1
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Jiao YX, Bu GW, Wu YW, Wu YK, Chen BB, She MT, Zhang YH, Lu YJ, Fan HY. DHX36-mediated G-quadruplexes unwinding is essential for oocyte and early embryo development in mice. Sci Bull (Beijing) 2025; 70:1295-1310. [PMID: 40023726 DOI: 10.1016/j.scib.2025.02.017] [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: 08/11/2024] [Revised: 01/18/2025] [Accepted: 01/25/2025] [Indexed: 03/04/2025]
Abstract
DHX36 plays a crucial role in regulating transcriptional and post-transcriptional processes through its interaction with G-quadruplexes (G4s). The mechanisms by which DHX36 regulates G4s vary across different cell types and physiological conditions. Oocyte-specific conditional knockout (CKO) mice were utilized to study the impact of DHX36 deficiency on female fertility. The results show that the CKO mice exhibit severely impaired hormone response, ovulation, and complete infertility. The CKO germinal vesicle (GV) oocytes display large nucleoli, aberrant chromatin configuration, decreased chromatin accessibility, disturbed transcriptome, and inhibited meiosis progression. Following fertilization, the embryos derived from the CKO oocytes arrest at the zygote or 2-cell stage. Notably, we observed inadequate rRNA transcription in growing GV oocytes, as well as insufficient pre-rRNA processing and translation activity in fully-grown GV oocytes. Using a G4 probe and antibody, we found increased G4s formation at the chromatin and cytoplasm of CKO GV oocytes; these G4s mainly originate from the rDNA and pre-rRNA. Furthermore, the distribution of DHX36 was found to be spatiotemporally synchronized with that of pre-rRNA and G4s in early mouse embryos. In vitro experiments confirmed that DHX36 directly binds with pre-rRNA through the RHAU-specific motif (RSM). Overexpression of DHX36 could partially alleviate the pre-rRNA accumulation in fully-grown CKO oocytes. In conclusion, this study highlights the physiological significance of DHX36 in maintaining female fertility, underscoring its critical role in rRNA homeostasis and chromatin configuration through G4-unwinding mechanism in mouse oocytes.
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Affiliation(s)
- Yu-Xuan Jiao
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Guo-Wei Bu
- Center for Biomedical Research, Shaoxing Institute, Zhejiang University, Shaoxing 312000, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yu-Ke Wu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Bao-Bao Chen
- Center for Biomedical Research, Shaoxing Institute, Zhejiang University, Shaoxing 312000, China
| | - Meng-Ting She
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Yi-Hang Zhang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Yu-Jing Lu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Center for Biomedical Research, Shaoxing Institute, Zhejiang University, Shaoxing 312000, China; Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China.
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2
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Kamzeeva PN, Alferova VA, Korshun VA, Varizhuk AM, Aralov AV. 5'-UTR G-Quadruplex-Mediated Translation Regulation in Eukaryotes: Current Understanding and Methodological Challenges. Int J Mol Sci 2025; 26:1187. [PMID: 39940956 PMCID: PMC11818886 DOI: 10.3390/ijms26031187] [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: 12/09/2024] [Revised: 01/23/2025] [Accepted: 01/28/2025] [Indexed: 02/16/2025] Open
Abstract
RNA G-quadruplexes (rG4s) in 5'-UTRs represent complex regulatory elements capable of both inhibiting and activating mRNA translation through diverse mechanisms in eukaryotes. This review analyzes the evolution of our understanding of 5'-UTR rG4-mediated translation regulation, from early discoveries of simple translation inhibitors to the current recognition of their multifaceted regulatory roles. We discuss canonical and non-canonical rG4 structures, their interactions with regulatory proteins, including helicases and FMRP, and their function in both cap-dependent and IRES-mediated translation. Special attention is given to the synergistic effects between rG4s and upstream open reading frames (uORFs), stress-responsive translation regulation, and their role in repeat-associated non-AUG (RAN) translation linked to neurodegenerative diseases. We critically evaluate methodological challenges in the field, including limitations of current detection methods, reporter system artifacts, and the necessity to verify rG4 presence in endogenous transcripts. Recent technological advances, including genome editing and high-throughput sequencing approaches, have revealed that rG4 effects are more complex and context-dependent than initially thought. This review highlights the importance of developing more robust methodologies for studying rG4s at endogenous levels and carefully reevaluating previously identified targets, while emphasizing their potential as therapeutic targets in various diseases.
