gutierrez-Santiago, Francisco Navarro
Summary: Ribosomes are vital for protein production, and their biogenesis is regulated by cellular energy status and stress signals. In eukaryotic cells, stress signals and newly-synthesized ribosomes require transcription by RNA polymerases. The Target of Rapamycin pathway in eukaryotes influences RNA polymerase transcription to ensure proper ribosome production. This review focuses on how TOR regulates transcription in Saccharomyces cerevisiae and the coordination of three RNA polymerases.
Article
Gastroenterology & Hepatology
Lei Sun, Arabella Wan, Zhuolong Zhou, Dongshi Chen, Heng Liang, Chuwei Liu, Shijia Yan, Yi Niu, Ziyou Lin, Siyue Zhan, Shanfeng Wang, Xianzhang Bu, Weiling He, Xiongbin Lu, Anlong Xu, Guohui Wan
Summary: The study identified an RNA-binding protein RALY as a critical regulator in colorectal cancer metabolism, promoting the post-transcriptional processing of miRNAs that downregulate metabolism-associated genes and reprogram mitochondrial metabolism in cancer cells. Increased levels of RALY were associated with poor prognosis in CRC patients expressing low levels of mitochondrion-associated genes, and this effect was facilitated by N6-methyladenosine switch under reactive oxygen species stress. Inhibition of m6A methylation abolished RALY recognition of pri-miRNAs, leading to inhibition of colorectal tumor growth and progression both in vivo and in organoid models.
Article
Neurosciences
Neal D. Amin, Gokhan Senturk, Giancarlo Costaguta, Shawn Driscoll, Brendan O'Leary, Dario Bonanomi, Samuel L. Pfaff
Summary: This study found that microRNA (miRNA) can govern different gene network outputs at different expression levels, and miRNA-dependent phenotypes emerge at specific dose ranges due to hidden regulatory inflection points in their gene networks.
Article
Biochemistry & Molecular Biology
Jianzhou Cui, Yi Yuan, Muthu K. Shanmugam, Durkeshwari Anbalagan, Tuan Zea Tan, Gautam Sethi, Alan Prem Kumar, Lina H. K. Lim
Summary: The study investigated the relationship between miR-196a and BRAM1 in renal cancer using TCGA analysis, RT-PCR, and mouse models, revealing the oncogenic role of miR-196a and tumor-suppressive role of Bram1. Dysregulated miR-196a and Bram1 may serve as potential prognostic biomarkers and therapeutic targets in renal cancer.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Review
Plant Sciences
Lu Zhang, Yu Xiang, Shengbo Chen, Min Shi, Xianda Jiang, Zhuoli He, Shuai Gao
Summary: This review focuses on the recent research progress in understanding miRNA biogenesis and stability control in plants, discussing the importance of miRNAs in plant growth, development, and stress responses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ajeet P. Singh, Huacheng Luo, Meghana Matur, Melanie A. Eshelman, Karina Hamamoto, Arati Sharma, Julia Lesperance, Suming Huang
Summary: MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) play crucial roles in regulating gene expression. The interaction between HOTTIP lncRNA and miRNAs in leukemogenesis is not well understood. Research shows that HOTTIP directly controls certain miRNA genes, impacting HOX cluster miRNAs expression and promoting leukemogenesis through chromatin remodeling. Inactivation of HOTTIP or miR-196b induces apoptosis and affects FAS gene expression in AML cells.
Editorial Material
Cell Biology
W. Mike Henne
Summary: Cells survive by sensing and adapting to their environment to maintain homeostasis, involving quality-control pathways, changes to organelle shape, and interorganelle communication. Several reviews in this issue discuss these organelle homeostasis principles and their alterations in disease.
DEVELOPMENTAL CELL
(2021)
Article
Biotechnology & Applied Microbiology
Haixia Liu, Mei Song, Xiaoyan Sun, Xin Zhang, Huayan Miao, Yankui Wang
Summary: TBX1 acts as a tumor suppressor in cervical cancer by inhibiting cell proliferation, migration, and invasion, and may function through regulation of miR-6727-5p.
