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Sivagurunathan N, Rahamathulla MP, Al-Dossary H, Calivarathan L. Emerging Role of Long Noncoding RNAs in Regulating Inflammasome-Mediated Neurodegeneration in Parkinson's Disease. Mol Neurobiol 2024; 61:4619-4632. [PMID: 38105409 DOI: 10.1007/s12035-023-03809-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
Parkinson's disease (PD) is one of the complex neurodegenerative disorders, primarily characterized by motor deficits, including bradykinesia, tremor, rigidity, and postural instability. The underlying pathophysiology involves the progressive loss of dopaminergic neurons within the substantia nigra pars compacta, leading to dopamine depletion in the basal ganglia circuitry. While motor symptoms are hallmark features of PD, emerging research highlights a wide range of non-motor symptoms, including cognitive impairments, mood disturbances, and autonomic dysfunctions. Inflammasome activation is pivotal in inducing neuroinflammation and promoting disease onset, progression, and severity of PD. Several studies have shown that long noncoding RNAs (lncRNAs) modulate inflammasomes in the pathogenesis of neurodegenerative diseases. Dysregulation of lncRNAs is linked to aberrant gene expression and cellular processes in neurodegeneration, causing the activation of inflammasomes that contribute to neuroinflammation and neurodegeneration. Inflammasomes are cytosolic proteins that form complexes upon activation, inducing inflammation and neuronal cell death. This review explores the significance of lncRNAs in regulating inflammasomes in PD, primarily focusing on specific lncRNAs such as nuclear paraspeckle assembly transcript 1 (NEATNEAT1), X-inactive specific transcript (XIST), growth arrest-specific 5 (GAS5), and HOX transcript antisense RNA (HOTAIR), which have been shown to activate or inhibit the NLRP3 inflammasome and induce the release of proinflammatory cytokines. Moreover, some lncRNAs mediate inflammasome activation through miRNA interactions. Understanding the roles of lncRNAs in inflammasome regulation provides new therapeutic targets for controlling neuroinflammation and reducing the progression of neurodegeneration. Identifying lncRNA-mediated regulatory pathways paves the way for novel therapies in the battle against these devastating neurodegenerative disorders.
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Affiliation(s)
- Narmadhaa Sivagurunathan
- Molecular Pharmacology & Toxicology Laboratory, Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Neelakudi Campus, Thiruvarur, 610005, India
| | - Mohamudha Parveen Rahamathulla
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Kingdom of Saudi Arabia
| | - Hussein Al-Dossary
- University Hospital, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Kingdom of Saudi Arabia
| | - Latchoumycandane Calivarathan
- Molecular Pharmacology & Toxicology Laboratory, Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Neelakudi Campus, Thiruvarur, 610005, India.
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Scholda J, Nguyen TTA, Kopp F. Long noncoding RNAs as versatile molecular regulators of cellular stress response and homeostasis. Hum Genet 2024; 143:813-829. [PMID: 37782337 PMCID: PMC11294412 DOI: 10.1007/s00439-023-02604-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023]
Abstract
Normal cell and body functions need to be maintained and protected against endogenous and exogenous stress conditions. Different cellular stress response pathways have evolved that are utilized by mammalian cells to recognize, process and overcome numerous stress stimuli in order to maintain homeostasis and to prevent pathophysiological processes. Although these stress response pathways appear to be quite different on a molecular level, they all have in common that they integrate various stress inputs, translate them into an appropriate stress response and eventually resolve the stress by either restoring homeostasis or inducing cell death. It has become increasingly appreciated that non-protein-coding RNA species, such as long noncoding RNAs (lncRNAs), can play critical roles in the mammalian stress response. However, the precise molecular functions and underlying modes of action for many of the stress-related lncRNAs remain poorly understood. In this review, we aim to provide a framework for the categorization of mammalian lncRNAs in stress response and homeostasis based on their experimentally validated modes of action. We describe the molecular functions and physiological roles of selected lncRNAs and develop a concept of how lncRNAs can contribute as versatile players in mammalian stress response and homeostasis. These concepts may be used as a starting point for the identification of novel lncRNAs and lncRNA functions not only in the context of stress, but also in normal physiology and disease.
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Affiliation(s)
- Julia Scholda
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Thi Thuy Anh Nguyen
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Florian Kopp
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria.
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3
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Cheng Y, Wang S, Zhang H, Lee JS, Ni C, Guo J, Chen E, Wang S, Acharya A, Chang TC, Buszczak M, Zhu H, Mendell JT. A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence. Cell 2024:S0092-8674(24)00693-7. [PMID: 38981482 DOI: 10.1016/j.cell.2024.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/20/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
Cellular senescence is an irreversible state of cell-cycle arrest induced by various stresses, including aberrant oncogene activation, telomere shortening, and DNA damage. Through a genome-wide screen, we discovered a conserved small nucleolar RNA (snoRNA), SNORA13, that is required for multiple forms of senescence in human cells and mice. Although SNORA13 guides the pseudouridylation of a conserved nucleotide in the ribosomal decoding center, loss of this snoRNA minimally impacts translation. Instead, we found that SNORA13 negatively regulates ribosome biogenesis. Senescence-inducing stress perturbs ribosome biogenesis, resulting in the accumulation of free ribosomal proteins (RPs) that trigger p53 activation. SNORA13 interacts directly with RPL23, decreasing its incorporation into maturing 60S subunits and, consequently, increasing the pool of free RPs, thereby promoting p53-mediated senescence. Thus, SNORA13 regulates ribosome biogenesis and the p53 pathway through a non-canonical mechanism distinct from its role in guiding RNA modification. These findings expand our understanding of snoRNA functions and their roles in cellular signaling.
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Affiliation(s)
- Yujing Cheng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Siwen Wang
- Division of Vascular Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jong-Sun Lee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jason Guo
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric Chen
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shenming Wang
- Division of Vascular Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - Asha Acharya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tsung-Cheng Chang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Alard EL, Capraro F, Rekad Z, Stojic L, Mardakheh FK. TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods 2024; 21:423-434. [PMID: 38374261 PMCID: PMC10927567 DOI: 10.1038/s41592-024-02181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells and under endogenous settings. Here we introduce TREX (targeted RNase H-mediated extraction of crosslinked RBPs)-a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD long noncoding RNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and previously unknown interactions that regulate ribosome biogenesis. With its applicability to different cell types, TREX is an RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
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Affiliation(s)
- Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giulia Guiducci
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sneha Krishnamurthy
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Emilie L Alard
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Federica Capraro
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Zeinab Rekad
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lovorka Stojic
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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Wang D, Zhang Z, Li X, He L. RNA binding protein PUM2 promotes IL-1β-induced apoptosis of chondrocytes via regulating FOXO3 expression. Heliyon 2024; 10:e25080. [PMID: 38356524 PMCID: PMC10865267 DOI: 10.1016/j.heliyon.2024.e25080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Objective RNA-binding proteins (RBPs) have been recently proven to be involved in the pathogenesis of several diseases. However, few studies elaborated RBPs in regulating osteoarthritis. This study aims to define the function and mechanism of RBPs-PUM2 in chondrocyte apoptosis during osteoarthritis. Methods Cartilage tissue samples and human juvenile chondrocyte cell line C28/I2 were collected for further study. PUM2 expression in the human tissues and cells was determined using qRT-PCR. Chondrocyte viability and apoptosis were determined by MTT and flow cytometry. ROS generation was determined by flow cytometry. The regulation of PUM2 on FOXO3 translation was evaluated by RNA immunoprecipitation, RNA pull-down, and Luciferase gene reporter analysis. Results PUM2 is upregulated in both cartilage tissue of osteoarthritis patients and IL-1β-stimulated chondrocytes. PUM2 overexpression reduces cell viability and promotes cell apoptosis and ROS generation of chondrocytes. PUM2 silencing increases cell viability and ameliorates cell apoptosis as well as ROS generation in chondrocytes induced by IL-1β. PUM2 inhibits FOXO3 expression via binding its mRNA 3'-UTR. PUM2 forms a signaling axis with FOXO3 in IL-1β induced chondrocyte damage. Conclusion PUM2 is upregulated in cartilage tissue of osteoarthritis and positively regulates chondrocytes apoptosis through controlling FOXO3 protein expression.
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Affiliation(s)
- Du Wang
- Department of Orthopedics, Wuhan Third Hospital, Tongren Hospital of Wuhan University, Wuhan, China
| | - ZhiLi Zhang
- Department of Surgery, Wuhan Third Hospital, Tongren Hospital of Wuhan University, Wuhan, China
| | - Xili Li
- Department of Radiology, Wuhan Third Hospital, Tongren Hospital of Wuhan University, Wuhan, China
| | - Ling He
- Department of Orthopedics, Wuhan Third Hospital, Tongren Hospital of Wuhan University, Wuhan, China
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Capela AM, Tavares-Marcos C, Estima-Arede HF, Nóbrega-Pereira S, Bernardes de Jesus B. NORAD-Regulated Signaling Pathways in Breast Cancer Progression. Cancers (Basel) 2024; 16:636. [PMID: 38339387 PMCID: PMC10854850 DOI: 10.3390/cancers16030636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Long non-coding RNA activated by DNA damage (NORAD) has recently been associated with pathologic mechanisms underlying cancer progression. Due to NORAD's extended range of interacting partners, there has been contradictory data on its oncogenic or tumor suppressor roles in BC. This review will summarize the function of NORAD in different BC subtypes and how NORAD impacts crucial signaling pathways in this pathology. Through the preferential binding to pumilio (PUM) proteins PUM1 and PUM2, NORAD has been shown to be involved in the control of cell cycle, angiogenesis, mitosis, DNA replication and transcription and protein translation. More recently, NORAD has been associated with PUM-independent roles, accomplished by interacting with other ncRNAs, mRNAs and proteins. The intricate network of NORAD-mediated signaling pathways may provide insights into the potential design of novel unexplored strategies to overcome chemotherapy resistance in BC treatment.
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Affiliation(s)
| | | | | | - Sandrina Nóbrega-Pereira
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.C.); (C.T.-M.); (H.F.E.-A.)
| | - Bruno Bernardes de Jesus
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.C.); (C.T.-M.); (H.F.E.-A.)