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Affiliation(s)
- Polina N. Kamzeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anna M. Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- RUDN University, 117198 Moscow, Russia
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3
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Meyer J, Payr M, Duss O, Hennig J. Exploring the dynamics of messenger ribonucleoprotein-mediated translation repression. Biochem Soc Trans 2024; 52:2267-2279. [PMID: 39601754 PMCID: PMC11668304 DOI: 10.1042/bst20231240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 10/14/2024] [Accepted: 10/21/2024] [Indexed: 11/29/2024]
Abstract
Translational control is crucial for well-balanced cellular function and viability of organisms. Different mechanisms have evolved to up- and down-regulate protein synthesis, including 3' untranslated region (UTR)-mediated translation repression. RNA binding proteins or microRNAs interact with regulatory sequence elements located in the 3' UTR and interfere most often with the rate-limiting initiation step of translation. Dysregulation of post-transcriptional gene expression leads to various kinds of diseases, emphasizing the significance of understanding the mechanisms of these processes. So far, only limited mechanistic details about kinetics and dynamics of translation regulation are understood. This mini-review focuses on 3' UTR-mediated translational regulation mechanisms and demonstrates the potential of using single-molecule fluorescence-microscopy for kinetic and dynamic studies of translation regulation in vivo and in vitro.
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Affiliation(s)
- Julia Meyer
- Department of Biochemistry IV – Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Marco Payr
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Candidate for Joint PhD Degree From EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Olivier Duss
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Janosch Hennig
- Department of Biochemistry IV – Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
- Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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4
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Zhao H, Lau HL, Zhang K, Kwok CK. Selective recognition of RNA G-quadruplex in vitro and in cells by L-aptamer-D-oligonucleotide conjugate. Nucleic Acids Res 2024; 52:13544-13560. [PMID: 39558155 DOI: 10.1093/nar/gkae1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 10/07/2024] [Accepted: 10/18/2024] [Indexed: 11/20/2024] Open
Abstract
RNA Guanine-quadruplexes (rG4s) are important nucleic acid structures that govern vital biological processes. Although numerous tools have been developed to target rG4s, few specific tools are capable of discerning individual rG4 of interest. Herein, we design and synthesize the first L-aptamer-antisense oligonucleotide (ASO) conjugate, L-Apt.4-1c-ASO15nt(APP), with a focus on recognizing the amyloid precursor protein (APP) rG4 region as an example. The L-aptamer module binds with the rG4 structure, whereas ASO hybridizes with flanking sequences. Together, these two modules enhance the precise recognition of APP rG4. We demonstrate that the L-Apt.4-1c-ASO15nt(APP) conjugate can interact with the APP rG4 region with sub-nanomolar binding affinity, and distinguish APP rG4 from other G4s and non-G4s in vitro and in cells. We also show that L-Apt.4-1c-ASO15nt(APP) can inhibit APP protein expression. Notably, we investigate the inhibitory mechanism of this newly developed tool, and reveal that it controls gene expression by hindering DHX36 protein from unraveling the rG4, as well as by promoting translational inhibition and RNase H-mediated mRNA knockdown activity. Our novel L-aptamer-ASO conjugate tool not only enables the specific recognition of rG4 region of interest, but also allows efficient gene control via targeting rG4-containing transcripts in cells.
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Affiliation(s)
- Haizhou Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Hill Lam Lau
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Kun Zhang
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
- Shenzhen Research Institute of City University of Hong Kong, 8 Yuexing 1st Road, Shenzhen Hi-Tech Industrial Park, Shenzhen, 518057, China
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5
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Fan W, Li Z, He X, Wang X, Sun M, Yang Z. SLC25A1 regulates placental development to ensure embryonic heart morphogenesis. Development 2024; 151:dev204290. [PMID: 39591637 DOI: 10.1242/dev.204290] [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: 07/28/2024] [Accepted: 10/07/2024] [Indexed: 11/28/2024]
Abstract
22q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal microdeletion syndrome. Congenital heart defects are prevalent in 22q11.2DS but the etiology is still poorly understood. In this study, we aimed to gain mechanistic insights into the heart defects that result from 22q11.2 deletion, with a focus on Slc25a1, which is located in the deletion segment. Whereas global knockout of Slc25a1 in mice produced a variety of heart malformations, cardiac deletion of Slc25a1 had little effect on heart development. We then found that trophoblast-specific Slc25a1 deletion recapitulated heart anomalies in the global knockout mice. Further study identified SLC25A1 as a regulator of trophoblast and placental development through modulation of histone H3K27 acetylation at the promoters and enhancers of key genes involved in trophoblast differentiation. Finally, administration of recombinant human pregnancy-specific glycoprotein 1 (PSG1), a trophoblast-derived secretory glycoprotein, partially corrected placental and embryonic heart defects. This study defines the role of SLC25A1 in heart development by regulating placental development, and provides new insights to understand the etiology of 22q11.2DS.