Article
Multidisciplinary Sciences
Essam Darwish, Ritesh Ghosh, Abraham Ontiveros-Cisneros, Huy Cuong Tran, Marcus Petersson, Liesbeth De Milde, Martyna Broda, Alain Goossens, Alex Van Moerkercke, Kasim Khan, Olivier Van Aken
Summary: Plants respond to mechanical stimuli by regulating their growth and defense mechanisms. This study identifies the molecular mechanisms of touch signaling and reveals that Piezo ion channels do not play a major role in touch-induced gene expression and thigmomorphogenesis. Instead, the receptor-like kinase Feronia acts as a strong negative regulator of the touch signaling pathway dependent on jasmonic acid. Furthermore, the calmodulin-binding transcriptional activators CAMTA1/2/3 are key regulators of the touch signaling pathway independent of jasmonic acid.
Article
Biochemistry & Molecular Biology
Dandan Zheng, Meng Cao, Siyu Zuo, Xin Xia, Chunchun Zhi, Yanbing Lin, Sitong Deng, Xiaoqin Yuan
Summary: High expression of RANBP1 in CRC is associated with poor prognosis, promoting cell proliferation and invasion, and influencing the expression of YAP by regulating miRNAs and the Hippo pathway, forming a positive feedback loop to enhance CRC progression.
Review
Cell Biology
Megan Rowton, Alexander Guzzetta, Ariel B. Rydeen, Ivan P. Moskowitz
Summary: Congenital Heart Disease (CHD), malformations of the heart at birth, is the most common life-threatening birth defect. The research challenge lies in elucidating the genetic determinants of CHD and linking CHD ontogeny to a molecular understanding of heart development. Tight temporal control of progenitor differentiation is crucial for normal organ size, spatial organization, and cellular physiology.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Marlene C. Gerner, Andrea Bileck, Lukas Janker, Liesa S. Ziegler, Thomas Oehlinger, Pierre Raeven, Ernst W. Muellner, Ulrich Salzer, Christopher Gerner, Klaus G. Schmetterer, David M. Baron
Summary: Research has shown that red blood cells can impact T-cell activation and proliferation, with packed red blood cells inhibiting T-cell activation through direct cell-cell contact and impacting the production of reactive oxygen species. Downstream signaling events requiring reactive oxygen species for full functionality are affected, with PRBCs more efficiently inhibiting T-cell activation compared to antioxidants. These immunomodulating effects may be responsible for clinical observations associated with transfusion of PRBCs.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Cell Biology
Cheuk Wang Fung, Shaopu Zhou, Han Zhu, Xiuqing Wei, Zhenguo Wu, Angela Ruohao Wu
Summary: This study provides insights into the role of Pax7 lineage during embryonic development, using lineage tracing and single-cell transcriptomics. It reveals transcription factors and differentiation events, and identifies a bipotent progenitor population in early stages.
Article
Biochemistry & Molecular Biology
Lorena Perez-Carrillo, Isaac Gimenez-Escamilla, Maria Garcia-Manzanares, Juan Carlos Trivino, Sandra Feijoo-Bandin, Alana Aragon-Herrera, Francisca Lago, Luis Martinez-Dolz, Manuel Portoles, Estefania Tarazon, Esther Rosello-Lleti
Summary: Ischemic cardiomyopathy (ICM) is associated with abnormal microRNA expression levels and altered gene expression profile. This study focuses on the analysis of microRNA maturation defects and the role of the microRNA biogenesis pathway and redox-sensitive microRNAs (redoximiRs) in ICM. The findings suggest a decrease in microRNA maturation in ICM patients due to a decrease in pre-microRNA export and cytoplasmic processing, regulated by hypoxia. The study also reveals deregulation of redoximiRs, particularly miR-122-5p, which correlates with ejection fraction.