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7
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Gu J, Lu J, Yang J, Liu Y, Zhu X, Zhang J, Shen H, Li X, Yu Z, Li H. Norad Competently Binds with Pum2 to Regulate Neuronal Apoptosis and Play a Neuroprotective Role After SAH in Mice. Neuroscience 2023; 535:108-123. [PMID: 37913857 DOI: 10.1016/j.neuroscience.2023.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 08/14/2023] [Accepted: 08/19/2023] [Indexed: 11/03/2023]
Abstract
Subarachnoid Hemorrhage (SAH) is a cerebrovascular disorder that has been found to have severe consequences, including a high mortality and disability rate. Research has indicated that neuronal death, particularly apoptosis, plays a major role in the neurological impairment that follows SAH. RNA-binding protein Pum2 can interfere with translation or other biological functions by connecting to the UGUAHAUA sequence on RNA. Noncoding RNA activated by DNA damage (Norad) contains some Pum2 recognition sequences, which may bind to Pum2 protein and affect its capacity to attach to target mRNA. The time course expression of Norad and Pum2 after SAH is analyzed by establishing a mouse SAH model. Subsequently, the purpose of this study is to investigate the potential role and mechanism of the Norad-Pum2 axis after SAH using lentivirus overexpression of Pum2 and knockdown of Norad. Analysis of Pum2 and Norad levels reveal that the former is significantly reduce and the latter is significantly increased in the SAH group compared to the sham group. Subsequent overexpression of Pum2 and Norad knockdown is found to reduce SAH-induced oxidative stress, neuronal apoptosis, and ultimately improve behavioral and cognitive changes in SAH mice. Our study indicates that Norad-Pum2 acts as a neuromodulator in SAH, and that by increasing Pum2 and decreasing Norad levels, SAH-induced neuronal apoptosis can be reduced and neurological deficits alleviated. Consequently, Norad-Pum2 may be a promising therapeutic target for SAH.
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Affiliation(s)
- Junyi Gu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Jinxin Lu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Jian Yang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Yangyang Liu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Xunan Zhu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Juyi Zhang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Haitao Shen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Xiang Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Zhengquan Yu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China.
| | - Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China.
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Zhang L, Xu J, Li M, Chen X. The role of long noncoding RNAs in liquid-liquid phase separation. Cell Signal 2023; 111:110848. [PMID: 37557974 DOI: 10.1016/j.cellsig.2023.110848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
Long noncoding RNAs (lncRNAs), which are among the most well-characterized noncoding RNAs, have attracted much attention due to their regulatory functions and potential therapeutic options in many types of disease. Liquid-liquid phase separation (LLPS), the formation of droplet condensates, is involved in various cellular processes, but the molecular interactions of lncRNAs in LLPS are unclear. In this review, we describe the research development on LLPS, including descriptions of various methods established to identify LLPS, summarize the physiological and pathological functions of LLPS, identify the molecular interactions of lncRNAs in LLPS, and present the potential applications of leveraging LLPS in the clinic. The aim of this review is to update the knowledge on the association between LLPS and lncRNAs, which might provide a new direction for the treatment of LLPS-mediated disease.
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Affiliation(s)
- Le Zhang
- Center for Reproductive Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China
| | - Jinjin Xu
- Department of Imaging Medicine, The People's Hospital of the Inner Mongolia Autonomous Region, Hohhot 010017, Inner Mongolia, China
| | - Muxuan Li
- The First Clinical Medical College of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China
| | - Xiujuan Chen
- Center for Reproductive Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China.
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Zhang J, Jiang J, Zhou H, Li S, Bian W, Hu L, Zhang D, Xu C, Sun Y. LncRNA NORAD defects deteriorate the formation of age-related macular degeneration. Aging (Albany NY) 2023; 15:7513-7532. [PMID: 37517088 PMCID: PMC10457045 DOI: 10.18632/aging.204917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/23/2023] [Indexed: 08/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in the development of age-related macular degeneration (AMD). However, the effect of long non-coding RNA activated by DNA damage (NORAD) on AMD remains unknown. This study aimed to investigate the effect of NORAD on RPE cell senescence and degeneration. Irradiated adult retinal pigment epithelial cell line-19 (ARPE-19) and sodium iodate-treated mice were used as in vitro and in vivo AMD models. Results showed that irradiation-induced AMD characteristics of ARPE-19 and NORAD-knockdown aggravated cell cycle arrest in the G2/M phase, cell apoptosis and cell senescence along with the increased expression of phosphorylated P53 (p-P53) and P21. AMD factors C3, ICAM-1, APP, APOE, and VEGF-A were also increased by NORAD-knockdown. Moreover, NORAD-knockdown increased irradiation-induced reduction of mitochondrial homeostasis factors, (i.e., TFAM and POLG) and mitochondrial respiratory chain complex genes (i.e., ND1 and ND5) along with mitochondrial reactive oxygen species (ROS). We also identified a strong interaction of NORAD and PGC-1α and sirtuin 1 (SIRT1) in ARPE-19; that is, NORAD knockdown increases the acetylation of PGC-1α. In NORAD knockout mice, NORAD-knockout accelerated the sodium iodate-reduced retinal thickness reduction, function impairment and loss of retinal pigment in the fundus. Therefore, NORAD-knockdown accelerates retinal cell senescence, apoptosis, and AMD markers via PGC-1α acetylation, mitochondrial ROS, and the p-P53-P21signaling pathway, in which NORAD-mediated effect on PGC-1α acetylation might occur through the direct interaction with PGC-1α and SIRT1.
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Affiliation(s)
- Jinfeng Zhang
- College of Pharmacy, Binzhou Medical University, Shandong, China
| | - Jing Jiang
- College of Pharmacy, Binzhou Medical University, Shandong, China
| | - Hongyu Zhou
- College of Pharmacy, Binzhou Medical University, Shandong, China
| | - Shenjun Li
- Non-Clinical Research Department, RemeGen Co., Ltd, Shandong, China
| | - Weihua Bian
- College of Pharmacy, Binzhou Medical University, Shandong, China
| | - Lifu Hu
- Non-Clinical Research Department, RemeGen Co., Ltd, Shandong, China
| | - Daolai Zhang
- College of Pharmacy, Binzhou Medical University, Shandong, China
| | - Cong Xu
- College of Pharmacy, Binzhou Medical University, Shandong, China
| | - Yeying Sun
- College of Pharmacy, Binzhou Medical University, Shandong, China
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10
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Widyarti S, Wibowo S, Sabarudin A, Abhirama I, Sumitro SB. Dysfunctional energy and future perspective of low dose H 2O 2 as protective agent in neurodegenerative disease. Heliyon 2023; 9:e18123. [PMID: 37519743 PMCID: PMC10372669 DOI: 10.1016/j.heliyon.2023.e18123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 05/21/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
The number of people with neurodegenerative disease continues to increase every year. A new perspective is needed to overcome this disease. In this review, researchers collected information about dysfunctional energy in neurodegenerative diseases driven by mitochondria. Mitochondrial dysregulation can cause damage to the neuron system. The increase in the amount and interaction of α-synuclein with SAMM50 and GABARAPL1 in the mitochondria is one of the factors causing neurodegenerative disease. As an energy provider in the body, the existence of harmonization in the regulation of mitochondria, specifically the mitochondrial outer membrane, is important. Low-dose hydrogen peroxide (H2O2) has neuroprotective abilities to overcome the impairment function of mitochondria in neurodegenerative patients. Based on computational simulation of this case, it can be used as a basic concept for the development of the role of H2O2 in neurodegenerative diseases.
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Affiliation(s)
- Sri Widyarti
- Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang 65145, East Java, Indonesia
| | - Syahputra Wibowo
- Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang 65145, East Java, Indonesia
- Postdoctoral Fellow, Faculty of Biology, Gadjah Mada University, Teknika Selatan Sekip Utara, 55281 Yogyakarta, Indonesia
| | - Akhmad Sabarudin
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang 65145, East Java, Indonesia
| | - Intan Abhirama
- Department of Neurology, Bogor Senior Hospital, Jl.Raya Tajur 16137, West Java, Indonesia
| | - Sutiman Bambang Sumitro
- Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang 65145, East Java, Indonesia
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11
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Yang Q, Fang D, Chen J, Hu S, chen N, Jiang J, Zeng M, Luo M. LncRNAs associated with oxidative stress in diabetic wound healing: Regulatory mechanisms and application prospects. Theranostics 2023; 13:3655-3674. [PMID: 37441585 PMCID: PMC10334824 DOI: 10.7150/thno.85823] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Diabetes is a group of chronic diseases with blood glucose imbalance, and long-term hyperglycaemia causes sustained damage to various organs of the body, resulting in vascular lesions, neuropathy and impaired wound healing. Diabetic wound formation involves a variety of complex mechanisms, and they are characterized by a persistent chronic inflammatory response, degradation of angiogenesis and imbalance of extracellular matrix regulation, all of which are related to oxidative stress. Additionally, repair and healing of diabetic wounds require the participation of a variety of cells, cytokines, genes, and other factors, which together constitute a complex biological regulatory network. Recent studies have shown that long noncoding RNAs (lncRNAs) can be involved in the regulation of several key biological pathways and cellular functions demonstrating their critical role in diabetic wound healing. LncRNAs are a major family of RNAs with limited or no protein-coding function. Numerous studies have recently reported a strong link between oxidative stress and lncRNAs. Given that both lncRNAs and oxidative stress have been identified as potential drivers of diabetic wound healing, their link in diabetic wound healing can be inferred. However, the specific mechanism of oxidative stress related to lncRNAs in diabetic wound healing is still unclear, and elucidating the functions of lncRNAs in these processes remains a major challenge. This article reviews the mechanisms of lncRNAs related to oxidative stress in several stages of diabetic wound healing and discusses diagnostic and treatment potential of lncRNAs to treat diabetic wounds by improving oxidative stress, as well as the challenges of using lncRNAs for this purpose. It is hoped that these results will provide new targets and strategies for the diagnosis and treatment of impaired wound healing in diabetic patients.
