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Camilleri-Robles C, Amador R, Tiebe M, Teleman A, Serras F, Guigó R, Corominas M. Long non-coding RNAs involved in Drosophila development and regeneration. NAR Genom Bioinform 2024; 6:lqae091. [PMID: 39157585 PMCID: PMC11327875 DOI: 10.1093/nargab/lqae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024] Open
Abstract
The discovery of functional long non-coding RNAs (lncRNAs) changed their initial concept as transcriptional noise. LncRNAs have been identified as regulators of multiple biological processes, including chromatin structure, gene expression, splicing, mRNA degradation, and translation. However, functional studies of lncRNAs are hindered by the usual lack of phenotypes upon deletion or inhibition. Here, we used Drosophila imaginal discs as a model system to identify lncRNAs involved in development and regeneration. We examined a subset of lncRNAs expressed in the wing, leg, and eye disc development. Additionally, we analyzed transcriptomic data from regenerating wing discs to profile the expression pattern of lncRNAs during tissue repair. We focused on the lncRNA CR40469, which is upregulated during regeneration. We generated CR40469 mutant flies that developed normally but showed impaired wing regeneration upon cell death induction. The ability of these mutants to regenerate was restored by the ectopic expression of CR40469. Furthermore, we found that the lncRNA CR34335 has a high degree of sequence similarity with CR40469 and can partially compensate for its function during regeneration in the absence of CR40469. Our findings point to a potential role of the lncRNA CR40469 in trans during the response to damage in the wing imaginal disc.
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Affiliation(s)
- Carlos Camilleri-Robles
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Raziel Amador
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marcel Tiebe
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Florenci Serras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Montserrat Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
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2
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Much C, Lasda EL, Pereira IT, Vallery TK, Ramirez D, Lewandowski JP, Dowell RD, Smallegan MJ, Rinn JL. The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation. Nat Commun 2024; 15:6821. [PMID: 39122712 PMCID: PMC11316132 DOI: 10.1038/s41467-024-50402-0] [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: 09/21/2023] [Accepted: 07/10/2024] [Indexed: 08/12/2024] Open
Abstract
Numerous studies have now demonstrated that lncRNAs can influence gene expression programs leading to cell and organismal phenotypes. Typically, lncRNA perturbations and concomitant changes in gene expression are measured on the timescale of many hours to days. Thus, we currently lack a temporally grounded understanding of the primary, secondary, and tertiary relationships of lncRNA-mediated transcriptional and epigenetic regulation-a prerequisite to elucidating lncRNA mechanisms. To begin to address when and where a lncRNA regulates gene expression, we genetically engineer cell lines to temporally induce the lncRNA Firre. Using this approach, we are able to monitor lncRNA transcriptional regulatory events from 15 min to four days. We observe that upon induction, Firre RNA regulates epigenetic and transcriptional states in trans within 30 min. These early regulatory events result in much larger transcriptional changes after 12 h, well before current studies monitor lncRNA regulation. Moreover, Firre-mediated gene expression changes are epigenetically remembered for days. Overall, this study suggests that lncRNAs can rapidly regulate gene expression by establishing persistent epigenetic and transcriptional states.
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Affiliation(s)
- Christian Much
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Erika L Lasda
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Isabela T Pereira
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Tenaya K Vallery
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Daniel Ramirez
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80302, USA
| | - Jordan P Lewandowski
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80302, USA
| | - Michael J Smallegan
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA.
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80302, USA.
| | - John L Rinn
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA.
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80303, USA.
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3
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Habib AM, Cox JJ, Okorokov AL. Out of the dark: the emerging roles of lncRNAs in pain. Trends Genet 2024; 40:694-705. [PMID: 38926010 DOI: 10.1016/j.tig.2024.04.009] [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: 02/27/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/28/2024]
Abstract
The dark genome, the nonprotein-coding part of the genome, is replete with long noncoding RNAs (lncRNAs). These functionally versatile transcripts, with specific temporal and spatial expression patterns, are critical gene regulators that play essential roles in health and disease. In recent years, FAAH-OUT was identified as the first lncRNA associated with an inherited human pain insensitivity disorder. Several other lncRNAs have also been studied for their contribution to chronic pain and genome-wide association studies are frequently identifying single nucleotide polymorphisms that map to lncRNAs. For a long time overlooked, lncRNAs are coming out of the dark and into the light as major players in human pain pathways and as potential targets for new RNA-based analgesic medicines.
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Affiliation(s)
- Abdella M Habib
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar
| | - James J Cox
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, UK.
| | - Andrei L Okorokov
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, UK.
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4
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Lovell CD, Jiwrajka N, Amerman HK, Cancro MP, Anguera MC. Xist Deletion in B Cells Results in Systemic Lupus Erythematosus Phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594175. [PMID: 38798403 PMCID: PMC11118349 DOI: 10.1101/2024.05.15.594175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease preferentially observed in females. X-linked gene expression in XX females is normalized to that of XY males by X-Chromosome Inactivation (XCI). However, B cells from female SLE patients and mouse models of SLE exhibit mislocalization of Xist RNA, a critical regulator of XCI, and aberrant expression of X-linked genes, suggesting that impairment of XCI may contribute to disease. Here, we find that a subset of female mice harboring a conditional deletion of Xis t in B cells ("Xist cKO") spontaneously develop SLE phenotypes, including expanded activated B cell subsets, disease-specific autoantibodies, and glomerulonephritis. Moreover, pristane-induced SLE-like disease is more severe in Xist cKO mice. Activated B cells from Xist cKO mice with SLE phenotypes have increased expression of proinflammatory X-linked genes implicated in SLE. Together, this work indicates that impaired XCI maintenance in B cells directly contributes to the female-bias of SLE.
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Srinivas T, Siqueira E, Guil S. Techniques for investigating lncRNA transcript functions in neurodevelopment. Mol Psychiatry 2024; 29:874-890. [PMID: 38145986 PMCID: PMC11176085 DOI: 10.1038/s41380-023-02377-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023]
Abstract
Long noncoding RNAs (lncRNAs) are sequences of 200 nucleotides or more that are transcribed from a large portion of the mammalian genome. While hypothesized to have a variety of biological roles, many lncRNAs remain largely functionally uncharacterized due to unique challenges associated with their investigation. For example, some lncRNAs overlap with other genomic loci, are expressed in a cell-type-specific manner, and/or are differentially processed at the post-transcriptional level. The mammalian CNS contains a vast diversity of lncRNAs, and lncRNAs are highly abundant in the mammalian brain. However, interrogating lncRNA function in models of the CNS, particularly in vivo, can be complex and challenging. Here we review the breadth of methods used to investigate lncRNAs in the CNS, their merits, and the understanding they can provide with respect to neurodevelopment and pathophysiology. We discuss remaining challenges in the field and provide recommendations to assay lncRNAs based on current methods.
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Affiliation(s)
- Tara Srinivas
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain.
- Germans Trias i Pujol Health Science Research Institute, 08916, Badalona, Barcelona, Catalonia, Spain.
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Tang W, Wu S, Tang Y, Ma J, Ao Y, Liu L, Wei K. Microarray analysis identifies lncFirre as a potential regulator of obesity-related acute lung injury. Life Sci 2024; 340:122459. [PMID: 38307237 DOI: 10.1016/j.lfs.2024.122459] [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: 11/08/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
AIMS The inflammatory response in acute lung injury/acute respiratory distress syndrome (ALI/ARDS) is heightened in obesity. The aim of this study was to investigate whether lncRNAs are involved in the effects of obesity on acute lung injury and to find possible effector lncRNAs. MAIN METHODS Microarray analysis was used to assess the transcriptional profiles of lncRNAs and mRNAs in lung tissues from normal (CON), high-fat diet induced obese (DIO), and obese ALI mice (DIO-ALI). GO and KEGG analyses were employed to explore the biological functions of differentially expressed genes. A lncRNA-mRNA co-expression network was constructed to identify specific lncRNA. Lung tissues and peripheral blood samples from patients with obesity and healthy lean donors were utilized to confirm the expression characteristics of lncFirre through qRT-PCR. lncFirre was knocked down in MH-S macrophages to explore its function. ELISA and Griess reagent kit were used to detect PGE2 and NO. Flow cytometry was used to detect macrophages polarization. KEY FINDINGS There were 475 lncRNAs and 404 mRNAs differentially expressed between DIO and CON, while 1348 lncRNAs and 1349 mRNAs between DIO-ALI and DIO. Obesity increased lncFirre expression in both mice and patients, and PA elevated lncFirre in MH-S. PA exacerbated the inflammation and proinflammatory polarization of MH-S induced by LPS. LncFirre knockdown inhibited the secretion of PGE2 and NO, M1 differentiation while promoted the M2 differentiation in PA and LPS co-challenged MH-S. SIGNIFICANCE Interfering with lncFirre effectively inhibit inflammation in MH-S, lncFirre can serve as a promising target for treating obesity-related ALI.
