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Shatskikh AS, Fefelova EA, Klenov MS. Functions of RNAi Pathways in Ribosomal RNA Regulation. Noncoding RNA 2024; 10:19. [PMID: 38668377 PMCID: PMC11054153 DOI: 10.3390/ncrna10020019] [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: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.
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Affiliation(s)
- Aleksei S. Shatskikh
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia;
| | - Elena A. Fefelova
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Mikhail S. Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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2
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Ruggiero V, Fagioli C, de Pretis S, Di Carlo V, Landsberger N, Zacchetti D. Complex CDKL5 translational regulation and its potential role in CDKL5 deficiency disorder. Front Cell Neurosci 2023; 17:1231493. [PMID: 37964795 PMCID: PMC10642286 DOI: 10.3389/fncel.2023.1231493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
CDKL5 is a kinase with relevant functions in correct neuronal development and in the shaping of synapses. A decrease in its expression or activity leads to a severe neurodevelopmental condition known as CDKL5 deficiency disorder (CDD). CDD arises from CDKL5 mutations that lie in the coding region of the gene. However, the identification of a SNP in the CDKL5 5'UTR in a patient with symptoms consistent with CDD, together with the complexity of the CDKL5 transcript leader, points toward a relevant translational regulation of CDKL5 expression with important consequences in physiological processes as well as in the pathogenesis of CDD. We performed a bioinformatics and molecular analysis of the 5'UTR of CDKL5 to identify translational regulatory features. We propose an important role for structural cis-acting elements, with the involvement of the eukaryotic translational initiation factor eIF4B. By evaluating both cap-dependent and cap-independent translation initiation, we suggest the presence of an IRES supporting the translation of CDKL5 mRNA and propose a pathogenic effect of the C>T -189 SNP in decreasing the translation of the downstream protein.
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Affiliation(s)
- Valeria Ruggiero
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudio Fagioli
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano de Pretis
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valerio Di Carlo
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Nicoletta Landsberger
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Daniele Zacchetti
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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3
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Yang Y, Chen Z, Le H. CTCF-mediated H3K27me3 enrichment on the LncRNA MALAT1 promoter regulates the cardiomyocytes from I/R-induced apoptosis through targeting miR-26b-5p. Mol Cell Toxicol 2023. [DOI: 10.1007/s13273-022-00246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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4
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Adnane S, Marino A, Leucci E. LncRNAs in human cancers: signal from noise. Trends Cell Biol 2022; 32:565-573. [DOI: 10.1016/j.tcb.2022.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 12/31/2022]
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5
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Vendramin R, Katopodi V, Cinque S, Konnova A, Knezevic Z, Adnane S, Verheyden Y, Karras P, Demesmaeker E, Bosisio FM, Kucera L, Rozman J, Gladwyn-Ng I, Rizzotto L, Dassi E, Millevoi S, Bechter O, Marine JC, Leucci E. Activation of the integrated stress response confers vulnerability to mitoribosome-targeting antibiotics in melanoma. J Exp Med 2021; 218:e20210571. [PMID: 34287642 PMCID: PMC8424468 DOI: 10.1084/jem.20210571] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
The ability to adapt to environmental stress, including therapeutic insult, contributes to tumor evolution and drug resistance. In suboptimal conditions, the integrated stress response (ISR) promotes survival by dampening cytosolic translation. We show that ISR-dependent survival also relies on a concomitant up-regulation of mitochondrial protein synthesis, a vulnerability that can be exploited using mitoribosome-targeting antibiotics. Accordingly, such agents sensitized to MAPK inhibition, thus preventing the development of resistance in BRAFV600E melanoma models. Additionally, this treatment compromised the growth of melanomas that exhibited elevated ISR activity and resistance to both immunotherapy and targeted therapy. In keeping with this, pharmacological inactivation of ISR, or silencing of ATF4, rescued the antitumoral response to the tetracyclines. Moreover, a melanoma patient exposed to doxycycline experienced complete and long-lasting response of a treatment-resistant lesion. Our study indicates that the repurposing of mitoribosome-targeting antibiotics offers a rational salvage strategy for targeted therapy in BRAF mutant melanoma and a therapeutic option for NRAS-driven and immunotherapy-resistant tumors.