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Affiliation(s)
- Qinzhi Yang
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Luzhou Municipal Key Laboratory of Thrombosis and Vascular Biology, Luzhou, Sichuan, China
| | - Dan Fang
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Luzhou Municipal Key Laboratory of Thrombosis and Vascular Biology, Luzhou, Sichuan, China
| | - Jinxiang Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Luzhou Municipal Key Laboratory of Thrombosis and Vascular Biology, Luzhou, Sichuan, China
| | - Shaorun Hu
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Luzhou Municipal Key Laboratory of Thrombosis and Vascular Biology, Luzhou, Sichuan, China
| | - Ni chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Luzhou Municipal Key Laboratory of Thrombosis and Vascular Biology, Luzhou, Sichuan, China
| | - Jun Jiang
- Department of General Surgery (Thyroid Surgery), the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, China
| | - Min Zeng
- Department of Pharmacy, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Mao Luo
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- Luzhou Municipal Key Laboratory of Thrombosis and Vascular Biology, Luzhou, Sichuan, China
- Department of Pharmacy, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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12
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 426] [Impact Index Per Article: 426.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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13
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Mammalian pumilio proteins control cellular morphology, migration, and adhesion. Sci Rep 2023; 13:3002. [PMID: 36810759 PMCID: PMC9944931 DOI: 10.1038/s41598-023-30004-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023] Open
Abstract
Pumilio proteins are RNA-binding proteins that control mRNA translation and stability by binding to the 3' UTR of target mRNAs. Mammals have two canonical Pumilio proteins, PUM1 and PUM2, which are known to act in many biological processes, including embryonic development, neurogenesis, cell cycle regulation and genomic stability. Here, we characterized a new role of both PUM1 and PUM2 in regulating cell morphology, migration, and adhesion in T-REx-293 cells, in addition to previously known defects in growth rate. Gene ontology analysis of differentially expressed genes in PUM double knockout (PDKO) cells for both cellular component and biological process showed enrichment in categories related to adhesion and migration. PDKO cells had a collective cell migration rate significantly lower than that of WT cells and displayed changes in actin morphology. In addition, during growth, PDKO cells aggregated into clusters (clumps) due to an inability to escape cell-cell contacts. Addition of extracellular matrix (Matrigel) alleviated the clumping phenotype. Collagen IV (ColIV), a major component of Matrigel, was shown to be the driving force in allowing PDKO cells to monolayer appropriately, however, ColIV protein levels remained unperturbed in PDKO cells. This study characterizes a novel cellular phenotype associated with cellular morphology, migration, and adhesion which can aid in developing better models for PUM function in both developmental processes and disease.
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14
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Saga Y, Shimoyama Y, Yamada Y, Morikawa N, Kawata T. The cytosolic lncRNA dutA affects STATa signaling and developmental commitment in Dictyostelium. Genes Cells 2023; 28:111-128. [PMID: 36504347 DOI: 10.1111/gtc.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/27/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
STATa is a pivotal transcription factor for Dictyostelium development. dutA is the most abundant RNA transcribed by RNA polymerase II in Dictyostelium, and its functional interplay with STATa has been suggested. This study demonstrates that dutA RNA molecules are distributed as spot-like structures in the cytoplasm, and that its cell type-specific expression changes dramatically during development. dutA RNA was exclusively detectable in the prespore region of slugs and then predominantly localized in prestalk cells, including the organizer region, at the Mexican hat stage before most dutA transcripts, excluding those in prestalk O cells, disappeared as culmination proceeded. dutA RNA was not translated into small peptides from any potential open reading frame, which confirmed that it is a cytoplasmic lncRNA. Ectopic expression of dutA RNA in the organizer region of slugs caused a prolonged slug migration period. In addition, buffered suspension-cultured cells of the strain displayed reduced STATa nuclear translocation and phosphorylation on Tyr702. Analysis of gene expression in various dutA mutants revealed changes in the levels of several STATa-regulated genes, such as the transcription factors mybC and gtaG, which might affect the phenotype. dutA RNA may regulate several mRNA species, thereby playing an indirect role in STATa activation.
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Affiliation(s)
- Yukika Saga
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan.,Department of Pharmacology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Yudai Shimoyama
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Yoko Yamada
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan.,Department of Materials and Life Sciences, Sophia University, Tokyo, Japan
| | - Naoki Morikawa
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Takefumi Kawata
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
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15
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Wei L, Xia H, Liang Z, Yu H, Liang Z, Yang X, Li Y. Disrupted expression of long non-coding RNAs in the human oocyte: the possible epigenetic culprits leading to recurrent oocyte maturation arrest. J Assist Reprod Genet 2022; 39:2215-2225. [PMID: 36018477 PMCID: PMC9596671 DOI: 10.1007/s10815-022-02596-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/10/2022] [Indexed: 11/26/2022] Open
Abstract
PURPOSE To depict the lncRNA expression during human oocyte maturation and explore the lncRNAs leading to recurrent oocyte maturation arrest. METHODS LncRNA sequencing was performed on pooled RNA from 20 oocytes of each group (recurrent oocyte maturation arrest (ROMA), of germinal vesicle (GV), metaphase I (MI), or metaphase II (MII) stages. Bioinformatics software was deployed to compare the lncRNA differential expression between the normal and ROMA oocytes. The co-expression of lncRNA/mRNA was illustrated with the Cytoscape software. The pooled RNA from every 10 oocytes of each group (ROMA, GV, MI, MII) was extracted for further qPCR validation. RESULTS There were 17 downregulated and 3 upregulated lncRNAs in the ROMA oocyte. Among them, co-expression analysis indicated that NEAT1 and NORAD were both downregulated. Basing on the KEGG enrichment analysis, PRCKA and JAK3 might be the target genes in the PI3K-Akt pathway and modulated by NEAT1 and NORAD. As validated by qPCR, the expressional levels of lncRNA candidates (NEAT1 and NORAD) and their target genes (PRKCA and JAK3) were confirmed to be extremely lower in the ROMA oocyte than in the normal oocyte. CONCLUSION By targeting the PI3K-Akt pathway genes PRKCA and JAK3, the abnormal expression of NEAT1 and NORAD is suggested to impede oocyte maturation and impair oocyte genome integrity.
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Affiliation(s)
- Lina Wei
- Division of Histology and Embryology, International Joint Laboratory for Embryonic Development and Prenatal Medicine, Medical College, Jinan University, Guangzhou, China
| | - Huayang Xia
- Center for Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Zhongkun Liang
- Center for Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Hao Yu
- Urology Department, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Zhenjie Liang
- Center for Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Xi Yang
- Center for Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yi Li
- Center for Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China.
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16
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Rajasekaran S, Khan E, Ching SR, Khan M, Siddiqui J, Gradia DF, Lin C, Bouley SJ, Mercadante D, Manning AL, Gerber AP, Walker J, Miles W. PUMILIO competes with AUF1 to control DICER1 RNA levels and miRNA processing. Nucleic Acids Res 2022; 50:7048-7066. [PMID: 35736218 PMCID: PMC9262620 DOI: 10.1093/nar/gkac499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
DICER1 syndrome is a cancer pre-disposition disorder caused by mutations that disrupt the function of DICER1 in miRNA processing. Studying the molecular, cellular and oncogenic effects of these mutations can reveal novel mechanisms that control cell homeostasis and tumor biology. Here, we conduct the first analysis of pathogenic DICER1 syndrome allele from the DICER1 3'UTR. We find that the DICER1 syndrome allele, rs1252940486, abolishes interaction with the PUMILIO RNA binding protein with the DICER1 3'UTR, resulting in the degradation of the DICER1 mRNA by AUF1. This single mutational event leads to diminished DICER1 mRNA and protein levels, and widespread reprogramming of miRNA networks. The in-depth characterization of the rs1252940486 DICER1 allele, reveals important post-transcriptional regulatory events that control DICER1 levels.
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Affiliation(s)
- Swetha Rajasekaran
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Samuel R Ching
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Misbah Khan
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Jalal K Siddiqui
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Daniela F Gradia
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Chenyu Lin
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Stephanie J Bouley
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dayna L Mercadante
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Amity L Manning
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - André P Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - James A Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wayne O Miles
- To whom correspondence should be addressed. Tel: +1 614 366 2869;
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17
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Ross CJ, Ulitsky I. Discovering functional motifs in long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1708. [PMID: 34981665 DOI: 10.1002/wrna.1708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 12/27/2022]
Abstract
Long noncoding RNAs (lncRNAs) are products of pervasive transcription that closely resemble messenger RNAs on the molecular level, yet function through largely unknown modes of action. The current model is that the function of lncRNAs often relies on specific, typically short, conserved elements, connected by linkers in which specific sequences and/or structures are less important. This notion has fueled the development of both computational and experimental methods focused on the discovery of functional elements within lncRNA genes, based on diverse signals such as evolutionary conservation, predicted structural elements, or the ability to rescue loss-of-function phenotypes. In this review, we outline the main challenges that the different methods need to overcome, describe the recently developed approaches, and discuss their respective limitations. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Caroline Jane Ross
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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18
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Gao XY, Yang T, Gu Y, Sun XH. Mitochondrial Dysfunction in Parkinson’s Disease: From Mechanistic Insights to Therapy. Front Aging Neurosci 2022; 14:885500. [PMID: 35795234 PMCID: PMC9250984 DOI: 10.3389/fnagi.2022.885500] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/30/2022] [Indexed: 12/02/2022] Open
Abstract
Parkinson’s disease (PD) is one of the most common neurodegenerative movement disorders worldwide. There are currently no cures or preventative treatments for PD. Emerging evidence indicates that mitochondrial dysfunction is closely associated with pathogenesis of sporadic and familial PD. Because dopaminergic neurons have high energy demand, cells affected by PD exhibit mitochondrial dysfunction that promotes the disease-defining the loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc). The mitochondrion has a particularly important role as the cellular “powerhouse” of dopaminergic neurons. Therefore, mitochondria have become a promising therapeutic target for PD treatments. This review aims to describe mitochondrial dysfunction in the pathology of PD, outline the genes associated with familial PD and the factors related to sporadic PD, summarize current knowledge on mitochondrial quality control in PD, and give an overview of therapeutic strategies for targeting mitochondria in neuroprotective interventions in PD.