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Affiliation(s)
- Wenjing Tang
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Siqi Wu
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yin Tang
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jingyue Ma
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yichan Ao
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Ling Liu
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Ke Wei
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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7
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Brezski A, Murtagh J, Schulz MH, Zarnack K. A systematic analysis of circRNAs in subnuclear compartments. RNA Biol 2024; 21:1-16. [PMID: 39257052 DOI: 10.1080/15476286.2024.2395718] [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] [Revised: 06/21/2024] [Accepted: 08/13/2024] [Indexed: 09/12/2024] Open
Abstract
CircRNAs are an important class of RNAs with diverse cellular functions in human physiology and disease. A thorough knowledge of circRNAs including their biogenesis and subcellular distribution is important to understand their roles in a wide variety of processes. However, the analysis of circRNAs from total RNA sequencing data remains challenging. Therefore, we developed Calcifer, a versatile workflow for circRNA annotation. Using Calcifer, we analysed APEX-Seq data to compare circRNA occurrence between whole cells, nucleus and subnuclear compartments. We generally find that circRNAs show higher abundance in whole cells compared to nuclear samples, consistent with their accumulation in the cytoplasm. The notable exception is the single-exon circRNA circCANX(9), which is unexpectedly enriched in the nucleus. In addition, we observe that circFIRRE prevails over the linear lncRNA FIRRE in both the cytoplasm and the nucleus. Zooming in on the subnuclear compartments, we show that circRNAs are strongly depleted from nuclear speckles, indicating that excess splicing factors in this compartment counteract back-splicing. Our results thereby provide valuable insights into the subnuclear distribution of circRNAs. Regarding circRNA function, we surprisingly find that the majority of all detected circRNAs possess complete open reading frames with potential for cap-independent translation. Overall, we show that Calcifer is an easy-to-use, versatile and sustainable workflow for the annotation of circRNAs which expands the repertoire of circRNA tools and allows to gain new insights into circRNA distribution and function.
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Affiliation(s)
- Andre Brezski
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Justin Murtagh
- Department of Medicine, Institute for Computational Genomic Medicine and Institute of Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Marcel H Schulz
- Department of Medicine, Institute for Computational Genomic Medicine and Institute of Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt am Main, Hesse, Germany
- Cardio-Pulmonary Institute, Goethe University Frankfurt, Frankfurt am Main, Hesse, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Hesse, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Hesse, Germany
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8
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Zhang L, Sun H, Chen X. Long noncoding RNAs in human reproductive processes and diseases. Mol Reprod Dev 2024; 91:e23728. [PMID: 38282314 DOI: 10.1002/mrd.23728] [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: 07/29/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 01/30/2024]
Abstract
Infertility has become a global disease burden. Although assisted reproductive technologies are widely used, the assisted reproduction birth rate is no more than 30% worldwide. Therefore, understanding the mechanisms of reproduction can provide new strategies to improve live birth rates and clinical outcomes of enhanced implantation. Long noncoding RNAs (lncRNAs) have been reported to exert regulatory roles in various biological processes and diseases in many species. In this review, we especially focus on the role of lncRNAs in human reproduction. We summarize the function and mechanisms of lncRNAs in processes vital to reproduction, such as spermatogenesis and maturation, sperm motility and morphology, follicle development and maturation, embryo development and implantation. Then, we highlight the importance and diverse potential of lncRNAs as good diagnostic molecular biomarkers and therapeutic targets for infertility treatment.
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Affiliation(s)
- Le Zhang
- Center for Reproductive Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Hailong Sun
- Center for Reproductive Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Xiujuan Chen
- Center for Reproductive Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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9
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Li W, Lv Y, Sun Y. Roles of non-coding RNA in megakaryocytopoiesis and thrombopoiesis: new target therapies in ITP. Platelets 2023; 34:2157382. [PMID: 36550091 DOI: 10.1080/09537104.2022.2157382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Noncoding RNAs (ncRNAs) are a group of RNA molecules that cannot encode proteins, and a better understanding of the complex interaction networks coordinated by ncRNAs will provide a theoretical basis for the development of therapeutics targeting the regulatory effects of ncRNAs. Platelets are produced upon the differentiation of hematopoietic stem cells into megakaryocytes, 1011 per day, and are renewed every 8-9 days. The process of thrombopoiesis is affected by multiple factors, in which ncRNAs also exert a significant regulatory role. This article reviewed the regulatory roles of ncRNAs, mainly microRNAs (miRNAs), circRNAs (circular RNAs), and long non-coding RNAs (lncRNAs), in thrombopoiesis in recent years as well as their roles in primary immune thrombocytopenia (ITP).
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Affiliation(s)
- Wuquan Li
- College of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yan Lv
- College of Life Science, Yantai University, Yantai, China
| | - Yeying Sun
- College of Pharmacy, Binzhou Medical University, Yantai, China
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10
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Mikaeili H, Habib AM, Yeung CWL, Santana-Varela S, Luiz AP, Panteleeva K, Zuberi S, Athanasiou-Fragkouli A, Houlden H, Wood JN, Okorokov AL, Cox JJ. Molecular basis of FAAH-OUT-associated human pain insensitivity. Brain 2023; 146:3851-3865. [PMID: 37222214 PMCID: PMC10473560 DOI: 10.1093/brain/awad098] [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: 11/03/2022] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 05/25/2023] Open
Abstract
Chronic pain affects millions of people worldwide and new treatments are needed urgently. One way to identify novel analgesic strategies is to understand the biological dysfunctions that lead to human inherited pain insensitivity disorders. Here we report how the recently discovered brain and dorsal root ganglia-expressed FAAH-OUT long non-coding RNA (lncRNA) gene, which was found from studying a pain-insensitive patient with reduced anxiety and fast wound healing, regulates the adjacent key endocannabinoid system gene FAAH, which encodes the anandamide-degrading fatty acid amide hydrolase enzyme. We demonstrate that the disruption in FAAH-OUT lncRNA transcription leads to DNMT1-dependent DNA methylation within the FAAH promoter. In addition, FAAH-OUT contains a conserved regulatory element, FAAH-AMP, that acts as an enhancer for FAAH expression. Furthermore, using transcriptomic analyses in patient-derived cells we have uncovered a network of genes that are dysregulated from disruption of the FAAH-FAAH-OUT axis, thus providing a coherent mechanistic basis to understand the human phenotype observed. Given that FAAH is a potential target for the treatment of pain, anxiety, depression and other neurological disorders, this new understanding of the regulatory role of the FAAH-OUT gene provides a platform for the development of future gene and small molecule therapies.