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Affiliation(s)
- Roberto Vendramin
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sonia Cinque
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Angelina Konnova
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Zorica Knezevic
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sara Adnane
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Yvessa Verheyden
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Panagiotis Karras
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, Katholieke Universiteit Leuven, Belgium
| | - Ewout Demesmaeker
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Lukas Kucera
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Jan Rozman
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | | | - Lara Rizzotto
- Trace, Leuven Cancer Institute, Katholieke Universiteit Leuven, Belgium
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Stefania Millevoi
- Cancer Research Centre of Toulouse, Institut national de la santé et de la recherche médicale Joint Research Unit 1037, Toulouse, France
- Université Toulouse III Paul Sabatier, Toulouse, France
- Laboratoire d’Excellence “TOUCAN,” Toulouse, France
| | - Oliver Bechter
- Department of General Medical Oncology, Leuven Cancer Institute, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, Katholieke Universiteit Leuven, Belgium
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
- Trace, Leuven Cancer Institute, Katholieke Universiteit Leuven, Belgium
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6
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Zaniani NR, Oroujalian A, Valipour A, Peymani M. LAMTOR5 expression level is a biomarker for colorectal cancer and lncRNA LAMTOR5-AS1 predicting miRNA sponging effect. Mol Biol Rep 2021; 48:6093-6101. [PMID: 34374893 DOI: 10.1007/s11033-021-06623-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/03/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Strong evidence indicated that high expression of HBXIP (also known as LAMTOR5) promotes cancer cells proliferation and helps cancer progression. Long non-coding RNAs (lncRNA) have also a crucial role in developing cancer. In this study, we aimed to determine the expression of LAMTOR5 and its nearby lncRNA, LAMTOR5-AS1 and investigate their potential as a biomarker in colorectal cancer (CRC) patients. METHODS 75 tissues of colorectal tumors and non-tumor adjacent normal sampled in this study. After RNA procedure then RT-qPCR was applied for expression analysis. Moreover, in silico investigation also enrolled for predicting sponging effect of lncRNA with miRNAs. RESULTS LAMTOR5 transcription level significantly overexpressed (p value < 0.001) and has shown a diagnostic potential (AUC = 0.8) in CRC. LAMTOR5-AS1 did not indicate any remarkable expression change overall, but showed a significant overexpressed in elderly patients (> 60) with CRC (p value < 0.0097). Moreover, the correlation analysis between LAMTOR5 and LAMTOR5-AS1 revealed a significant association in CRC (p value = 0.0074) which can be partly explained by its predicting act as a mediator with sponging effect on hsa-miR-let-7b-3p and hsa-miR-20a-5p. CONCLUSION LAMTOR5 gene can be considered as prognostic biomarker for CRC. LAMTOR5-AS5 which is a nearby lncRNA of this gene could play a regulatory impact through its sponging effect on hsa-miR-let-7b-3p and hsa-miR-20a-5p which both have shown a significant impact on overall survival rate in CRC patients in high expression levels.
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Affiliation(s)
- Najmeh Riahi Zaniani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Andisheh Oroujalian
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Ali Valipour
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
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Non-Coding, RNAPII-Dependent Transcription at the Promoters of rRNA Genes Regulates Their Chromatin State in S. cerevisiae. Noncoding RNA 2021; 7:ncrna7030041. [PMID: 34287362 PMCID: PMC8293398 DOI: 10.3390/ncrna7030041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022] Open
Abstract
Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.
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8
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Oocyte specific lncRNA variant Rose influences oocyte and embryo development. Noncoding RNA Res 2021; 6:107-113. [PMID: 34278057 PMCID: PMC8258604 DOI: 10.1016/j.ncrna.2021.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/11/2021] [Accepted: 06/23/2021] [Indexed: 11/21/2022] Open
Abstract
Fully grown mammalian oocytes store a large amount of RNA synthesized during the transcriptionally active growth stage. A large part of the stored RNA belongs to the long non-coding class which contain either transcriptional noise or important contributors to cellular physiology. Despite the expanding number of studies related to lncRNAs, their influence on oocyte physiology remains enigmatic. We found an oocyte specific antisense, long non-coding RNA, "Rose" (lncRNA in Oocyte Specifically Expressed) expressed in two variants containing two and three non-coding exons, respectively. Rose is localized in the nucleus of transcriptionally active oocyte and in embryo with polysomal occupancy in the cytoplasm. Experimental overexpression of Rose in fully grown oocyte did not show any differences in meiotic maturation. However, knocking down Rose resulted in abnormalities in oocyte cytokinesis and impaired preimplantation embryo development. In conclusion, we have identified an oocyte-specific maternal lncRNA that is essential for successful mammalian oocyte and embryo development.