Article
Biochemistry & Molecular Biology
Ammad Ahmad Farooqi, Ru Wen, Rukset Attar, Simona Taverna, Ghazala Butt, Baojun Xu
Summary: This article reviews the modulation mechanism of natural product berbamine in different cancers and oncogenic cell-signaling pathways. It also analyzes the activation of the TGF/SMAD pathway by berbamine and nanotechnological strategies for efficient delivery. Furthermore, berbamine demonstrates potent anti-cancer and anti-metastatic effects in tumor-bearing mice. However, the regulatory role of berbamine in non-coding RNAs remains insufficiently studied, and further research is needed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Correction
Multidisciplinary Sciences
Lijuan Kan, Stanislav Ott, Brian Joseph, Eun Sil Park, Wei Dai, Ralph E. Kleiner, Adam Claridge-Chang, Eric C. Lai
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Seungjae Lee, Lu Wei, Binglong Zhang, Raeann Goering, Sonali Majumdar, Jiayu Wen, J. Matthew Taliaferro, Eric C. Lai
Summary: ELAV/Hu factors, a conserved family of RNA binding proteins, orchestrate multiple broad programs of neuronal mRNA processing and isoform diversification in both Drosophila and mammalian neurons. Their impacts on splicing, particularly in relation to 3' UTR extensions, play vital roles in regulating neural mRNA processing events.
Article
Developmental Biology
Fernando Bejarano, Chih-Hsuan Chang, Kailiang Sun, Joshua W. Hagen, Wu-Min Deng, Eric C. Lai
Summary: Research has shown that misexpression of miRNAs may have broader phenotypic impacts during disease situations, with the ability to modify the activity of pro-apoptotic factors. Studies have identified a subset of miRNAs that can inhibit irradiation-induced cell death and promote survival of mutant clones in larval development. Interestingly, some anti-apoptotic miRNAs do not target apoptotic factors, revealing unexpected functional synergies in disease or cancer-relevant settings.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Daniel L. Garaulet, Albertomaria Moro, Eric C. Lai
Summary: The study revealed that in fruit flies, the behavior of virgin females is regulated by factors such as miR-iab-4/8, Hth, and Dsx, with a double-negative regulatory pathway specifying the virgin behavioral state in the ventral nerve cord.
Review
Genetics & Heredity
Lu Wei, Eric C. Lai
Summary: The process of APA can alter regulatory capacity and coding potential of genes, leading to the formation of characteristic 3' UTR isoforms in neurons. However, our understanding of APA mechanisms and biology is still limited.
FRONTIERS IN GENETICS
(2022)
Article
Biology
Brian Joseph, Chaz Scala, Shu Kondo, Eric C. Lai
Summary: In this study, the mechanisms regulating the choice between intronic ratchet points (RPs) and recursive splicing (RS) exons in Drosophila were investigated. It was found that competition between splice donors can suppress the inclusion of cryptic exons, exonic sequences can influence the choice of RS-exon usage, and splicing can suppress the utilization of RPs. The study highlights the multiple factors influencing splicing of RS-exons in Drosophila.
LIFE SCIENCE ALLIANCE
(2022)
Article
Biology
Adrienne Samani, Rylie M. Hightower, Andrea L. Reid, Katherine G. English, Michael A. Lopez, J. Scott Doyle, Michael J. Conklin, David A. Schneider, Marcas M. Bamman, Jeffrey J. Widrick, David K. Crossman, Min Xie, David Jee, Eric C. Lai, Matthew S. Alexander
Summary: miR-486 plays a significant role in muscle function, with reduced expression associated with Duchenne muscular dystrophy. It is essential for normal muscle function and contributes to pathological remodeling in dystrophin-deficient muscle. Additionally, it serves as a useful biomarker for disease progression. The use of multiple omic platforms is effective in identifying in vivo miR-486 target transcripts.