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Affiliation(s)
- Hajar Mikaeili
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Abdella M Habib
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Charlix Wai-Lok Yeung
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Sonia Santana-Varela
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Ana P Luiz
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Kseniia Panteleeva
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Sana Zuberi
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | | | - Henry Houlden
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Andrei L Okorokov
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
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11
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Tenorio M, Serwatowska J, Fernandez-Valverde SL, Oktaba K, Cortez D. Genome-wide analysis of RNA-chromatin interactions in lizards as a mean for functional lncRNA identification. BMC Genomics 2023; 24:444. [PMID: 37550606 PMCID: PMC10405410 DOI: 10.1186/s12864-023-09545-5] [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: 03/30/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are defined as transcribed molecules longer than 200 nucleotides with little to no protein-coding potential. LncRNAs can regulate gene expression of nearby genes (cis-acting) or genes located on other chromosomes (trans-acting). Several methodologies have been developed to capture lncRNAs associated with chromatin at a genome-wide level. Analysis of RNA-DNA contacts can be combined with epigenetic and RNA-seq data to define potential lncRNAs involved in the regulation of gene expression. RESULTS We performed Chromatin Associated RNA sequencing (ChAR-seq) in Anolis carolinensis to obtain the genome-wide map of the associations that RNA molecules have with chromatin. We analyzed the frequency of DNA contacts for different classes of RNAs and were able to define cis- and trans-acting lncRNAs. We integrated the ChAR-seq map of RNA-DNA contacts with epigenetic data for the acetylation of lysine 16 on histone H4 (H4K16ac), a mark connected to actively transcribed chromatin in lizards. We successfully identified three trans-acting lncRNAs significantly associated with the H4K16ac signal, which are likely involved in the regulation of gene expression in A. carolinensis. CONCLUSIONS We show that the ChAR-seq method is a powerful tool to explore the RNA-DNA map of interactions. Moreover, in combination with epigenetic data, ChAR-seq can be applied in non-model species to establish potential roles for predicted lncRNAs that lack functional annotations.
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Affiliation(s)
- Mariela Tenorio
- Center for Genome Sciences, National Autonomous University of Mexico (UNAM), Cuernavaca, Mexico
| | | | - Selene L Fernandez-Valverde
- Center for Research and Advanced Studies (Cinvestav), Irapuato, Mexico
- School of Biotechnology and Biomolecular Sciences and the RNA Institute, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Katarzyna Oktaba
- Center for Research and Advanced Studies (Cinvestav), Irapuato, Mexico
| | - Diego Cortez
- Center for Genome Sciences, National Autonomous University of Mexico (UNAM), Cuernavaca, Mexico.
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12
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Zheng C, Wei Y, Zhang Q, Sun M, Wang Y, Hou J, Zhang P, Lv X, Su D, Jiang Y, Gumin J, Sahni N, Hu B, Wang W, Chen X, McGrail DJ, Zhang C, Huang S, Xu H, Chen J, Lang FF, Hu J, Chen Y. Multiomics analyses reveal DARS1-AS1/YBX1-controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. SCIENCE ADVANCES 2023; 9:eadf3984. [PMID: 37540752 PMCID: PMC10403220 DOI: 10.1126/sciadv.adf3984] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
The glioblastoma (GBM) stem cell-like cells (GSCs) are critical for tumorigenesis/therapeutic resistance of GBM. Mounting evidence supports tumor-promoting function of long noncoding RNAs (lncRNAs), but their role in GSCs remains poorly understood. By combining CRISPRi screen with orthogonal multiomics approaches, we identified a lncRNA DARS1-AS1-controlled posttranscriptional circuitry that promoted the malignant properties of GBM cells/GSCs. Depleting DARS1-AS1 inhibited the proliferation of GBM cells/GSCs and self-renewal of GSCs, prolonging survival in orthotopic GBM models. DARS1-AS1 depletion also impaired the homologous recombination (HR)-mediated double-strand break (DSB) repair and enhanced the radiosensitivity of GBM cells/GSCs. Mechanistically, DARS1-AS1 interacted with YBX1 to promote target mRNA binding and stabilization, forming a mixed transcriptional/posttranscriptional feed-forward loop to up-regulate expression of the key regulators of G1-S transition, including E2F1 and CCND1. DARS1-AS1/YBX1 also stabilized the mRNA of FOXM1, a master transcription factor regulating GSC self-renewal and DSB repair. Our findings suggest DARS1-AS1/YBX1 axis as a potential therapeutic target for sensitizing GBM to radiation/HR deficiency-targeted therapy.
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Affiliation(s)
- Caishang Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qiang Zhang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yunfei Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiakai Hou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiangdong Lv
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yujie Jiang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Statistics, Rice University, Houston, TX 77005, USA
| | - Joy Gumin
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nidhi Sahni
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA
| | - Baoli Hu
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Pediatric Neurosurgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- Molecular and Cellular Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel J. McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
- Lerner Research Institute, Cleveland, OH 44195, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, and Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Suyun Huang
- Department of Human and Molecular Genetics, Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA
| | - Han Xu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Frederick F. Lang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Hu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Cancer Biology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Neuroscience Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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13
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Ivanov KI, Samuilova OV, Zamyatnin AA. The emerging roles of long noncoding RNAs in lymphatic vascular development and disease. Cell Mol Life Sci 2023; 80:197. [PMID: 37407839 PMCID: PMC10322780 DOI: 10.1007/s00018-023-04842-4] [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: 11/08/2022] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Recent advances in RNA sequencing technologies helped uncover what was once uncharted territory in the human genome-the complex and versatile world of long noncoding RNAs (lncRNAs). Previously thought of as merely transcriptional "noise", lncRNAs have now emerged as essential regulators of gene expression networks controlling development, homeostasis and disease progression. The regulatory functions of lncRNAs are broad and diverse, and the underlying molecular mechanisms are highly variable, acting at the transcriptional, post-transcriptional, translational, and post-translational levels. In recent years, evidence has accumulated to support the important role of lncRNAs in the development and functioning of the lymphatic vasculature and associated pathological processes such as tumor-induced lymphangiogenesis and cancer metastasis. In this review, we summarize the current knowledge on the role of lncRNAs in regulating the key genes and pathways involved in lymphatic vascular development and disease. Furthermore, we discuss the potential of lncRNAs as novel therapeutic targets and outline possible strategies for the development of lncRNA-based therapeutics to treat diseases of the lymphatic system.
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Affiliation(s)
- Konstantin I Ivanov
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation.
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | - Olga V Samuilova
- Department of Biochemistry, Sechenov First Moscow State Medical University, Moscow, Russian Federation
- HSE University, Moscow, Russian Federation
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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14
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Li Y, Zhai H, Tong L, Wang C, Xie Z, Zheng K. LncRNA Functional Screening in Organismal Development. Noncoding RNA 2023; 9:36. [PMID: 37489456 PMCID: PMC10366883 DOI: 10.3390/ncrna9040036] [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: 05/10/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023] Open
Abstract
Controversy continues over the functional prevalence of long non-coding RNAs (lncRNAs) despite their being widely investigated in all kinds of cells and organisms. In animals, lncRNAs have aroused general interest from exponentially increasing transcriptomic repertoires reporting their highly tissue-specific and developmentally dynamic expression, and more importantly, from growing experimental evidence supporting their functionality in facilitating organogenesis and individual fitness. In mammalian testes, while a great multitude of lncRNA species are identified, only a minority of them have been shown to be useful, and even fewer have been demonstrated as true requirements for male fertility using knockout models to date. This noticeable gap is attributed to the virtual existence of a large number of junk lncRNAs, the lack of an ideal germline culture system, difficulty in loss-of-function interrogation, and limited screening strategies. Facing these challenges, in this review, we discuss lncRNA functionality in organismal development and especially in mouse testis, with a focus on lncRNAs with functional screening.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Huicong Zhai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Lingxiu Tong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Cuicui Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhiming Xie
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
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15
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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: 483] [Impact Index Per Article: 483.0] [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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16
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Mattick JS. RNA out of the mist. Trends Genet 2023; 39:187-207. [PMID: 36528415 DOI: 10.1016/j.tig.2022.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
Abstract
RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia; UNSW RNA Institute, UNSW, Sydney, NSW 2052, Australia.