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Affiliation(s)
- Xiao-Yan Gao
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Science Experiment Center, China Medical University, Shenyang, China
| | - Tuo Yang
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Ying Gu
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiao-Hong Sun
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Science Experiment Center, China Medical University, Shenyang, China
- *Correspondence: Xiao-Hong Sun,
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19
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Li X, Zhu M, Zang M, Cao D, Xie Z, Liang H, Bian Z, Zhao T, Hu Z, Xu EY. PUMILIO-mediated translational control of somatic cell cycle program promotes folliculogenesis and contributes to ovarian cancer progression. Cell Mol Life Sci 2022; 79:279. [PMID: 35507203 PMCID: PMC11072887 DOI: 10.1007/s00018-022-04254-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023]
Abstract
Translational control is a fundamental mechanism regulating animal germ cell development. Gonadal somatic cells provide support and microenvironment for germ cell development to ensure fertility, yet the roles of translational control in gonadal somatic compartment remain largely undefined. We found that mouse homolog of conserved fly germline stem cell factor Pumilio, PUM1, is absent in oocytes of all growing follicles after the primordial follicle stage, instead, it is highly expressed in somatic compartments of ovaries. Global loss of Pum1, not oocyte-specific loss of Pum1, led to a significant reduction in follicular number and size as well as fertility. Whole-genome identification of PUM1 targets in ovarian somatic cells revealed an enrichment of cell proliferation pathway, including 48 key regulators of cell phase transition. Consistently granulosa cells proliferation is reduced and the protein expression of the PUM-bound Cell Cycle Regulators (PCCR) were altered accordingly in mutant ovaries, and specifically in granulosa cells. Increase in negative regulator expression and decrease in positive regulators in the mutant ovaries support a coordinated translational control of somatic cell cycle program via PUM proteins. Furthermore, postnatal knockdown, but not postnatal oocyte-specific loss, of Pum1 in Pum2 knockout mice reduced follicular growth and led to similar expression alteration of PCCR genes, supporting a critical role of PUM-mediated translational control in ovarian somatic cells for mammalian female fertility. Finally, expression of human PUM protein and its regulated cell cycle targets exhibited significant correlation with ovarian cancer and prognosis for cancer survival. Hence, PUMILIO-mediated cell cycle regulation represents an important mechanism in mammalian female reproduction and human cancer biology.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Reproductive Medicine (Suzhou Centre), The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Mengyi Zhu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Min Zang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Dandan Cao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhengyao Xie
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Haibo Liang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zexin Bian
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Tingting Zhao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine (Suzhou Centre), The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Eugene Yujun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Department of Neurology, Center for Reproductive Science, Feinberg School of Medicine, Northwestern University Feinberg School of Medicine, Chicago, USA.
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20
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Thomas A, Rehfeld F, Zhang H, Chang TC, Goodarzi M, Gillet F, Mendell JT. RBM33 directs the nuclear export of transcripts containing GC-rich elements. Genes Dev 2022; 36:550-565. [PMID: 35589130 PMCID: PMC9186391 DOI: 10.1101/gad.349456.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/03/2022] [Indexed: 12/13/2022]
Abstract
Although splicing is a major driver of RNA nuclear export, many intronless RNAs are efficiently exported to the cytoplasm through poorly characterized mechanisms. For example, GC-rich sequences promote nuclear export in a splicing-independent manner, but how GC content is recognized and coupled to nuclear export is unknown. Here, we developed a genome-wide screening strategy to investigate the mechanism of export of NORAD, an intronless cytoplasmic long noncoding RNA (lncRNA). This screen revealed an RNA binding protein, RBM33, that directs the nuclear export of NORAD and numerous other transcripts. RBM33 directly binds substrate transcripts and recruits components of the TREX-NXF1/NXT1 RNA export pathway. Interestingly, high GC content emerged as the feature that specifies RBM33-dependent nuclear export. Accordingly, RBM33 directly binds GC-rich elements in target transcripts. These results provide a broadly applicable strategy for the genetic dissection of nuclear export mechanisms and reveal a long-sought nuclear export pathway for transcripts with GC-rich sequences.
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Affiliation(s)
- Anu Thomas
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Frederick Rehfeld
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Tsung-Cheng Chang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Mohammad Goodarzi
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Frank Gillet
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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21
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From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. Nat Rev Genet 2022; 23:229-243. [PMID: 34837040 DOI: 10.1038/s41576-021-00427-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide sequencing has led to the discovery of thousands of long non-coding RNA (lncRNA) loci in the human genome, but evidence of functional significance has remained controversial for many lncRNAs. Genetically engineered model organisms are considered the gold standard for linking genotype to phenotype. Recent advances in CRISPR-Cas genome editing have led to a rapid increase in the use of mouse models to more readily survey lncRNAs for functional significance. Here, we review strategies to investigate the physiological relevance of lncRNA loci by highlighting studies that have used genetic mouse models to reveal key in vivo roles for lncRNAs, from fertility to brain development. We illustrate how an investigative approach, starting with whole-gene deletion followed by transcription termination and/or transgene rescue strategies, can provide definitive evidence for the in vivo function of mammalian lncRNAs.
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22
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Liu X, Xu M, Li P, Zhang W, Zeng LH, Yang Y, Yang G. Roles of lncRNAs in the transcription regulation of HIV-1. Biomed J 2022; 45:580-593. [PMID: 35364293 PMCID: PMC9486250 DOI: 10.1016/j.bj.2022.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (LncRNAs) is a class of RNA molecules that are more than 200bp but cannot be translated into proteins. More and more studies have proved that lncRNA plays a crucial role in various biological functions and disease processes, including virus infection. It's worth noting that studies have also shown that lncRNAs play an essential role in the pathogenesis of human immunodeficiency virus 1 (HIV-1), one of the lethal virus that can destroy immune system. Although lncRNA-mediated gene regulation involves a variety of mechanisms, such as transcription regulation, translation regulation, protein modification, and the formation of RNA-protein complexes, in this review, we primarily focus on the role of lncRNAs in HIV-1 transcription regulation, which is one of the most important mechanisms that control the activation and development of HIV-1. This review also briefly summarizes the latest research progress of lncRNAs related to HIV-1 infection and its potential application in HIV-1 therapy. Although there are antiretroviral drugs that interfere with the function of HIV-1 virus-encoded proteins, this treatment for the HIV-1 virus is limited by its ability to produce drug resistance. Hence, a further understanding of HIV-1 transcription regulation by lncRNAs might help develop non-traditional antiviral therapy strategies.
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Affiliation(s)
- Xingzhu Liu
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Mengjiao Xu
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ping Li
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Wenyuan Zhang
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ling-Hui Zeng
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China.
| | - Yadong Yang
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Geng Yang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China.
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23
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Li G, Ma L, He S, Luo R, Wang B, Zhang W, Song Y, Liao Z, Ke W, Xiang Q, Feng X, Wu X, Zhang Y, Wang K, Yang C. WTAP-mediated m 6A modification of lncRNA NORAD promotes intervertebral disc degeneration. Nat Commun 2022; 13:1469. [PMID: 35304463 PMCID: PMC8933458 DOI: 10.1038/s41467-022-28990-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent RNA modification at the posttranscriptional level and involved in various diseases and cellular processes. However, the underlying mechanism of m6A regulation in intervertebral disc degeneration (IVDD) remains elusive. Here, we show that methylation of the lncRNA NORAD significantly increases in senescent nucleus pulposus cells (NPCs) by m6A sequencing. Subsequent loss- and gain-of-function experiments reveal WTAP is increased in senescent NPCs due to an epigenetic increase in H3K4me3 of the promoter mediated by KDM5a, and significantly promotes NORAD m6A modification. Furthermore, YTHDF2-mediated decay of NORAD is enhanced in senescent NPCs, and then deficiency of NORAD results in less sequestraion of PUMILIO proteins, contributing to the augmented activity of PUM1/2, thus repressing the expression of target E2F3 mRNAs and promoting the cellular senescence. Here, we show interruption of NORAD m6A modification or the NORAD/PUMILIO/E2F3 axis could serve as a potential therapeutic target to inhibit the senescence of NPCs and development of IVDD. Intervertebral disc degeneration (IVDD) is the leading cause of low back pain and Nucleus pulposus cell senescence contributes a lot to its progression. Here, the authors reveal WTAP-mediated m6A modification of lncRNA NORAD promotes IVDD.
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Affiliation(s)
- Gaocai Li
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Liang Ma
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Shujie He
- Department of Cardiology, Union Hospital, and Key Laboratory of Biological Targeted Therapy of the Ministry of Education, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Rongjin Luo
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Bingjin Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Weifeng Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yu Song
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Zhiwei Liao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Wencan Ke
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Qian Xiang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Xiaobo Feng
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Xinghuo Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yukun Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Kun Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
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24
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Suppression of lncRNA NORAD may affect cell migration and apoptosis in gastric cancer cells. Mol Biol Rep 2022; 49:3289-3296. [PMID: 35083614 DOI: 10.1007/s11033-022-07167-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Gastric cancer (GC) is a major malignancy that threatens people's lives worldwide. Long noncoding RNA (lncRNA) non-coding RNA activated by DNA damage (NORAD) is known to be a potential oncogene in many cancers and may promote cell migration and metastasis, and decrease apoptosis rate. MATERIAL AND METHODS NORAD expression was measured in 70 pairs of GC tissues and their adjacent normal tissues (ANTs) by quantitative real-time polymerase chain reaction. Si-NORAD gene knockdown study and cellular assays were conducted to assess the correlation between NORAD expression and cell viability, apoptosis, migration, and metastasis. RESULTS NORAD was significantly overexpressed in GC tissues compared to ANTs (P value < 0.0001). The receiver operating characteristic curve indicated the AUC of 0.721 with the sensitivity and specificity of 78.57 and 61.43, respectively (P value < 0.0001). NORAD downregulation leads to decreased cell viability (P value < 0.001) and migration (P value < 0.01), increased apoptosis rate (P value < 0.0001), and increased protein level for PTEN, E-cadherin, and Bax, but decreased protein level for Bcl-2. CONCLUSION Generally, NORAD may serve as a potential diagnostic biomarker in GC.