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Gu W, Wang L, Gu R, Ouyang H, Bao B, Zheng L, Xu B. Defects of cohesin loader lead to bone dysplasia associated with transcriptional disturbance. J Cell Physiol 2021; 236:8208-8225. [PMID: 34170011 DOI: 10.1002/jcp.30491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 02/05/2023]
Abstract
Cohesin loader nipped-B-like protein (Nipbl) is increasingly recognized for its important role in development and cancer. Cornelia de Lange Syndrome (CdLS), mostly caused by heterozygous mutations of Nipbl, is an autosomal dominant disease characterized by multiorgan malformations. However, the regulatory role and underlying mechanism of Nipbl in skeletal development remain largely elusive. In this study, we constructed a Nipbl-a Cas9-knockout (KO) zebrafish, which displayed severe retardation of global growth and skeletal development. Deficiency of Nipbl remarkably compromised cell growth and survival, and osteogenic differentiation of mammalian osteoblast precursors. Furthermore, Nipbl depletion impaired the cell cycle process, and caused DNA damage accumulation and cellular senescence. In addition, nucleolar fibrillarin expression, global rRNA biogenesis, and protein translation were defective in the Nipbl-depleted osteoblast precursors. Interestingly, an integrated stress response inhibitor (ISRIB), partially rescued Nipbl depletion-induced cellular defects in proliferation and apoptosis, osteogenesis, and nucleolar function. Simultaneously, we performed transcriptome analysis of Nipbl deficiency on human neural crest cells and mouse embryonic fibroblasts in combination with Nipbl ChIP-Seq. We found that Nipbl deficiency caused thousands of differentially expressed genes including some important genes in bone and cartilage development. In conclusion, Nipbl deficiency compromised skeleton development through impairing osteoblast precursor cell proliferation and survival, and osteogenic differentiation, and also disturbing the expression of some osteogenesis-regulatory genes. Our study elucidated that Nipbl played a pivotal role in skeleton development, and supported the fact that treatment of ISRIB may provide an early intervention strategy to alleviate the bone dysplasia of CdLS.
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Affiliation(s)
- Weihuai Gu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lihong Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renjie Gu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huiya Ouyang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Baicheng Bao
- Hospital of Stomatology, Orthodontic Department, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liwei Zheng
- State Key Laboratory of Oral Diseases, Department of Pediatric Dentistry, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Baoshan Xu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong, China
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10
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Aquino JB, Sierra R, Montaldo LA. Diverse cellular origins of adult blood vascular endothelial cells. Dev Biol 2021; 477:117-132. [PMID: 34048734 DOI: 10.1016/j.ydbio.2021.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/26/2021] [Accepted: 05/14/2021] [Indexed: 12/11/2022]
Abstract
During embryonic stages, vascular endothelial cells (ECs) originate from the mesoderm, at specific extraembryonic and embryonic regions, through a process called vasculogenesis. In the adult, EC renewal/replacement mostly depend on local resident ECs or endothelial progenitor cells (EPCs). Nevertheless, contribution from circulating ECs/EPCs was also reported. In addition, cells lacking from EC/EPC markers with in vitro extended plasticity were shown to originate endothelial-like cells (ELCs). Most of these cells consist of mesenchymal stromal progenitors, which would eventually get mobilized from the bone marrow after injury. Based on that, current knowledge on different mouse and human bone marrow stromal cell (BM-SC) subpopulations, able to contribute with mesenchymal stromal/stem cells (MSCs), is herein reviewed. Such analyses underline an unexpected heterogeneity among sinusoidal LepR+ stromal/CAR cells. For instance, in a recent report a subgroup of LepR+ stromal/CAR progenitors, which express GLAST and is traced in Wnt1Cre;R26RTom mice, was found to contribute with ELCs in vivo. These GLAST + Wnt1+ BM-SCs were shown to get mobilized to the peripheral blood and to contribute with liver regeneration. Other sources of ELCs, such as adipose, neural and dental pulp tissues, were also published. Finally, mechanisms likely involved in the enhanced cellular plasticity properties of bone marrow/adipose tissue stromal cells, able to originate ELCs, are assessed. In the future, strategies to analyze the in vivo expression profile of stromal cells, with MSC properties, in combination with screening of active genomic regions at the single cell-level, during early postnatal development and/or after injury, will likely help understanding properties of these ELC sources.