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17
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Lian J, Walker RG, D'Amico A, Vujic A, Mills MJ, Messemer KA, Mendello KR, Goldstein JM, Leacock KA, Epp S, Stimpfl EV, Thompson TB, Wagers AJ, Lee RT. Functional substitutions of amino acids that differ between GDF11 and GDF8 impact skeletal development and skeletal muscle. Life Sci Alliance 2023; 6:e202201662. [PMID: 36631218 PMCID: PMC9834663 DOI: 10.26508/lsa.202201662] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 01/13/2023] Open
Abstract
Growth differentiation factor 11 (GDF11) and GDF8 (MSTN) are closely related TGF-β family proteins that interact with nearly identical signaling receptors and antagonists. However, GDF11 appears to activate SMAD2/3 more potently than GDF8 in vitro and in vivo. The ligands possess divergent structural properties, whereby substituting unique GDF11 amino acids into GDF8 enhanced the activity of the resulting chimeric GDF8. We investigated potentially distinct endogenous activities of GDF11 and GDF8 in vivo by genetically modifying their mature signaling domains. Full recoding of GDF8 to that of GDF11 yielded mice lacking GDF8, with GDF11 levels ∼50-fold higher than normal, and exhibiting modestly decreased muscle mass, with no apparent negative impacts on health or survival. Substitution of two specific amino acids in the fingertip region of GDF11 with the corresponding GDF8 residues resulted in prenatal axial skeletal transformations, consistent with Gdf11-deficient mice, without apparent perturbation of skeletal or cardiac muscle development or homeostasis. These experiments uncover distinctive features between the GDF11 and GDF8 mature domains in vivo and identify a specific requirement for GDF11 in early-stage skeletal development.
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Affiliation(s)
- John Lian
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Ryan G Walker
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Andrea D'Amico
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Ana Vujic
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Melanie J Mills
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Kathleen A Messemer
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Kourtney R Mendello
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Jill M Goldstein
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Krystynne A Leacock
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Soraya Epp
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Emma V Stimpfl
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Thomas B Thompson
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, OH, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Joslin Diabetes Center, Boston, MA, USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA, USA
| | - Richard T Lee
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
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18
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Landshammer A, Bolondi A, Kretzmer H, Much C, Buschow R, Rose A, Wu HJ, Mackowiak SD, Braendl B, Giesselmann P, Tornisiello R, Parsi KM, Huey J, Mielke T, Meierhofer D, Maehr R, Hnisz D, Michor F, Rinn JL, Meissner A. T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife 2023; 12:e83077. [PMID: 36719724 PMCID: PMC9889090 DOI: 10.7554/elife.83077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously unannotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically associating domain. We termed it T-REX17 (Transcript Regulating Endoderm and activated by soX17) and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of T-REX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. Taken together, our study identified and characterized T-REX17 as a transiently expressed and essential non-coding regulator in early human endoderm differentiation.
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Affiliation(s)
- Alexandro Landshammer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Christian Much
- Department of Biochemistry, University of Colorado Boulder and BioFrontiers InstituteBoulderUnited States
| | - René Buschow
- Max Planck Institute for Molecular Genetics, Microscopy Core FacilityBerlinGermany
| | - Alina Rose
- Helmholtz Institute for Metabolic, Obesity and Vascular ResearchLeipzigGermany
| | - Hua-Jun Wu
- Department of Data Science, Dana-Farber Cancer Institute, Department of Biostatistics, Harvard T. H. Chan School of Public HealthBostonUnited States
- Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center and Peking University Cancer Hospital and InstituteBeijingChina
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Bjoern Braendl
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Pay Giesselmann
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Rosaria Tornisiello
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jack Huey
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Microscopy Core FacilityBerlinGermany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Core FacilityBerlinGermany
| | - René Maehr
- Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center and Peking University Cancer Hospital and InstituteBeijingChina
- Diabetes Center of Excellence, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Franziska Michor
- Department of Stem Cell and Regenerative Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Data Science, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T. H. Chan School of Public HealthBostonUnited States
- The Ludwig Center at Harvard, Boston, MA 02215, USA, and Center for Cancer Evolution, Dana-Farber Cancer InstituteBostonUnited States
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder and BioFrontiers InstituteBoulderUnited States
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
- Department of Stem Cell and Regenerative Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
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19
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Gal-Oz ST, Shay T. Genetics of Sex Differences in Immunity. Curr Top Microbiol Immunol 2023; 441:1-19. [PMID: 37695423 DOI: 10.1007/978-3-031-35139-6_1] [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] [Indexed: 09/12/2023]
Abstract
Women have a stronger immune response and a higher frequency of most autoimmune diseases than men. While much of the difference between men and women is due to the effect of gonadal hormones, genetic differences play a major role in the difference between the immune response and disease frequencies in women and men. Here, we focus on the immune differences between the sexes that are not downstream of the gonadal hormones. These differences include the gene content of the sex chromosomes, the inactivation of chromosome X in women, the consequences of non-random X inactivation and escape from inactivation, and the states that are uniquely met by the immune system of women-pregnancy, birth, and breast feeding. While these female-specific states are temporary and involve gonadal hormonal changes, they may leave a long-lasting footprint on the health of women, for example, by fetal cells that remain in the mother's body for decades. We also briefly discuss the immune phenotype of congenital sex chromosomal aberrations and experimental models that enable hormonal and the non-hormonal effects of the sex chromosomes to be disentangled. The increasing human life expectancy lengthens the period during which gonadal hormones levels are reduced in both sexes. A better understanding of the non-hormonal effects of sex chromosomes thus becomes more important for improving the life quality during that period.
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Affiliation(s)
- Shani T Gal-Oz
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Tal Shay
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
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20
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Arunima A, van Schaik EJ, Samuel JE. The emerging roles of long non-coding RNA in host immune response and intracellular bacterial infections. Front Cell Infect Microbiol 2023; 13:1160198. [PMID: 37153158 PMCID: PMC10160451 DOI: 10.3389/fcimb.2023.1160198] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/07/2023] [Indexed: 05/09/2023] Open
Abstract
The long non-coding RNAs (lncRNAs) are evolutionarily conserved classes of non-coding regulatory transcripts of > 200 nucleotides in length. They modulate several transcriptional and post-transcriptional events in the organism. Depending on their cellular localization and interactions, they regulate chromatin function and assembly; and alter the stability and translation of cytoplasmic mRNAs. Although their proposed range of functionality remains controversial, there is increasing research evidence that lncRNAs play a regulatory role in the activation, differentiation and development of immune signaling cascades; microbiome development; and in diseases such as neuronal and cardiovascular disorders; cancer; and pathogenic infections. This review discusses the functional roles of different lncRNAs in regulation of host immune responses, signaling pathways during host-microbe interaction and infection caused by obligate intracellular bacterial pathogens. The study of lncRNAs is assuming significance as it could be exploited for development of alternative therapeutic strategies for the treatment of severe and chronic pathogenic infections caused by Mycobacterium, Chlamydia and Rickettsia infections, as well as commensal colonization. Finally, this review summarizes the translational potential of lncRNA research in development of diagnostic and prognostic tools for human diseases.
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21
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Løvendorf MB, Holm A, Petri A, Thrue CA, Uchida S, Venø MT, Kauppinen S. Knockdown of Circular RNAs Using LNA-Modified Antisense Oligonucleotides. Nucleic Acid Ther 2023; 33:45-57. [PMID: 36445751 DOI: 10.1089/nat.2022.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Circular RNAs (circRNAs) constitute an abundant class of covalently closed noncoding RNA molecules that are formed by backsplicing from eukaryotic protein-coding genes. Recent studies have shown that circRNAs can act as microRNA or protein decoys, as well as transcriptional regulators. However, the functions of most circRNAs are still poorly understood. Because circRNA sequences overlap with their linear parent transcripts, depleting specific circRNAs without affecting host gene expression remains a challenge. In this study, we assessed the utility of LNA-modified antisense oligonucleotides (ASOs) to knock down circRNAs for loss-of-function studies. We found that, while most RNase H-dependent gapmer ASOs mediate effective knockdown of their target circRNAs, some gapmers reduce the levels of the linear parent transcript. The circRNA targeting specificity can be enhanced using design-optimized gapmer ASOs, which display potent and specific circRNA knockdown with a minimal effect on the host genes. In summary, our results demonstrate that LNA-modified ASOs complementary to backsplice-junction sequences mediate robust knockdown of circRNAs in vitro and, thus, represent a useful tool to explore the biological roles of circRNAs in loss-of-function studies in cultured cells and animal models.