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25
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Fernández-Alvarez AJ, Thomas MG, Pascual ML, Habif M, Pimentel J, Corbat AA, Pessoa JP, La Spina PE, Boscaglia L, Plessis A, Carmo-Fonseca M, Grecco HE, Casado M, Boccaccio GL. Smaug1 membrane-less organelles respond to AMPK/mTOR and affect mitochondrial function‡. J Cell Sci 2021; 135:273619. [PMID: 34859817 DOI: 10.1242/jcs.253591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
Smaug is a conserved translational regulator that binds numerous mRNAs, including nuclear transcripts that encode mitochondrial enzymes. Smaug orthologs form cytosolic membrane-less organelles (MLOs) in several organisms and cell types. We have performed single-molecule FISH assays that revealed that SDHB and UQCRC1 mRNAs associate with Smaug1 bodies in U2OS cells. Loss of function of Smaug1 and Smaug2 affected both mitochondrial respiration and morphology of the mitochondrial network. Phenotype rescue by Smaug1 transfection depends on the presence of its RNA binding domain. Moreover, we identified specific Smaug1 domains involved in MLO formation, and found that impaired Smaug1 MLO condensation correlates with mitochondrial defects. Mitochondrial Complex I inhibition by rotenone -but not strong mitochondrial uncoupling by CCCP- rapidly induced Smaug1 MLOs dissolution. Metformin and rapamycin elicited similar effects, which were blocked by pharmacological inhibition of AMPK. Finally, we found that Smaug1 MLO dissolution weakens the interaction with target mRNAs, thus enabling their release. We propose that mitochondrial respiration and the AMPK/mTOR balance controls the condensation and dissolution of Smaug1 MLOs, thus regulating nuclear mRNAs that encode key mitochondrial proteins.
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Affiliation(s)
- Ana J Fernández-Alvarez
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - María Gabriela Thomas
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Malena L Pascual
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Martín Habif
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Jerónimo Pimentel
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Agustín A Corbat
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - João P Pessoa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Pablo E La Spina
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | | | - Anne Plessis
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Hernán E Grecco
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Marta Casado
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia 46010, Spain, and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid 28029, Spain
| | - Graciela L Boccaccio
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina.,Department of Molecular and Cellular Biology and Physiology (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, C1428EHA Buenos Aires, Argentina
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26
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Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:118-141. [PMID: 34791665 PMCID: PMC9808899 DOI: 10.1111/nyas.14713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023]
Abstract
The human transcriptome contains many types of noncoding RNAs, which rival the number of protein-coding species. From long noncoding RNAs (lncRNAs) that are over 200 nucleotides long to piwi-interacting RNAs (piRNAs) of only 20 nucleotides, noncoding RNAs play important roles in regulating transcription, epigenetic modifications, translation, and cell signaling. Roles for noncoding RNAs in disease mechanisms are also being uncovered, and several species have been identified as potential drug targets. On May 11-14, 2021, the Keystone eSymposium "Noncoding RNAs: Biology and Applications" brought together researchers working in RNA biology, structure, and technologies to accelerate both the understanding of RNA basic biology and the translation of those findings into clinical applications.
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Affiliation(s)
| | - Edith Heard
- European Molecular Biology Laboratory (EMBL), Heidelberg, Heidelberg, Germany
- Collège de France, Paris, France
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Sciences, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, China
| | | | - Sofia A Quinodoz
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor and Genetics Program, Stony Brook University, Stony Brook, New York
| | - Sarah D Diermeier
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Allison M Porman
- Biochemistry and Molecular Genetics Department, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Dhiraj Kumar
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xiaohua Shen
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Juan Pablo Unfried
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), Pamplona, Spain
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital; and Department for BioMedical Research University of Bern, Bern, Switzerland
- School of Biology and Environmental Science and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Adelheid Lempradl
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, Michigan
| | - Sean E McGeary
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
- Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Lamia Wahba
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Anna Marie Pyle
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
- Connecticut and Howard Hughes Medical Institute, Chevy Chase, Maryland
| | | | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Róża K Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California
- Howard Hughes Medical Institute, Stanford University, Stanford, California
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College of Cornell University, New York, New York
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, California
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, California
| | - Joshua T Mendell
- Department of Molecular Biology, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine; and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lin He
- Division of Cellular and Developmental Biology, Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, California
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center and Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Bioland Laboratory; Program of Molecular Medicine, Zhongshan School of Medicine, Sun Yat-sen University; and Fountain-Valley Institute for Life Sciences, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences Guangzhou, Guangzhou, China
| | - John L Rinn
- Department of Biochemistry, BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado
| | - Mukesh Kumar Lalwani
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, Scotland, United Kingdom
| | - Murat Can Kalem
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, New York
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, New York
| | - Xuhang Liu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, New York
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27
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Abstract
Although long noncoding RNAs (lncRNAs) are generally expressed at low levels, emerging evidence has revealed that many play important roles in gene regulation by a variety of mechanisms as they engage with proteins. Given that the abundance of proteins often greatly exceeds that of their interacting lncRNAs, quantification of the relative abundance, or even the exact stoichiometry in some cases, within lncRNA-protein complexes is helpful for understanding of the mechanism(s) of action of lncRNAs. We discuss methods used to examine lncRNA and protein expression at the single cell, subcellular, and suborganelle levels, the average and local lncRNA concentration in cells, as well as how lncRNAs can modulate the functions of their interacting proteins even at a low stoichiometric concentration.
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Affiliation(s)
- Man Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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28
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Mercer M, Jang S, Ni C, Buszczak M. The Dynamic Regulation of mRNA Translation and Ribosome Biogenesis During Germ Cell Development and Reproductive Aging. Front Cell Dev Biol 2021; 9:710186. [PMID: 34805139 PMCID: PMC8595405 DOI: 10.3389/fcell.2021.710186] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/07/2021] [Indexed: 01/21/2023] Open
Abstract
The regulation of mRNA translation, both globally and at the level of individual transcripts, plays a central role in the development and function of germ cells across species. Genetic studies using flies, worms, zebrafish and mice have highlighted the importance of specific RNA binding proteins in driving various aspects of germ cell formation and function. Many of these mRNA binding proteins, including Pumilio, Nanos, Vasa and Dazl have been conserved through evolution, specifically mark germ cells, and carry out similar functions across species. These proteins typically influence mRNA translation by binding to specific elements within the 3′ untranslated region (UTR) of target messages. Emerging evidence indicates that the global regulation of mRNA translation also plays an important role in germ cell development. For example, ribosome biogenesis is often regulated in a stage specific manner during gametogenesis. Moreover, oocytes need to produce and store a sufficient number of ribosomes to support the development of the early embryo until the initiation of zygotic transcription. Accumulating evidence indicates that disruption of mRNA translation regulatory mechanisms likely contributes to infertility and reproductive aging in humans. These findings highlight the importance of gaining further insights into the mechanisms that control mRNA translation within germ cells. Future work in this area will likely have important impacts beyond germ cell biology.
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Affiliation(s)
- Marianne Mercer
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Seoyeon Jang
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Chunyang Ni
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Michael Buszczak
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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29
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Long non-coding RNAs: novel regulators of cellular physiology and function. Pflugers Arch 2021; 474:191-204. [PMID: 34791525 PMCID: PMC8766390 DOI: 10.1007/s00424-021-02641-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/19/2022]
Abstract
Long non-coding RNAs were once considered as “junk” RNA produced by aberrant DNA transcription. They are now understood to play central roles in diverse cellular processes from proliferation and migration to differentiation, senescence and DNA damage control. LncRNAs are classed as transcripts longer than 200 nucleotides that do not encode a peptide. They are relevant to many physiological and pathophysiological processes through their control of fundamental molecular functions. This review summarises the recent progress in lncRNA research and highlights the far-reaching physiological relevance of lncRNAs. The main areas of lncRNA research encompassing their characterisation, classification and mechanisms of action will be discussed. In particular, the regulation of gene expression and chromatin landscape through lncRNA control of proteins, DNA and other RNAs will be introduced. This will be exemplified with a selected number of lncRNAs that have been described in numerous physiological contexts and that should be largely representative of the tens-of-thousands of mammalian lncRNAs. To some extent, these lncRNAs have inspired the current thinking on the central dogmas of epigenetics, RNA and DNA mechanisms.
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30
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Xiong X, Liu J, He Q, Dai R, Zhang H, Cao Z, Liao Y, Liu B, Zhou Y, Chen J, Liu J, Chen M. Long non-coding RNA NORAD aggravates acute myocardial infarction by promoting fibrosis and apoptosis via miR-577/COBLL1 axis. ENVIRONMENTAL TOXICOLOGY 2021; 36:2256-2265. [PMID: 34355838 DOI: 10.1002/tox.23339] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Acute myocardial infarction (AMI) is one of the most common and serious cardiovascular diseases. With high morbidity and mortality, AMI has attracted the most attention. Emerging studies indicated that long noncoding RNAs (lncRNAs) play an important role in the progression of AMI. However, the role of NORAD in AMI remained unclear. The current study aimed to investigate the function and mechanism of NORAD in AMI. Bioinformatics tools and a wide range of assays including RT-qPCR, flow cytometry, TTC staining, western blot, luciferase reporter and caspase-3 activity assays were conducted to investigate the function and mechanism of NORAD in AMI. We found out that NORAD was significantly upregulated in AMI rats. Knockdown of NORAD alleviated H9c2 cell injury by reducing apoptosis and decreasing expression levels of fibrogenic factors. In addition, NORAD inhibition ameliorated AMI in a rat model by decreasing infarct size and fibrosis. We confirmed that NORAD bound to miR-577, which was downregulated in ischemia-reperfusion (I/R) rats and hypoxia-exposed H9c2 cells. Additionally, miR-577 combined with the 3'UTR of COBLL1, which was upregulated in I/R rats and hypoxia-exposed H9c2 cells. At last, rescue assay validated that the suppressive effects of NORAD knockdown on apoptosis and expression levels of fibrogenic factors were counteracted by COBLL1 overexpression. Overall, NORAD aggravates acute myocardial infarction by promoting fibrosis and apoptosis via the miR-577/COBLL1 axis. This novel discovery suggested that NORAD may serve as a potential therapeutic target for AMI patients.