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Affiliation(s)
- Jorge B Aquino
- CONICET-Universidad Austral, Instituto de Investigaciones en Medicina Traslacional (IIMT), Developmental Biology & Regenerative Medicine Laboratory, Argentina.
| | - Romina Sierra
- CONICET-Universidad Austral, Instituto de Investigaciones en Medicina Traslacional (IIMT), Developmental Biology & Regenerative Medicine Laboratory, Argentina
| | - Laura A Montaldo
- CONICET-Universidad Austral, Instituto de Investigaciones en Medicina Traslacional (IIMT), Developmental Biology & Regenerative Medicine Laboratory, Argentina
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11
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MicroRNAs and long non-coding RNAs as novel regulators of ribosome biogenesis. Biochem Soc Trans 2021; 48:595-612. [PMID: 32267487 PMCID: PMC7200637 DOI: 10.1042/bst20190854] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/14/2022]
Abstract
Ribosome biogenesis is the fine-tuned, essential process that generates mature ribosomal subunits and ultimately enables all protein synthesis within a cell. Novel regulators of ribosome biogenesis continue to be discovered in higher eukaryotes. While many known regulatory factors are proteins or small nucleolar ribonucleoproteins, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) are emerging as a novel modulatory layer controlling ribosome production. Here, we summarize work uncovering non-coding RNAs (ncRNAs) as novel regulators of ribosome biogenesis and highlight their links to diseases of defective ribosome biogenesis. It is still unclear how many miRNAs or lncRNAs are involved in phenotypic or pathological disease outcomes caused by impaired ribosome production, as in the ribosomopathies, or by increased ribosome production, as in cancer. In time, we hypothesize that many more ncRNA regulators of ribosome biogenesis will be discovered, which will be followed by an effort to establish connections between disease pathologies and the molecular mechanisms of this additional layer of ribosome biogenesis control.
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12
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Aprile M, Katopodi V, Leucci E, Costa V. LncRNAs in Cancer: From garbage to Junk. Cancers (Basel) 2020; 12:cancers12113220. [PMID: 33142861 PMCID: PMC7692075 DOI: 10.3390/cancers12113220] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Sequencing-based transcriptomics has significantly redefined the concept of genome complexity, leading to the identification of thousands of lncRNA genes identification of thousands of lncRNA genes whose products possess transcriptional and/or post-transcriptional regulatory functions that help to shape cell functionality and fate. Indeed, it is well-established now that lncRNAs play a key role in the regulation of gene expression through epigenetic and posttranscriptional mechanims. The rapid increase of studies reporting lncRNAs alteration in cancers has also highlighted their relevance for tumorigenesis. Herein we describe the most prominent examples of well-established lncRNAs having oncogenic and/or tumor suppressive activity. We also discuss how technical advances have provided new therapeutic strategies based on their targeting, and also report the challenges towards their use in the clinical settings.
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Affiliation(s)
- Marianna Aprile
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy;
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, LKI, Herestraat 49, 3000 Leuven, Belgium; (V.K.); (E.L.)
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, LKI, Herestraat 49, 3000 Leuven, Belgium; (V.K.); (E.L.)
| | - Valerio Costa
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy;
- Correspondence:
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13
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Lu Z, Yu Y, Ding X, Jin D, Wang G, Zhou Y, Zhu Y, Na L, He Y, Wang Q. LncRNA FLJ33360 accelerates the metastasis in hepatocellular carcinoma by targeting miRNA-140/MMP9 axis. Am J Transl Res 2020; 12:583-591. [PMID: 32194906 PMCID: PMC7061837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
This study aims to detect expression level of long non-coding RNA (lncRNA) FLJ33360 in hepatocellular carcinoma (HCC) and its regulatory effects on accelerating malignant progression of HCC. Expression levels of FLJ33360 in 29 matched HCC tissues and paracancerous tissues were detected by quantitative real-time polymerase chain reaction (qRT-PCR). After transfection of sh-FLJ33360#1 in Bel-7402 and HepG2 cells, changes in migratory and invasive capacities were evaluated by Transwell and wound healing assay. Potential miRNAs targeting FLJ33360 were verified. The correlation between expression levels of FLJ33360 and miRNA-140 in HCC tissues was determined. At last, potential influences of FLJ33360/miRNA-140 regulatory loop on HCC phenotypes were determined by rescue experiments. FLJ33360 was upregulated in HCC tissues relative to paracancerous ones. After knockdown of FLJ33360, migratory and invasive capacities in Bel-7402 and HepG2 cells were attenuated. There were five miRNA candidates predicted to bind FLJ33360, and miRNA-140 was the most differentially expressed by FLJ33360 regulation. Dual-luciferase reporter gene assay confirmed the binding between FLJ33360 and miRNA-140. Besides, their expression levels were negatively correlated in HCC tissues. Moreover, knockdown of miRNA-140 could stimulate metastatic ability in HCC. At last, rescue experiments verified the involvement of miRNA-140 in FLJ33360-regulated HCC progression. LncRNA FLJ33360 is upregulated in HCC. It accelerates the metastasis of HCC through targeting miRNA-140/MMP9 axis.