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Affiliation(s)
| | - Anja Holm
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark.,Department of Clinical Experimental Research, Rigshopitalet, Glostrup, Denmark
| | - Andreas Petri
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
| | - Charlotte Albæk Thrue
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
| | - Shizuka Uchida
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
| | | | - Sakari Kauppinen
- Department of Clinical Medicine, Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
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22
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Gcanga L, Tamgue O, Ozturk M, Pillay S, Jacobs R, Chia JE, Mbandi SK, Davids M, Dheda K, Schmeier S, Alam T, Roy S, Suzuki H, Brombacher F, Guler R. Host-Directed Targeting of LincRNA-MIR99AHG Suppresses Intracellular Growth of Mycobacterium tuberculosis. Nucleic Acid Ther 2022; 32:421-437. [PMID: 35895506 PMCID: PMC7613730 DOI: 10.1089/nat.2022.0009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) kills 1.6 million people worldwide every year, and there is an urgent need for targeting host-pathogen interactions as a strategy to reduce mycobacterial resistance to current antimicrobials. Noncoding RNAs are emerging as important regulators of numerous biological processes and avenues for exploitation in host-directed therapeutics. Although long noncoding RNAs (lncRNAs) are abundantly expressed in immune cells, their functional role in gene regulation and bacterial infections remains understudied. In this study, we identify an immunoregulatory long intergenic noncoding RNA, lincRNA-MIR99AHG, which is upregulated in mouse and human macrophages upon IL-4/IL-13 stimulation and downregulated after clinical Mtb HN878 strain infection and in peripheral blood mononuclear cells from active TB patients. To evaluate the functional role of lincRNA-MIR99AHG, we used antisense locked nucleic acid (LNA) GapmeR-mediated antisense oligonucleotide (ASO) lncRNA knockdown experiments. Knockdown of lincRNA-MIR99AHG with ASOs significantly reduced intracellular Mtb growth in mouse and human macrophages and reduced pro-inflammatory cytokine production. In addition, in vivo treatment of mice with MIR99AHG ASOs reduced the mycobacterial burden in the lung and spleen. Furthermore, in macrophages, lincRNA-MIR99AHG is translocated to the nucleus and interacts with high affinity to hnRNPA2/B1 following IL-4/IL-13 stimulation and Mtb HN878 infection. Together, these findings identify lincRNA-MIR99AHG as a positive regulator of inflammation and macrophage polarization to promote Mtb growth and a possible target for adjunctive host-directed therapy against TB.
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Affiliation(s)
- Lorna Gcanga
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Ousman Tamgue
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa.,Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Mumin Ozturk
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Shandre Pillay
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Raygaana Jacobs
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Julius Ebua Chia
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- Division of Immunology, Department of Pathology, South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Malika Davids
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunology, UCT Lung Institute, University of Cape Town, Cape Town, South Africa.,South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Keertan Dheda
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunology, UCT Lung Institute, University of Cape Town, Cape Town, South Africa.,South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.,Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical medicine, London, United Kingdom
| | - Sebastian Schmeier
- College of Science, School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Tanvir Alam
- Information and Computing Technology Division, College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Sugata Roy
- RIKEN Center for Integrative Medical Sciences, Cellular Function Conversion Technology Team, Yokohama, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Cellular Function Conversion Technology Team, Yokohama, Japan
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Address correspondence to: Frank Brombacher, PhD, International Centre for Genetic Engineering and Biotechnology (ICGEB) Department of Pathology, Cape Town Component, Cape Town 7925, South Africa
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Department of Pathology, Cape Town Component, Cape Town, South Africa.,Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC) University of Cape Town, Cape Town, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Reto Guler, PhD, Division of Immunology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town 7925, South Africa
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23
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Much C, Smallegan MJ, Hwang T, Hanson SD, Dumbović G, Rinn JL. Evolutionary divergence of Firre localization and expression. RNA (NEW YORK, N.Y.) 2022; 28:842-853. [PMID: 35304421 PMCID: PMC9074896 DOI: 10.1261/rna.079070.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/06/2022] [Indexed: 06/03/2023]
Abstract
Long noncoding RNAs (lncRNAs) are rapidly evolving and thus typically poorly conserved in their sequences. How these sequence differences affect the characteristics and potential functions of lncRNAs with shared synteny remains unclear. Here we show that the syntenically conserved lncRNA Firre displays distinct expression and localization patterns in human and mouse. Single molecule RNA FISH reveals that in a range of cell lines, mouse Firre (mFirre) is predominantly nuclear, while human FIRRE (hFIRRE) is distributed between the cytoplasm and nucleus. This localization pattern is maintained in human/mouse hybrid cells expressing both human and mouse Firre, implying that the localization of the lncRNA is species autonomous. We find that the majority of hFIRRE transcripts in the cytoplasm are comprised of isoforms that are enriched in RRD repeats. We furthermore determine that in various tissues, mFirre is more highly expressed than its human counterpart. Our data illustrate that the rapid evolution of syntenic lncRNAs can lead to variations in lncRNA localization and abundance, which in turn may result in disparate lncRNA functions even in closely related species.
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Affiliation(s)
- Christian Much
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Michael J Smallegan
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80302, USA
| | - Taeyoung Hwang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Skylar D Hanson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Gabrijela Dumbović
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - John L Rinn
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80302, USA
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24
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Robinson EK, Worthington A, Poscablo D, Shapleigh B, Salih MM, Halasz H, Seninge L, Mosqueira B, Smaliy V, Forsberg EC, Carpenter S. lincRNA-Cox2 Functions to Regulate Inflammation in Alveolar Macrophages during Acute Lung Injury. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1886-1900. [PMID: 35365562 PMCID: PMC9038212 DOI: 10.4049/jimmunol.2100743] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/05/2022] [Indexed: 12/15/2022]
Abstract
Our respiratory system is vital to protect us from the surrounding nonsterile environment; therefore, it is critical for a state of homeostasis to be maintained through a balance of inflammatory cues. Recent studies have shown that actively transcribed noncoding regions of the genome are emerging as key regulators of biological processes, including inflammation. lincRNA-Cox2 is one such example of an inflammatory inducible long intergenic noncoding RNA functioning to fine-tune immune gene expression. Using bulk and single-cell RNA sequencing, in addition to FACS, we find that lincRNA-Cox2 is most highly expressed in the lung and is most upregulated after LPS-induced lung injury (acute lung injury [ALI]) within alveolar macrophages, where it functions to regulate inflammation. We previously reported that lincRNA-Cox2 functions to regulate its neighboring protein Ptgs2 in cis, and in this study, we use genetic mouse models to confirm its role in regulating gene expression more broadly in trans during ALI. Il6, Ccl3, and Ccl5 are dysregulated in the lincRNA-Cox2-deficient mice and can be rescued to wild type levels by crossing the deficient mice with our newly generated lincRNA-Cox2 transgenic mice, confirming that this gene functions in trans. Many genes are specifically regulated by lincRNA-Cox2 within alveolar macrophages originating from the bone marrow because the phenotype can be reversed by transplantation of wild type bone marrow into the lincRNA-Cox2-deficient mice. In conclusion, we show that lincRNA-Cox2 is a trans-acting long noncoding RNA that functions to regulate immune responses and maintain homeostasis within the lung at baseline and on LPS-induced ALI.