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Affiliation(s)
- Xiaojv Xiong
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinhua Liu
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin He
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Dai
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Zhang
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhe Cao
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanxi Liao
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Liu
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Zhou
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Chen
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jijun Liu
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Manhua Chen
- Department of Cardiovascular Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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31
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Mourtzi N, Siahanidou T, Tsifintaris M, Karamichali E, Tasiopoulou A, Sertedaki A, Pesmatzoglou M, Kapetanaki A, Liosis G, Baltatzis G, Vlachakis D, Chrousos GP, Giannakakis A. lncRNA NORAD is consistently detected in breastmilk exosomes and its expression is downregulated in mothers of preterm infants. Int J Mol Med 2021; 48:216. [PMID: 34651660 PMCID: PMC8559700 DOI: 10.3892/ijmm.2021.5049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/27/2021] [Indexed: 01/08/2023] Open
Abstract
Breast milk is the ideal food for infants and undoubtedly has immediate and long-term benefits. Breast milk contains extracellular vesicles (EVs) i.e., exosomes secreted by maternal breast cells. Exosomes carry genetic material, such as long non-coding RNAs (lncRNAs), which possibly participate in cell-to-cell communications, as they are known to regulate critical gene pathways. The aim of the present study was to screen human breastmilk exosomes for their lncRNA cargo and to examine exosomal lncRNA levels associated with milk obtained from mothers that gave birth at term or prematurely (<37 weeks of gestation). Samples were collected at 3 weeks postpartum from 20 healthy, breastfeeding mothers; 10 mothers had given birth at full-term and 10 mothers preterm. Exosomal RNA was extracted from all samples and the expression of 88 distinct lncRNAs was determined using reverse transcription-quantitative PCR. A total of 13 lncRNAs were detected in ≥85% of the samples, while 31 were detected in ≥50% of the samples. Differential expression analysis of the lncRNAs between the two groups revealed ≥2-fold differences, with generally higher lncRNA concentrations found in the milk of the mothers that gave birth at term compared with those that gave birth preterm. Among these, the non-coding RNA activated at DNA damage (NORAD) was prominently detected in both groups, and its expression was significantly downregulated in the breast milk exosomes of mothers who delivered preterm. On the whole, the present study demonstrates that breast milk lncRNAs may be important factors of normal early human development. Collectively, the presence of lncRNAs in human breast milk may explain the consistent inability of researchers to fully 'humanize' animal milk.
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Affiliation(s)
- Niki Mourtzi
- Laboratory of Molecular Endocrinology, Choremeio Research Center, First Department of Pediatrics, Children's Hospital 'Aghia Sophia', School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Tania Siahanidou
- First Department of Pediatrics, 'Aghia Sophia' Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Margaritis Tsifintaris
- Laboratory of Gene Expression, Molecular Diagnostics and Modern Therapeutics, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Eirini Karamichali
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Androniki Tasiopoulou
- Laboratory of Gene Expression, Molecular Diagnostics and Modern Therapeutics, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Amalia Sertedaki
- Laboratory of Molecular Endocrinology, Choremeio Research Center, First Department of Pediatrics, Children's Hospital 'Aghia Sophia', School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Margarita Pesmatzoglou
- First Department of Pediatrics, 'Aghia Sophia' Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | - George Liosis
- General and Maternity Hospital 'Helena Venizelou', 11521 Athens, Greece
| | - George Baltatzis
- First Department of Pathology, School of Health Sciences, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Antonis Giannakakis
- Laboratory of Gene Expression, Molecular Diagnostics and Modern Therapeutics, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
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32
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Chen Z, Rasheed M, Deng Y. The epigenetic mechanisms involved in mitochondrial dysfunction: Implication for Parkinson's disease. Brain Pathol 2021; 32:e13012. [PMID: 34414627 PMCID: PMC9048811 DOI: 10.1111/bpa.13012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/21/2021] [Accepted: 07/27/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial dysfunction is one of the crucial factors involved in PD’s pathogenicity, which emerges from a combination of genetic and environmental factors. These factors cause differential molecular expression in neurons, such as varied transcriptional regulation of genes, elevated oxidative stress, α‐synuclein aggregation and endogenous neurotoxins release, which induces epigenetic modifications and triggers energy crisis by damaging mitochondria of the dopaminergic neurons (DN). So far, these events establish a complicated relationship with underlying mechanisms of mitochondrial anomalies in PD, which has remained unclear for years and made PD diagnosis and treatment extremely difficult. Therefore, in this review, we endeavored to discuss the complex association of epigenetic modifications and other associated vital factors in mitochondrial dysfunction. We propose a hypothesis that describes a vicious cycle in which mitochondrial dysfunction and oxidative stress act as a hub for regulating DA neuron's fate in PD. Oxidative stress triggers the release of endogenous neurotoxins (CTIQs) that lead to mitochondrial dysfunction along with abnormal α‐synuclein aggregation and epigenetic modifications. These disturbances further intensify oxidative stress and mitochondrial damage, amplifying the synthesis of CTIQs and works vice versa. This vicious cycle may result in the degeneration of DN to hallmark Parkinsonism. Furthermore, we have also highlighted various endogenous compounds and epigenetic marks (neurotoxic and neuroprotective), which may help for devising future diagnostic biomarkers and target specific drugs using novel PD management strategies.
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Affiliation(s)
- Zixuan Chen
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Madiha Rasheed
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yulin Deng
- School of Life Science, Beijing Institute of Technology, Beijing, China
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33
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Duan N, Arroyo M, Deng W, Cardoso MC, Leonhardt H. Visualization and characterization of RNA-protein interactions in living cells. Nucleic Acids Res 2021; 49:e107. [PMID: 34313753 PMCID: PMC8501972 DOI: 10.1093/nar/gkab614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/14/2021] [Accepted: 07/07/2021] [Indexed: 12/26/2022] Open
Abstract
RNA–protein interactions are the structural and functional basis of significant numbers of RNA molecules. RNA–protein interaction assays though, still mainly depend on biochemical tests in vitro. Here, we establish a convenient and reliable RNA fluorescent three-hybrid (rF3H) method to detect/interrogate the interactions between RNAs and proteins in cells. A GFP tagged highly specific RNA trap is constructed to anchor the RNA of interest to an artificial or natural subcellular structure, and RNA–protein interactions can be detected and visualized by the enrichment of RNA binding proteins (RBPs) at these structures. Different RNA trapping systems are developed and detection of RNA–protein complexes at multiple subcellular structures are assayed. With this new toolset, interactions between proteins and mRNA or noncoding RNAs are characterized, including the interaction between a long noncoding RNA and an epigenetic modulator. Our approach provides a flexible and reliable method for the characterization of RNA–protein interactions in living cells.
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Affiliation(s)
- Ningjun Duan
- Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany.,Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Maria Arroyo
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Wen Deng
- Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany.,College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany
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34
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Singh N. Role of mammalian long non-coding RNAs in normal and neuro oncological disorders. Genomics 2021; 113:3250-3273. [PMID: 34302945 DOI: 10.1016/j.ygeno.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/09/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes but have a crucial role in gene regulation. LncRNA is distinct, they are being transcribed using RNA polymerase II, and their functionality depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer. To date, ~40% of lncRNAs have been reported in the nervous system (NS) and are involved in the early development/differentiation of the NS to synaptogenesis. LncRNA expression patterns in the most common adult and pediatric tumor suggest them as potential biomarkers and provide a rationale for targeting them pharmaceutically. Here, we discuss the mechanisms of lncRNA synthesis, localization, and functions in transcriptional, post-transcriptional, and other forms of gene regulation, methods of lncRNA identification, and their potential therapeutic applications in neuro oncological disorders as explained by molecular mechanisms in other malignant disorders.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Department of Centre for Advance Research, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India.
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35
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Bella F, Campo S. Long non-coding RNAs and their involvement in bipolar disorders. Gene 2021; 796-797:145803. [PMID: 34175394 DOI: 10.1016/j.gene.2021.145803] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/22/2021] [Indexed: 01/22/2023]
Abstract
Non-coding RNAs (nc-RNAs) can be defined as RNA molecules that are not translated into proteins. Although the functional meaning of many nc-RNAs remains still to be verified, several of these molecules have a clear biological importance, which goes from translation of mRNAs to DNA replication. Indeed, regulatory nc-RNAs can be classified into two groups: short non-coding RNAs (sncRNAs) and long-non coding RNAs (lncRNAs). In the last years, lncRNAs have gained increasing importance in the study of gene regulation, helping authors understand the molecular mechanisms underlying cellular physiology and pathology. LncRNAs are greater than 200 bp and accumulate in nucleus, cytoplasm and exosomes with high tissue specificity, acting in cis or in trans in order to exert enhancer or silencer modulation on gene expression. Such regulatory features, which are widespread in human cells and tissues, can be disrupted in several morbid states. Recent evidences may suggest a disruption of lncRNAs in bipolar disorders, a cluster of severe, chronic and disabling psychiatric diseases, which are characterized by major depressive states cyclically alternating with manic episodes. Here, the authors reviewed genes, classification, biogenesis, structures, functions and databases regarding lncRNAs, and also focused on bipolar disorders, in which some lncRNAs, especially those involved in inflammation and neuronal development, has reported to be dysregulated.
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Affiliation(s)
- Fabrizio Bella
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, via Consolare Valeria, 1, Messina 98125 Italy
| | - Salvatore Campo
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, via Consolare Valeria, 1, Messina 98125 Italy.
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36
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Sun X, Feinberg MW. Vascular Endothelial Senescence: Pathobiological Insights, Emerging Long Noncoding RNA Targets, Challenges and Therapeutic Opportunities. Front Physiol 2021; 12:693067. [PMID: 34220553 PMCID: PMC8242592 DOI: 10.3389/fphys.2021.693067] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a stable form of cell cycle arrest in response to various stressors. While it serves as an endogenous pro-resolving mechanism, detrimental effects ensue when it is dysregulated. In this review, we introduce recent advances for cellular senescence and inflammaging, the underlying mechanisms for the reduction of nicotinamide adenine dinucleotide in tissues during aging, new knowledge learned from p16 reporter mice, and the development of machine learning algorithms in cellular senescence. We focus on pathobiological insights underlying cellular senescence of the vascular endothelium, a critical interface between blood and all tissues. Common causes and hallmarks of endothelial senescence are highlighted as well as recent advances in endothelial senescence. The regulation of cellular senescence involves multiple mechanistic layers involving chromatin, DNA, RNA, and protein levels. New targets are discussed including the roles of long noncoding RNAs in regulating endothelial cellular senescence. Emerging small molecules are highlighted that have anti-aging or anti-senescence effects in age-related diseases and impact homeostatic control of the vascular endothelium. Lastly, challenges and future directions are discussed including heterogeneity of endothelial cells and endothelial senescence, senescent markers and detection of senescent endothelial cells, evolutionary differences for immune surveillance in mice and humans, and long noncoding RNAs as therapeutic targets in attenuating cellular senescence. Accumulating studies indicate that cellular senescence is reversible. A better understanding of endothelial cellular senescence through lifestyle and pharmacological interventions holds promise to foster a new frontier in the management of cardiovascular disease risk.