LIFE SCIENCE ALLIANCE
(2022)
Article
Biochemistry & Molecular Biology
Renfu Shang, Dmitry A. Kretov, Scott Adamson, Thomas Treiber, Nora Treiber, Jeffrey Vedanayagam, Jeffrey H. Chuang, Gunter Meister, Daniel Cifuentes, Eric C. Lai
Summary: A study has revealed the important regulatory role of conserved loop sequences in the generation of miRNAs in vertebrates, particularly in the cleavage of pre-mir-144. This regulatory role involves the ILF3 complex and reshaping of the apical loop of pre-mir-144, allowing for cleavage by Dicer. Furthermore, these findings extend our understanding of nuclear and cytoplasmic regulatory events in miRNA maturation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Seungjae Lee, Yen-Chung Chen, Austin E. Gillen, J. Matthew Taliaferro, Bart Deplancke, Hongjie Li, Eric C. Lai
Summary: Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs) through alternative polyadenylation (APA). This study explores the cell-type expression of 3' UTRs in over 250 adult Drosophila cell types using single nucleus RNA-sequencing data. The researchers reveal tissue-specific APA/ALE programs and dynamic 3' UTR patterns across cell lineages, providing a foundation for future investigations of alternative isoforms in this model organism.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Seungjae Lee, David Jee, Sid Srivatsava, Acong Yang, Abhinav Ramidi, Renfu Shang, Diane Bortoamiol-Becet, Sebastien Pfeffer, Shuo Gu, Jiayu Wen, Eric C. Lai
Summary: Canonical miRNA hairpins are processed by Drosha and Dicer enzymes to form small RNAs loaded into Ago effector. Splicing generates unannotated hairpins, termed ssdRNAs, which associate with Dicer and/or Ago complexes. They contaminate the canonical miRNA pathway and are tailed by terminal nucleotidyltransferases. This intragenomic conflict constitutes a Red Queen's race.
Article
Genetics & Heredity
Jeffrey C. Vedanayagam, Ching-Jung Lin, Ranjith Papareddy, Michael Nodine, Alex Flynt, Jiayu Wen, Eric Lai
Summary: Recent studies have shown the important role of endogenous RNAi in suppressing selfish genes in the fruitfly Drosophila simulans. Hairpin RNA (hpRNA) loci generate endo-siRNAs that suppress X-linked meiotic drive loci. Comparative genomic analyses reveal an expanded network of hpRNA-target interactions in D. simulans. These findings provide insights into the emergence and potential roles of hpRNAs in sex chromosome conflict.
Article
Cell Biology
Eric C. Lai, Aaron A. Vogan
Summary: Killer meiotic drive elements are genetic entities that manipulate the sexual cycle to promote their own inheritance. Recent research has shown that many of these systems are caused by a single gene, and similar molecular genetic studies in fruit flies have identified individual loci that distort gamete sex. These meiotic drive elements can easily duplicate, forming gene families that provide the basis for their rapid functional diversification.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2023)
Review
Genetics & Heredity
Renfu Shang, Seungjae Lee, Gayan Senavirathne, Eric C. Lai
Summary: In this Review, the authors discuss how new technologies have advanced our understanding of miRNA biology. They provide an overview of miRNA biogenesis, function, and processing, and highlight the challenges for future research.
NATURE REVIEWS GENETICS
(2023)
Review
Biology
Seungjae Lee, Joseph Aubee, Eric C. Lai
Summary: Cell-type-specific gene expression is achieved through various regulatory strategies. The nervous system extensively uses cell-specific isoforms to specialize gene function. Alternative splicing and alternative polyadenylation are regulatory strategies involved in neural-specific isoform processing, and misregulation of these processes can lead to neural pathologies and mutant phenotypes.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemistry & Molecular Biology
Sweta Khanal, Matthew de Cruz, Britton Strickland, Kody Mansfield, Eric C. Lai, Alex Flynt
Summary: This study reveals that miR-1017, a highly expressed mirtron in Drosophila, can extend the lifespan of neurons through targeting its host transcript and affecting splicing.
NUCLEIC ACIDS RESEARCH
(2023)