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Affiliation(s)
- Elektra Kantzari Robinson
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Atesh Worthington
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA;,Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA; and
| | - Donna Poscablo
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA;,Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA; and
| | - Barbara Shapleigh
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Mays Mohammed Salih
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Haley Halasz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Lucas Seninge
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Benny Mosqueira
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Valeriya Smaliy
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - E. Camilla Forsberg
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA; and,Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
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25
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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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26
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Peltier DC, Roberts A, Reddy P. LNCing RNA to immunity. Trends Immunol 2022; 43:478-495. [DOI: 10.1016/j.it.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 12/29/2022]
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27
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Lin C, Li Y, Zhang E, Feillet F, Zhang S, Blau N. Importance of the long non-coding RNA (lncRNA) transcript HULC for the regulation of phenylalanine hydroxylase and treatment of phenylketonuria. Mol Genet Metab 2022; 135:171-178. [PMID: 35101330 DOI: 10.1016/j.ymgme.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
Abstract
More than 1280 variants in the phenylalanine hydroxylase (PAH) gene are responsible for a broad spectrum of phenylketonuria (PKU) phenotypes. While the genotype-phenotype correlation is reaching 88%, for some inconsistent phenotypes with the same genotype additional factors like tetrahydrobiopterin (BH4), the PAH co-chaperone DNAJC12, phosphorylation of the PAH residues or epigenetic factors may play an important role. Very recently an additional player, the long non-coding RNA (lncRNA) transcript HULC, was described to regulate PAH activity and enhance residual enzyme activity of some PAH variants (e.g., the most common p.R408W) by using HULC mimics. In this review we present an overview of the lncRNA function and in particular the interplay of the HUCL transcript with the PAH and discuss potential applications for the future treatment of some PKU patients.
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Affiliation(s)
- Chunru Lin
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Yajuan Li
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Eric Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - François Feillet
- INSERM, U1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy, France; Pediatric Department Reference Center for Inborn Errors of Metabolism Children University Hospital Nancy, Nancy, France
| | - Shuxing Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital Zürich, Zurich, Switzerland.
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28
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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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29
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Long non-coding RNAs associated with infection and vaccine-induced immunity. Essays Biochem 2021; 65:657-669. [PMID: 34528687 DOI: 10.1042/ebc20200072] [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: 12/14/2020] [Revised: 08/01/2021] [Accepted: 08/10/2021] [Indexed: 12/31/2022]
Abstract
The immune system responds to infection or vaccination through a dynamic and complex process that involves several molecular and cellular factors. Among these factors, long non-coding RNAs (lncRNAs) have emerged as significant players in all areas of biology, particularly in immunology. Most of the mammalian genome is transcribed in a highly regulated manner, generating a diversity of lncRNAs that impact the differentiation and activation of immune cells and affect innate and adaptive immunity. Here, we have reviewed the range of functions and mechanisms of lncRNAs in response to infectious disease, including pathogen recognition, interferon (IFN) response, and inflammation. We describe examples of lncRNAs exploited by pathogenic agents during infection, which indicate that lncRNAs are a fundamental part of the arms race between hosts and pathogens. We also discuss lncRNAs potentially implicated in vaccine-induced immunity and present examples of lncRNAs associated with the antibody response of subjects receiving Influenza or Yellow Fever vaccines. Elucidating the widespread involvement of lncRNAs in the immune system will improve our understanding of the factors affecting immune response to different pathogenic agents, to better prevent and treat disease.
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30
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31
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DiStefano JK, Gerhard GS. Long Noncoding RNAs and Human Liver Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:1-21. [PMID: 34416820 DOI: 10.1146/annurev-pathol-042320-115255] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome, exhibit a diverse range of biological functions, and exert effects through a variety of mechanisms. The sheer number of lncRNAs in the human genome has raised important questions about their potential biological significance and roles in human health and disease. Technological and computational advances have enabled functional annotation of a large number of lncRNAs. Though the number of publications related to lncRNAs has escalated in recent years, relatively few have focused on those involved in hepatic physiology and pathology. We provide an overview of evolving lncRNA classification systems and characteristics and highlight important advances in our understanding of the contribution of lncRNAs to liver disease, with a focus on nonalcoholic steatohepatitis, hepatocellular carcinoma, and cholestatic liver disease. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Johanna K DiStefano
- Diabetes and Fibrotic Disease Research Unit, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA;
| | - Glenn S Gerhard
- Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA;
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32
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Yin H, Wei C, Lee JT. Revisiting the consequences of deleting the X inactivation center. Proc Natl Acad Sci U S A 2021; 118:e2102683118. [PMID: 34161282 PMCID: PMC8237661 DOI: 10.1073/pnas.2102683118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian cells equalize X-linked dosages between the male (XY) and female (XX) sexes by silencing one X chromosome in the female sex. This process, known as "X chromosome inactivation" (XCI), requires a master switch within the X inactivation center (Xic). The Xic spans several hundred kilobases in the mouse and includes a number of regulatory noncoding genes that produce functional transcripts. Over three decades, transgenic and deletional analyses have demonstrated both the necessity and sufficiency of the Xic to induce XCI, including the steps of X chromosome counting, choice, and initiation of whole-chromosome silencing. One recent study, however, reported that deleting the noncoding sequences of the Xic surprisingly had no effect for XCI and attributed a sufficiency to drive counting to the coding gene, Rnf12/Rlim Here, we revisit the question by creating independent Xic deletion cell lines. Multiple independent clones carrying heterozygous deletions of the Xic display an inability to up-regulate Xist expression, consistent with a counting defect. This defect is rescued by a second site mutation in Tsix occurring in trans, bypassing the defect in counting. These findings reaffirm the essential nature of noncoding Xic elements for the initiation of XCI.
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Affiliation(s)
- Hao Yin
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02114
| | - Chunyao Wei
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02114
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114;
- Department of Genetics, Harvard Medical School, Boston, MA 02114
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33
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ArcRNAs and the formation of nuclear bodies. Mamm Genome 2021; 33:382-401. [PMID: 34085114 DOI: 10.1007/s00335-021-09881-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 01/13/2023]
Abstract
Long noncoding RNAs (lncRNAs) have long been collectively and passively defined as transcripts that do not encode proteins. However, extensive functional studies performed over the last decade have enabled the classification of lncRNAs into multiple categories according to their functions and/or molecular properties. Architectual RNAs (arcRNAs) are a group of lncRNAs that serve as architectural components of submicron-scale cellular bodies or nonmembranous organelles, which are composed of specific sets of proteins and nucleic acids involved in particular molecular processes. In this review, we focus on arcRNAs that function in the nucleus, which provide a structural basis for the formation of nuclear bodies, nonmembranous organelles in the cell nucleus. We will summarize the current list of arcRNAs and proteins associated with classic and more recently discovered nuclear bodies and discuss general rules that govern the formation of nuclear bodies, emphasizing weak multivalent interactions mediated by innately flexible biomolecules.
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34
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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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35
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Schmerer N, Schulte LN. Long noncoding RNAs in bacterial infection. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1664. [PMID: 33989449 DOI: 10.1002/wrna.1664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 11/10/2022]
Abstract
Infectious and inflammatory diseases remain major causes of mortality and morbidity worldwide. To combat bacterial infections, the mammalian immune system employs a myriad of regulators, which secure the effective initiation of inflammatory responses while preventing pathologies due to overshooting immunity. Recently, the human genome has been shown to be pervasively transcribed and to generate thousands of still poorly characterized long noncoding RNAs (lncRNAs). A growing body of literature suggests that lncRNAs play important roles in the regulatory circuitries controlling innate and adaptive immune responses to bacterial pathogens. This review provides an overview of the roles of lncRNAs in the interaction of human and rodent host cells with bacterial pathogens. Further decoding of the lncRNA networks that underlie pathological inflammation and immune subversion could provide new insights into the host cell mechanisms and microbial strategies that determine the outcome of bacterial infections. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nils Schmerer
- Institute for Lung Research, Philipps-University, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps-University, Marburg, Germany.,German Center for Lung Research, Giessen, Germany
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36
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Fernandes N, Buchan JR. RNAs as Regulators of Cellular Matchmaking. Front Mol Biosci 2021; 8:634146. [PMID: 33898516 PMCID: PMC8062979 DOI: 10.3389/fmolb.2021.634146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/22/2021] [Indexed: 12/30/2022] Open
Abstract
RNA molecules are increasingly being identified as facilitating or impeding the interaction of proteins and nucleic acids, serving as so-called scaffolds or decoys. Long non-coding RNAs have been commonly implicated in such roles, particularly in the regulation of nuclear processes including chromosome topology, regulation of chromatin state and gene transcription, and assembly of nuclear biomolecular condensates such as paraspeckles. Recently, an increased awareness of cytoplasmic RNA scaffolds and decoys has begun to emerge, including the identification of non-coding regions of mRNAs that can also function in a scaffold-like manner to regulate interactions of nascently translated proteins. Collectively, cytoplasmic RNA scaffolds and decoys are now implicated in processes such as mRNA translation, decay, protein localization, protein degradation and assembly of cytoplasmic biomolecular condensates such as P-bodies. Here, we review examples of RNA scaffolds and decoys in both the nucleus and cytoplasm, illustrating common themes, the suitability of RNA to such roles, and future challenges in identifying and better understanding RNA scaffolding and decoy functions.