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Affiliation(s)
- Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.,Nebraska Center for the Prevention of Obesity Diseases Through Dietary Molecules, University of Nebraska-Lincoln, Lincoln, NE, United States.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
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37
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NORAD-induced Pumilio phase separation is required for genome stability. Nature 2021; 595:303-308. [PMID: 34108682 DOI: 10.1038/s41586-021-03633-w] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/11/2021] [Indexed: 01/10/2023]
Abstract
Liquid-liquid phase separation is a major mechanism of subcellular compartmentalization1,2. Although the segregation of RNA into phase-separated condensates broadly affects RNA metabolism3,4, whether and how specific RNAs use phase separation to regulate interacting factors such as RNA-binding proteins (RBPs), and the phenotypic consequences of such regulatory interactions, are poorly understood. Here we show that RNA-driven phase separation is a key mechanism through which a long noncoding RNA (lncRNA) controls the activity of RBPs and maintains genomic stability in mammalian cells. The lncRNA NORAD prevents aberrant mitosis by inhibiting Pumilio (PUM) proteins5-8. We show that NORAD can out-compete thousands of other PUM-binding transcripts to inhibit PUM by nucleating the formation of phase-separated PUM condensates, termed NP bodies. Dual mechanisms of PUM recruitment, involving multivalent PUM-NORAD and PUM-PUM interactions, enable NORAD to competitively sequester a super-stoichiometric amount of PUM in NP bodies. Disruption of NORAD-driven PUM phase separation leads to PUM hyperactivity and genome instability that is rescued by synthetic RNAs that induce the formation of PUM condensates. These results reveal a mechanism by which RNA-driven phase separation can regulate RBP activity and identify an essential role for this process in genome maintenance. The repetitive sequence architecture of NORAD and other lncRNAs9-11 suggests that phase separation may be a widely used mechanism of lncRNA-mediated regulation.
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38
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Maimaiti A, Wang X, Pei Y, Nuermaimaiti N, Tuersunniyazi A, Abula Y, Feng Z, Jiang L, Shi X, Kasimu M. Identification and validation of a novel eight mutant-derived long non-coding RNAs signature as a prognostic biomarker for genome instability in low-grade glioma. Aging (Albany NY) 2021; 13:15164-15192. [PMID: 34081618 PMCID: PMC8221298 DOI: 10.18632/aging.203079] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/11/2021] [Indexed: 04/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) comprise an integral part of the eukaryotic transcriptome. Alongside proteins, lncRNAs modulate lncRNA-based gene signatures of unstable transcripts, play a crucial role as antisense lncRNAs to control intracellular homeostasis and are implicated in tumorigenesis. However, the role of genomic instability-associated lncRNAs in low-grade gliomas (LGG) has not been fully explored. In this study, lncRNAs expression and somatic mutation profiles in low-grade glioma genome were used to identify eight novel mutant-derived genomic instability-associated lncRNAs including H19, FLG-AS1, AC091932.1, AC064875.1, AL138767.3, AC010273.2, AC131097.4 and ISX-AS1. Patients from the LGG gene mutagenome atlas were grouped into training and validation sets to test the performance of the signature. The genomic instability-associated lncRNAs signature (GILncSig) was then validated using multiple external cohorts. A total of 59 novel genomic instability-associated lncRNAs in LGG were used for least absolute shrinkage and selection operator (Lasso), single and multifactor Cox regression analysis using the training set. Furthermore, the independent predictive role of risk features in the training and validation sets were evaluated through survival analysis, receiver operating feature analysis and construction of a nomogram. Patients with IDH1 mutation status were grouped into two different risk groups based on the GILncSig score. The low-risk group showed a relatively higher rate of IDH1 mutations compared with patients in the high-risk group. Furthermore, patients in the low-risk group had better prognosis compared with patients in the high-risk group. In summary, this study reports a reliable prognostic prediction signature and provides a basis for further investigation of the role of lncRNAs on genomic instability. In addition, lncRNAs in the signature can be used as new targets for treatment of LGG.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Functional Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Xixian Wang
- Department of Functional Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Yinan Pei
- Department of Functional Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Nuerbiye Nuermaimaiti
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Disease in Central Asia, Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Abudireheman Tuersunniyazi
- Department of Functional Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Yaeraili Abula
- Department of Functional Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Zhaohai Feng
- Department of Functional Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Lei Jiang
- Department of Functional Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Xin Shi
- Department of Functional Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Maimaitijiang Kasimu
- Department of Functional Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
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Turner DJ, Turner M. RNA Binding Proteins As Regulators of Oxidative Stress Identified by a Targeted CRISPR-Cas9 Single Guide RNA Library. CRISPR J 2021; 4:427-437. [PMID: 34096786 PMCID: PMC8236562 DOI: 10.1089/crispr.2020.0116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome editing system has been broadly adopted for high-throughput genetic screens. However, the application of genome-wide single guide RNA (sgRNA) libraries can be challenging. We generated a custom sgRNA library, an order of magnitude smaller than genome-wide alternatives, to facilitate the genetic screening of RNA binding proteins (RBPs). We demonstrated the utility of our reagent in a genetic screen for RBPs that conveyed cellular resistance or sensitivity to oxidative stress induced by paraquat. This identified that CSDE1 and STRAP, proteins that interact with each other, convey sensitivity to oxidative stress and that Pumilio homologues (PUM1 and PUM2) convey resistance. Targeting eIF4-E1 and -A1 protected cells from high-dose paraquat, whereas eIF4E2 targeted cells did less well. We also found that G3BP1 promoted sensitivity to a low dose of paraquat but protected cells at a higher dose. Our study highlights the use of genetic screens to identify roles of RBPs and identifies novel genes regulating sensitivity to oxidative stress.
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Affiliation(s)
- David J. Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
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40
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Abstract
We have known for decades that long noncoding RNAs (lncRNAs) can play essential functions across most forms of life. The maintenance of chromosome length requires an lncRNA (e.g., hTERC) and two lncRNAs in the ribosome that are required for protein synthesis. Thus, lncRNAs can represent powerful RNA machines. More recently, it has become clear that mammalian genomes encode thousands more lncRNAs. Thus, we raise the question: Which, if any, of these lncRNAs could also represent RNA-based machines? Here we synthesize studies that are beginning to address this question by investigating fundamental properties of lncRNA genes, revealing new insights into the RNA structure-function relationship, determining cis- and trans-acting lncRNAs in vivo, and generating new developments in high-throughput screening used to identify functional lncRNAs. Overall, these findings provide a context toward understanding the molecular grammar underlying lncRNA biology.
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Affiliation(s)
- John L Rinn
- BioFrontiers Institute, Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA;
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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41
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Chorostecki U, Saus E, Gabaldón T. Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units. Comput Struct Biotechnol J 2021; 19:3245-3254. [PMID: 34141143 PMCID: PMC8192489 DOI: 10.1016/j.csbj.2021.05.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the functions of lncRNAS are largely mediated by their structures. However, our structural knowledge for most lncRNAS is limited to sequence-based computational predictions. Non-coding RNA activated by DNA damage (NORAD) is an atypical lncRNA due to its abundant expression and high sequence conservation. NORAD regulates genomic stability by interacting with proteins and microRNAs. Previous sequence-based characterization has identified a modular organization of NORAD composed of several NORAD repeat units (NRUs). These units comprise the protein-binding elements and are separated by regular spacers. Here, we experimentally determine for the first time the secondary structure of NORAD using the nextPARS approach. Our results suggest that the spacer regions provide structural stability to NRUs. Furthermore, we uncover two previously unreported NRUs, and determine the core structural motifs conserved across NRUs. Overall, these findings will help to elucidate the function and evolution of NORAD.
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Affiliation(s)
- Uciel Chorostecki
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, 29. 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, 29. 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, 29. 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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Guiducci G, Stojic L. Long Noncoding RNAs at the Crossroads of Cell Cycle and Genome Integrity. Trends Genet 2021; 37:528-546. [PMID: 33685661 DOI: 10.1016/j.tig.2021.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/28/2020] [Accepted: 01/18/2021] [Indexed: 12/14/2022]
Abstract
The cell cycle is controlled by guardian proteins that coordinate the process of cell growth and cell division. Alterations in these processes lead to genome instability, which has a causal link to many human diseases. Beyond their well-characterized role of influencing protein-coding genes, an increasing body of evidence has revealed that long noncoding RNAs (lncRNAs) actively participate in regulation of the cell cycle and safeguarding of genome integrity. LncRNAs are versatile molecules that act via a wide array of mechanisms. In this review, we discuss how lncRNAs are implicated in control of the cell cycle and maintenance of genome stability and how changes in lncRNA-regulatory networks lead to proliferative diseases such as cancer.
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Affiliation(s)
- Giulia Guiducci
- Barts Cancer Institute, Centre for Cancer Cell and Molecular Biology, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London EC1M 6BQ, UK
| | - Lovorka Stojic
- Barts Cancer Institute, Centre for Cancer Cell and Molecular Biology, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London EC1M 6BQ, UK.
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Chen Y, Li Z, Chen X, Zhang S. Long non-coding RNAs: From disease code to drug role. Acta Pharm Sin B 2021; 11:340-354. [PMID: 33643816 PMCID: PMC7893121 DOI: 10.1016/j.apsb.2020.10.001] [Citation(s) in RCA: 258] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/30/2022] Open
Abstract
Enormous studies have corroborated that long non-coding RNAs (lncRNAs) extensively participate in crucial physiological processes such as metabolism and immunity, and are closely related to the occurrence and development of tumors, cardiovascular diseases, nervous system disorders, nephropathy, and other diseases. The application of lncRNAs as biomarkers or intervention targets can provide new insights into the diagnosis and treatment of diseases. This paper has focused on the emerging research into lncRNAs as pharmacological targets and has reviewed the transition of lncRNAs from the role of disease coding to acting as drug candidates, including the current status and progress in preclinical research. Cutting-edge strategies for lncRNA modulation have been summarized, including the sources of lncRNA-related drugs, such as genetic technology and small-molecule compounds, and related delivery methods. The current progress of clinical trials of lncRNA-targeting drugs is also discussed. This information will form a latest updated reference for research and development of lncRNA-based drugs.