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Affiliation(s)
- Zhenhui Lu
- Department of Hepatobiliary Surgery, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
| | - Yingzi Yu
- Department of Infection Control, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
| | - Xiangchun Ding
- Department of Infectious Disease, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
| | - Dong Jin
- Department of Hepatobiliary Surgery, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
| | - Genwang Wang
- Department of Hepatobiliary Surgery, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
| | - Yu Zhou
- Department of Surgical Research Laborator, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
| | - Yongzhao Zhu
- Department of Surgical Research Laborator, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
| | - Li Na
- Department of Surgical Research Laborator, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
| | - Yaqin He
- Department of Surgical Research Laborator, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
| | - Qi Wang
- Department of Hepatobiliary Surgery, General Hospital of Ningxia Medical UniversityYinchuan, Ningxia, China
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14
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Spadafora C. Transgenerational epigenetic reprogramming of early embryos: a mechanistic model. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa009. [PMID: 32704385 PMCID: PMC7368376 DOI: 10.1093/eep/dvaa009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 05/10/2023]
Abstract
The notion that epigenetic information can be transmitted across generations is supported by mounting waves of data, but the underlying mechanisms remain elusive. Here, a model is proposed which combines different lines of experimental evidence. First, it has been shown that somatic tissues exposed to stressing stimuli release circulating RNA-containing extracellular vesicles; second, epididymal spermatozoa can take up, internalize and deliver the RNA-containing extracellular vesicles to oocytes at fertilization; third, early embryos can process RNA-based information. These elements constitute the building blocks upon which the model is built. The model proposes that a continuous stream of epigenetic information flows from parental somatic tissues to the developing embryos. The flow can cross the Weismann barrier, is mediated by circulating vesicles and epididymal spermatozoa, and has the potential to generate epigenetic traits that are then stably acquired in the offspring. In a broader perspective, it emerges that a natural 'assembly line' operates continuously, aiming at passing the parental epigenetic blueprint in growing embryos.
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Affiliation(s)
- Corrado Spadafora
- Institute of Translational Pharmacology, National Research Council (CNR), 100 Via del Fosso del Cavaliere, 00133 Rome, Italy
- Correspondence address. Institute of Translational Pharmacology, National Research Council (CNR), 100 Via del Fosso del Cavaliere, 00133 Rome, Italy. Tel: +39 0649917536; Fax: +39 064457529; E-mail: ;
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Reisacher C, Arbibe L. Not lost in host translation: The new roles of long noncoding RNAs in infectious diseases. Cell Microbiol 2019; 21:e13119. [PMID: 31634981 DOI: 10.1111/cmi.13119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) play a central role in the regulation of gene expression. Although they were initially described as mRNA-like transcripts not encoding proteins, global approaches such as ribosome profiling have shown that they frequently associate with ribosomes, opening the possibility that lncRNAs are a source of cryptic translation events with functional roles. Recent studies have shed more light on small ORFs borne by lncRNAs and encoding short peptides potentially involved in infectious immunity. This review outlines the main strategies used to determine the coding potential of lncRNAs and discusses our emerging understanding of the implication of the encoded peptides in infectious diseases.
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Affiliation(s)
- Caroline Reisacher
- Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
| | - Laurence Arbibe
- Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
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16
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Pirogov SA, Gvozdev VA, Klenov MS. Long Noncoding RNAs and Stress Response in the Nucleolus. Cells 2019; 8:cells8070668. [PMID: 31269716 PMCID: PMC6678565 DOI: 10.3390/cells8070668] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) perform diverse functions in the regulation of cellular processes. Here we consider a variety of lncRNAs found in the ribosome production center, the nucleolus, and focus on their role in the response to environmental stressors. Nucleolar lncRNAs ensure stress adaptation by cessation of resource-intensive ribosomal RNA (rRNA) synthesis and by inducing the massive sequestration of proteins within the nucleolus. Different cell states like quiescence and cancer are also controlled by specific lncRNAs in the nucleolus. Taken together, recent findings allow us to consider lncRNAs as multifunctional regulators of nucleolar activities, which are responsive to various physiological conditions.
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Affiliation(s)
- Sergei A Pirogov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Vladimir A Gvozdev
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia.
| | - Mikhail S Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia.
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