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Affiliation(s)
| | - J. Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, United States
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37
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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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38
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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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39
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Ramírez-Colmenero A, Oktaba K, Fernandez-Valverde SL. Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans. Front Genet 2020; 11:589697. [PMID: 33329735 PMCID: PMC7734150 DOI: 10.3389/fgene.2020.589697] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have important regulatory functions across eukarya. It is now clear that many of these functions are related to gene expression regulation through their capacity to recruit epigenetic modifiers and establish chromatin interactions. Several lncRNAs have been recently shown to participate in modulating chromatin within the spatial organization of the genome in the three-dimensional space of the nucleus. The identification of lncRNA candidates is challenging, as it is their functional characterization. Conservation signatures of lncRNAs are different from those of protein-coding genes, making identifying lncRNAs under selection a difficult task, and the homology between lncRNAs may not be readily apparent. Here, we review the evidence for these higher-order genome organization functions of lncRNAs in animals and the evolutionary signatures they display.
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Affiliation(s)
- América Ramírez-Colmenero
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Katarzyna Oktaba
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Selene L Fernandez-Valverde
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
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40
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Fang H, Bonora G, Lewandowski JP, Thakur J, Filippova GN, Henikoff S, Shendure J, Duan Z, Rinn JL, Deng X, Noble WS, Disteche CM. Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Nat Commun 2020; 11:6053. [PMID: 33247132 PMCID: PMC7695720 DOI: 10.1038/s41467-020-19879-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Firre encodes a lncRNA involved in nuclear organization. Here, we show that Firre RNA expressed from the active X chromosome maintains histone H3K27me3 enrichment on the inactive X chromosome (Xi) in somatic cells. This trans-acting effect involves SUZ12, reflecting interactions between Firre RNA and components of the Polycomb repressive complexes. Without Firre RNA, H3K27me3 decreases on the Xi and the Xi-perinucleolar location is disrupted, possibly due to decreased CTCF binding on the Xi. We also observe widespread gene dysregulation, but not on the Xi. These effects are measurably rescued by ectopic expression of mouse or human Firre/FIRRE transgenes, supporting conserved trans-acting roles. We also find that the compact 3D structure of the Xi partly depends on the Firre locus and its RNA. In common lymphoid progenitors and T-cells Firre exerts a cis-acting effect on maintenance of H3K27me3 in a 26 Mb region around the locus, demonstrating cell type-specific trans- and cis-acting roles of this lncRNA.
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Affiliation(s)
- He Fang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Giancarlo Bonora
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jordan P Lewandowski
- Department of Stem Cell and Regenerative Biology, Harvard University, Boston, MA, USA
| | | | - Galina N Filippova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John L Rinn
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
| | - Christine M Disteche
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Medicine, University of Washington, Seattle, WA, USA.
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41
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Miolo G, Bernardini L, Capalbo A, Favia A, Goldoni M, Pivetta B, Tessitori G, Corona G. Identification of a De Novo Xq26.2 Microduplication Encompassing FIRRE Gene in a Child with Intellectual Disability. Diagnostics (Basel) 2020; 10:diagnostics10121009. [PMID: 33255855 PMCID: PMC7760855 DOI: 10.3390/diagnostics10121009] [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: 10/28/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 12/30/2022] Open
Abstract
Long non-coding RNAs (lncRNAs), defined as transcripts of ≥200 nucleotides not translated into protein, have been involved in a wide range of regulatory functions. Their dysregulations have been associated with diverse pathological conditions such as cancer, schizophrenia, Parkinson’s, Huntington’s, Alzheimer’s diseases and Neurodevelopmental Disorders (NDDs), including autism spectrum disorders (ASDs). We report on the case of a five-year-old child with global developmental delay carrying a de novo microduplication on chromosome Xq26.2 region characterized by a DNA copy-number gain spanning about 147 Kb (chrX:130,813,232-130,960,617; GRCh37/hg19). This small microduplication encompassed the exons 2-12 of the functional intergenic repeating RNA element (FIRRE) gene (chrX:130,836,678-130,964,671; GRCh37/hg19) that encodes for a lncRNA involved in the maintenance of chromatin repression. The association of such a genetic alteration with a severe neurodevelopmental delay without clear dysmorphic features and congenital abnormalities indicative of syndromic condition further suggests that small Xq26.2 chromosomal region microduplications containing the FIRRE gene may be responsible for clinical phenotypes mainly characterized by structural or functioning neurological impairment.
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Affiliation(s)
- Gianmaria Miolo
- Medical Laboratory Department, Genetics Section, Pordenone Hospital, 33170 Pordenone, Italy; (B.P.); (G.T.)
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
- Correspondence: ; Tel.: +39-0434659097
| | - Laura Bernardini
- Medical Genetics Unit, Casa Sollievo della Sofferenza IRCCS Foundation, 71013 San Giovanni Rotondo, Italy; (L.B.); (A.C.); (M.G.)
| | - Anna Capalbo
- Medical Genetics Unit, Casa Sollievo della Sofferenza IRCCS Foundation, 71013 San Giovanni Rotondo, Italy; (L.B.); (A.C.); (M.G.)
| | - Anna Favia
- Department of Pediatrics, Pordenone Hospital, 33170 Pordenone, Italy;
| | - Marina Goldoni
- Medical Genetics Unit, Casa Sollievo della Sofferenza IRCCS Foundation, 71013 San Giovanni Rotondo, Italy; (L.B.); (A.C.); (M.G.)
| | - Barbara Pivetta
- Medical Laboratory Department, Genetics Section, Pordenone Hospital, 33170 Pordenone, Italy; (B.P.); (G.T.)
| | - Giovanni Tessitori
- Medical Laboratory Department, Genetics Section, Pordenone Hospital, 33170 Pordenone, Italy; (B.P.); (G.T.)
| | - Giuseppe Corona
- Immunopathology and Cancer Biomarkers Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy;
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42
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Abstract
The innate immune system relies on a germ-line-encoded repertoire of pattern recognition receptors (PRRs), activated by deeply conserved pathogen signatures, such as bacterial cell wall components or foreign nucleic acids. To enable effective defence against invading pathogens and prevent from deleterious inflammation, PRR-driven immune responses are tightly controlled by a dense network of nuclear and cytoplasmic regulators. Long non-coding RNAs (lncRNAs) are increasingly recognized as important components of these regulatory circuitries, providing positive and negative control of PRR-induced innate immune responses. The present review provides an overview of the presently known roles of lncRNAs in human and murine innate antiviral and antibacterial immunity. The emerging roles in host defence and inflammation suggest that further mechanistic insights into the cellular functions of lncRNAs will decisively advance our molecular understanding of immune-associated diseases and open new avenues for therapeutic intervention.