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Key Words
- AD, Alzheimer's disease
- ANRIL, antisense noncoding RNA gene at the INK4 locus
- ASO, antisense oligonucleotide
- ASncmtRNA
- ASncmtRNA, antisense noncoding mitochondrial RNA
- BCAR4, breast cancer anti-estrogen resistance 4
- BDNF-AS, brain-derived neurotrophic factor antisense
- CASC9, cancer susceptibility candidate 9
- CDK, cyclin dependent kinase 1
- CHRF, cardiac hypertrophy related factor
- CRISPR, clustered regularly interspaced short palindromic repeats
- Clinical trials
- DACH1, dachshund homolog 1
- DANCR, differentiation antagonizing non-protein coding RNA
- DKD, diabetic kidney disease
- DPF, diphenyl furan
- Delivery
- EBF3-AS, early B cell factor 3-antisense
- ENE, element for nuclear expression
- Erbb4-IR, Erb-B2 receptor tyrosine kinase 4-immunoreactivity
- FDA, U.S. Food and Drug Administration
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- GAS5, growth arrest specific 5
- Gene therapy
- HISLA, HIF-1α-stabilizing long noncoding RNA
- HOTAIR, HOX transcript antisense intergenic RNA
- HULC, highly upregulated in liver cancer
- LIPCAR, long intergenic noncoding RNA predicting cardiac remodeling
- LNAs, locked nucleic acids
- LncRNAs
- MALAT1, metastasis associated lung adenocarcinoma transcript 1
- MEG3, maternally expressed gene 3
- MHRT, myosin heavy chain associated RNA transcripts
- MM, multiple myeloma
- NEAT1, nuclear enriched abundant transcript 1
- NKILA, NF-kappaB interacting lncRNA
- NPs, nanoparticles
- Norad, non-coding RNA activated by DNA damage
- OIP5-AS1, opa-interacting protein 5 antisense transcript 1
- PD, Parkinson's disease
- PEG, polyethylene glycol
- PNAs, peptide nucleic acids
- PTO, phosphorothioate
- PVT1, plasmacytoma variant translocation 1
- RGD, arginine-glycine-aspartic acid peptide
- RISC, RNA-induced silencing complex
- SALRNA1, senescence associated long non-coding RNA 1
- SNHG1, small nucleolar RNA host gene 1
- Small molecules
- SncmtRNA, sense noncoding mitochondrial RNA
- THRIL, TNF and HNRNPL related immunoregulatory
- TTTY15, testis-specific transcript, Y-linked 15
- TUG1, taurine-upregulated gene 1
- TWIST1, twist family BHLH transcription factor 1
- Targeted drug
- TncRNA, trophoblast-derived noncoding RNA
- Translational medicine
- UCA1, urothelial carcinoma-associated 1
- UTF1, undifferentiated transcription factor 1
- XIST, X-inactive specific transcript
- lincRNA-p21, long intergenic noncoding RNA p21
- lncRNAs, long non-coding RNAs
- mtlncRNA, mitochondrial long noncoding RNA
- pHLIP, pH-low insertion peptide
- sgRNA, single guide RNA
- siRNAs, small interfering RNAs
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Constanty F, Shkumatava A. lncRNAs in development and differentiation: from sequence motifs to functional characterization. Development 2021; 148:148/1/dev182741. [PMID: 33441380 DOI: 10.1242/dev.182741] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of long noncoding RNAs (lncRNAs) with characterized developmental and cellular functions continues to increase, but our understanding of the molecular mechanisms underlying lncRNA functions, and how they are dictated by RNA sequences, remains limited. Relatively short, conserved sequence motifs embedded in lncRNA transcripts are often important determinants of lncRNA localization, stability and interactions. Identifying such RNA motifs remains challenging due to the substantial length of lncRNA transcripts and the rapid evolutionary turnover of lncRNA sequences. Nevertheless, the recent discovery of specific RNA elements, together with their experimental interrogation, has enabled the first step in classifying heterogeneous lncRNAs into sub-groups with similar molecular mechanisms and functions. In this Review, we focus on lncRNAs with roles in development, cell differentiation and normal physiology in vertebrates, and we discuss the sequence elements defining their functions. We also summarize progress on the discovery of regulatory RNA sequence elements, as well as their molecular functions and interaction partners.
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Affiliation(s)
- Florian Constanty
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | - Alena Shkumatava
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
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Role of PUM RNA-Binding Proteins in Cancer. Cancers (Basel) 2021; 13:cancers13010129. [PMID: 33401540 PMCID: PMC7796173 DOI: 10.3390/cancers13010129] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary PUM1 and PUM2 are RNA-binding Pumilio proteins controlling the accessibility of hundreds of mRNAs for translation in a variety of human tissues. As a result, PUMs exemplify one of the mechanisms safeguarding the cellular proteome. PUM expression is disturbed in cancer, resulting in dysregulation of their target mRNAs. These targets encode factors responsible for processes usually affected in cancer, such as proliferation, apoptosis, and the cell cycle. This review describes PUM1 and PUM2 ribonucleoprotein networks and highlights the mechanisms underlying the regulatory role of PUM proteins and, most importantly, the emerging impact of PUM dysregulation in cancer. It also emphasizes the importance of upcoming studies on PUM proteins in the context of cancer, as they may provide new therapeutic targets in the future. Abstract Until recently, post-transcriptional gene regulation (PTGR), in contrast to transcriptional regulation, was not extensively explored in cancer, even though it seems to be highly important. PUM proteins are well described in the PTGR of several organisms and contain the PUF RNA-binding domain that recognizes the UGUANAUA motif, located mostly in the 3′ untranslated region (3′UTR) of target mRNAs. Depending on the protein cofactors recruited by PUM proteins, target mRNAs are directed towards translation, repression, activation, degradation, or specific localization. Abnormal profiles of PUM expression have been shown in several types of cancer, in some of them being different for PUM1 and PUM2. This review summarizes the dysregulation of PUM1 and PUM2 expression in several cancer tissues. It also describes the regulatory mechanisms behind the activity of PUMs, including cooperation with microRNA and non-coding RNA machineries, as well as the alternative polyadenylation pathway. It also emphasizes the importance of future studies to gain a more complete picture of the role of PUM proteins in different types of cancer. Such studies may result in identification of novel targets for future cancer therapies.
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Abstract
Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.
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Ravanidis S, Doxakis E. RNA-Binding Proteins Implicated in Mitochondrial Damage and Mitophagy. Front Cell Dev Biol 2020; 8:372. [PMID: 32582692 PMCID: PMC7287033 DOI: 10.3389/fcell.2020.00372] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/27/2020] [Indexed: 01/19/2023] Open
Abstract
The mitochondrial lifecycle comprises biogenesis, fusion and cristae remodeling, fission, and breakdown by the autophagosome. This cycle is essential for maintaining proper cellular function, and inhibition of any of these processes results in deterioration of bioenergetics and swift induction of apoptosis, particularly in energy-craving cells such as myocytes and neurons. Regulation of gene expression is a fundamental step in maintaining mitochondrial plasticity, mediated by (1) transcription factors that control the expression of mitochondrial mRNAs and (2) RNA-binding proteins (RBPs) that regulate mRNA splicing, stability, targeting to mitochondria, and translation. More recently, RBPs have been also shown to interact with proteins modulating the mitochondrial lifecycle. Importantly, misexpression or mutations in RBPs give rise to mitochondrial dysfunctions, and there is strong evidence to support that these mitochondrial impairments occur early in disease development, constituting leading causes of pathogenesis. This review presents key aspects of the molecular network of the disease-relevant RBPs, including transactive response DNA-binding protein 43 (TDP43), fused in sarcoma (FUS), T-cell intracellular antigen 1 (TIA1), TIA-related protein (TIAR), and pumilio (PUM) that drive mitochondrial dysfunction in the nervous system.
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Affiliation(s)
- Stylianos Ravanidis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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Tietz KT, Gallagher TL, Mannings MC, Morrow ZT, Derr NL, Amacher SL. Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts. Dev Biol 2020; 462:129-140. [PMID: 32246943 DOI: 10.1016/j.ydbio.2020.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 01/06/2023]
Abstract
Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.
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Affiliation(s)
- Kiel T Tietz
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Thomas L Gallagher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Monica C Mannings
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zachary T Morrow
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nicolas L Derr
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Sharon L Amacher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University, Columbus, OH, 43210, USA.
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50
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Short Tandem Repeat-Enriched Architectural RNAs in Nuclear Bodies: Functions and Associated Diseases. Noncoding RNA 2020; 6:ncrna6010006. [PMID: 32093161 PMCID: PMC7151548 DOI: 10.3390/ncrna6010006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/31/2020] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Nuclear bodies are membraneless, phase-separated compartments that concentrate specific proteins and RNAs in the nucleus. They are believed to serve as sites for the modification, sequestration, and storage of specific factors, and to act as organizational hubs of chromatin structure to control gene expression and cellular function. Architectural (arc) RNA, a class of long noncoding RNA (lncRNA), plays essential roles in the formation of nuclear bodies. Herein, we focus on specific arcRNAs containing short tandem repeat-enriched sequences and introduce their biological functions and recently elucidated underlying molecular mechanism. In various neurodegenerative diseases, abnormal nuclear and cytoplasmic bodies are built on disease-causing RNAs or toxic RNAs with aberrantly expanded short tandem repeat-enriched sequences. We discuss the possible analogous functions of natural arcRNAs and toxic RNAs with short tandem repeat-enriched sequences. Finally, we describe the technical utility of short tandem repeat-enriched arcRNAs as a model for exploring the structures and functions of nuclear bodies, as well as the pathogenic mechanisms of neurodegenerative diseases.
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