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Affiliation(s)
- Katharina Walther
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany
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43
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Flores-Concha M, Oñate ÁA. Long Non-coding RNAs in the Regulation of the Immune Response and Trained Immunity. Front Genet 2020; 11:718. [PMID: 32793280 PMCID: PMC7393263 DOI: 10.3389/fgene.2020.00718] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/12/2020] [Indexed: 01/04/2023] Open
Affiliation(s)
- Manuel Flores-Concha
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Ángel A Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
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44
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Khelifi G, Hussein SMI. A New View of Genome Organization Through RNA Directed Interactions. Front Cell Dev Biol 2020; 8:517. [PMID: 32760716 PMCID: PMC7371936 DOI: 10.3389/fcell.2020.00517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/02/2020] [Indexed: 12/30/2022] Open
Affiliation(s)
- Gabriel Khelifi
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada.,Université Laval Cancer Research Center, Université Laval, Québec, QC, Canada.,Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
| | - Samer M I Hussein
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada.,Université Laval Cancer Research Center, Université Laval, Québec, QC, Canada.,Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
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45
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Chen L, Bao Y, Jiang S, Zhong XB. The Roles of Long Noncoding RNAs HNF1α-AS1 and HNF4α-AS1 in Drug Metabolism and Human Diseases. Noncoding RNA 2020; 6:ncrna6020024. [PMID: 32599764 PMCID: PMC7345002 DOI: 10.3390/ncrna6020024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNAs with a length of over 200 nucleotides that do not have protein-coding abilities. Recent studies suggest that lncRNAs are highly involved in physiological functions and diseases. lncRNAs HNF1α-AS1 and HNF4α-AS1 are transcripts of lncRNA genes HNF1α-AS1 and HNF4α-AS1, which are antisense lncRNA genes located in the neighborhood regions of the transcription factor (TF) genes HNF1α and HNF4α, respectively. HNF1α-AS1 and HNF4α-AS1 have been reported to be involved in several important functions in human physiological activities and diseases. In the liver, HNF1α-AS1 and HNF4α-AS1 regulate the expression and function of several drug-metabolizing cytochrome P450 (P450) enzymes, which also further impact P450-mediated drug metabolism and drug toxicity. In addition, HNF1α-AS1 and HNF4α-AS1 also play important roles in the tumorigenesis, progression, invasion, and treatment outcome of several cancers. Through interacting with different molecules, including miRNAs and proteins, HNF1α-AS1 and HNF4α-AS1 can regulate their target genes in several different mechanisms including miRNA sponge, decoy, or scaffold. The purpose of the current review is to summarize the identified functions and mechanisms of HNF1α-AS1 and HNF4α-AS1 and to discuss the future directions of research of these two lncRNAs.
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Affiliation(s)
- Liming Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
| | - Yifan Bao
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
| | - Suzhen Jiang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 51006, China
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
- Correspondence: ; Tel.: +01-860-486-3697
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46
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Tachiwana H, Yamamoto T, Saitoh N. Gene regulation by non-coding RNAs in the 3D genome architecture. Curr Opin Genet Dev 2020; 61:69-74. [PMID: 32387763 DOI: 10.1016/j.gde.2020.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 01/01/2023]
Abstract
Appropriate gene expression is essential for producing the correct amount of proteins at the right time, which is critical for living organisms. In the three-dimensional (3D) space of the nucleus, genomes are folded into higher order chromatin structures that are intimately associated with epigenetic factors, including histone modifications and nuclear long non-coding RNAs (lncRNAs). LncRNAs regulate transcription for both activation and repression, either in cis or in trans. Many ncRNAs are expressed in development-specific, differentiation-specific, and disease-specific manners, suggesting that they are critical regulators for organ generation and maintenance. In this review, we mainly describe the following ncRNAs: Xist, involved in X chromosome inactivation, Firre, which serves as a platform for trans-chromosomal associations, and UMLILO and ELEANORS, which co-regulate genes involved in the immune response and breast cancer, respectively. These ncRNAs are gene regulators in the context of the 3D genome structure.
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Affiliation(s)
- Hiroaki Tachiwana
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Tatsuro Yamamoto
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
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47
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Abstract
Long non-coding RNAs (lncRNAs) represent a major fraction of the transcriptome in multicellular organisms. Although a handful of well-studied lncRNAs are broadly recognized as biologically meaningful, the fraction of such transcripts out of the entire collection of lncRNAs remains a subject of vigorous debate. Here we review the evidence for and against biological functionalities of lncRNAs and attempt to arrive at potential modes of lncRNA functionality that would reconcile the contradictory conclusions. Finally, we discuss different strategies of phenotypic analyses that could be used to investigate such modes of lncRNA functionality.
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Affiliation(s)
- Fan Gao
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China
| | - Ye Cai
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China.
| | - Dongyang Xu
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China.
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48
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Long non-coding RNAs in immune regulation and their potential as therapeutic targets. Int Immunopharmacol 2020; 81:106279. [PMID: 32058929 DOI: 10.1016/j.intimp.2020.106279] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs (lncRNAs) are potent regulators of immune cell development and function. Their implication in multiple immune-mediated disorders highlights lncRNAs as exciting biomarkers and potential drug targets. Recent technological innovations in oligo-based therapeutics, development of RNA-targeting small molecules, and CRISPR-based approaches, position RNA as the next therapeutic frontier. Here, we review the latest advances made toward understanding the role of lncRNAs in human immunological disorders and further discuss RNA-targeting approaches that could be potentially exploited to manipulate lncRNA function as a clinical intervention.
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49
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Bansal P, Kondaveeti Y, Pinter SF. Forged by DXZ4, FIRRE, and ICCE: How Tandem Repeats Shape the Active and Inactive X Chromosome. Front Cell Dev Biol 2020; 7:328. [PMID: 32076600 PMCID: PMC6985041 DOI: 10.3389/fcell.2019.00328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Recent efforts in mapping spatial genome organization have revealed three evocative and conserved structural features of the inactive X in female mammals. First, the chromosomal conformation of the inactive X reveals a loss of topologically associated domains (TADs) present on the active X. Second, the macrosatellite DXZ4 emerges as a singular boundary that suppresses physical interactions between two large TAD-depleted "megadomains." Third, DXZ4 reaches across several megabases to form "superloops" with two other X-linked tandem repeats, FIRRE and ICCE, which also loop to each other. Although all three structural features are conserved across rodents and primates, deletion of mouse and human orthologs of DXZ4 and FIRRE from the inactive X have revealed limited impact on X chromosome inactivation (XCI) and escape in vitro. In contrast, loss of Xist or SMCHD1 have been shown to impair TAD erasure and gene silencing on the inactive X. In this perspective, we summarize these results in the context of new research describing disruption of X-linked tandem repeats in vivo, and discuss their possible molecular roles through the lens of evolutionary conservation and clinical genetics. As a null hypothesis, we consider whether the conservation of some structural features on the inactive X may reflect selection for X-linked tandem repeats on account of necessary cis- and trans-regulatory roles they may play on the active X, rather than the inactive X. Additional hypotheses invoking a role for X-linked tandem repeats on X reactivation, for example in the germline or totipotency, remain to be assessed in multiple developmental models spanning mammalian evolution.
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Affiliation(s)
- Prakhar Bansal
- Department of Genetics and Genome Sciences, School of Medicine, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, School of Medicine, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
| | - Stefan F. Pinter
- Department of Genetics and Genome Sciences, School of Medicine, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
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50
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Andergassen D, Smith ZD, Lewandowski JP, Gerhardinger C, Meissner A, Rinn JL. In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation. eLife 2019; 8:e47214. [PMID: 31738164 PMCID: PMC6860989 DOI: 10.7554/elife.47214] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022] Open
Abstract
Recent evidence has determined that the conserved X chromosome mega-structures controlled by the Firre and Dxz4 loci are not required for X chromosome inactivation (XCI) in cell lines. Here, we examined the in vivo contribution of these loci by generating mice carrying a single or double deletion of Firre and Dxz4. We found that these mutants are viable, fertile and show no defect in random or imprinted XCI. However, the lack of these elements results in many dysregulated genes on autosomes in an organ-specific manner. By comparing the dysregulated genes between the single and double deletion, we identified superloop, megadomain, and Firre locus-dependent gene sets. The largest transcriptional effect was observed in all strains lacking the Firre locus, indicating that this locus is the main driver for these autosomal expression signatures. Collectively, these findings suggest that these X-linked loci are involved in autosomal gene regulation rather than XCI biology.
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Affiliation(s)
- Daniel Andergassen
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
| | - Zachary D Smith
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
| | - Jordan P Lewandowski
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
| | - Alexander Meissner
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
| | - John L Rinn
- Department of BiochemistryUniversity of Colorado BoulderBoulderUnited States
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