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Affiliation(s)
- Wenli Fan
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing 210093, China
| | - Zixuan Li
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing 210093, China
| | - Xueke He
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing 210093, China
| | - Xiaodong Wang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing 210093, China
| | - Ming Sun
- Suqian Scientific Research Institute of Nanjing University Medical School, Nanjing University, Suqian, Jiangsu 223800, China
| | - Zhongzhou Yang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Medical School, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing 210093, China
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6
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Zhang Y, Zhao J, Chen X, Qiao Y, Kang J, Guo X, Yang F, Lyu K, Ding Y, Zhao Y, Sun H, Kwok CK, Wang H. DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m 6A reader YTHDF1. Nat Commun 2024; 15:9890. [PMID: 39543097 PMCID: PMC11564809 DOI: 10.1038/s41467-024-54000-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/28/2024] [Indexed: 11/17/2024] Open
Abstract
RNA structure constitutes a new layer of gene regulatory mechanisms. RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) is known to bind and unwind RNA G-quadruplex (rG4) structure but the transcriptome-wide RNA structure remodeling induced by DHX36 binding and the impact on RNA fate remain poorly understood. Here, we investigate the RNA structurome alteration induced by DHX36 depletion. Our findings reveal that DHX36 binding induces structural remodeling not only at the localized binding sites but also on the entire mRNA transcript most pronounced in 3'UTR regions. DHX36 binding increases structural accessibility at 3'UTRs which is correlated with decreased post-transcriptional mRNA abundance. Further analyses and experiments uncover that DHX36 binding sites are enriched for N6-methyladenosine (m6A) modification and YTHDF1 binding; and DHX36 induced structural changes may facilitate YTHDF1 binding to m6A sites leading to RNA degradation. Altogether, our findings uncover the structural remodeling effect of DHX36 binding and its impact on RNA abundance through regulating m6A dependent YTHDF1 binding.
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Grants
- 82172436 National Natural Science Foundation of China (National Science Foundation of China)
- 32300703 National Natural Science Foundation of China (National Science Foundation of China)
- 32270587 National Natural Science Foundation of China (National Science Foundation of China)
- National Key R&D Program of China to H.W. (2022YFA0806003);General Research Funds (GRF) from the Research Grants Council (RGC) of the Hong Kong Special Administrative Region (14115319, 14100620, 14106521 and 14105823 to H.W.);the research funds from Health@InnoHK program launched by Innovation Technology Commission, the Government of the Hong Kong SAR, China to H.W.; Collaborative Research Fund (CRF) from RGC to H.W. (C6018-19GF); Theme-based Research Scheme (TRS) from RGC (project number: T13-602/21-N); Hong Kong Epigenomics Project (EpiHK) Fund to H.W.; Area of Excellence Scheme (AoE) from RGC (project number: AoE/M-402/20); Health and Medical Research Fund (HMRF) from Health Bureau of the Hong Kong Special Administrative Region, China (project Code: 10210906 and 08190626 to H.W.).
- CUHK Direct Grant to X.C. (project No.: 2022.038)
- General Research Funds (GRF) from the Research Grants Council (RGC) of the Hong Kong Special Administrative Region (14120420, 14103522 and 14105123); Hong Kong Epigenomics Project (EpiHK) Fund
- General Research Funds (GRF) from the Research Grants Council (RGC) of the Hong Kong Special Administrative Region (CityU 11100123, CityU 11100222, CityU 11100421); National Natural Science Foundation of China (NSFC) Excellent Young Scientists Fund (Hong Kong and Macau) Project (32222089) to C.K.K.; Croucher Foundation Project (9509003) to C.K.K.; State Key Laboratory of Marine Pollution Seed Collaborative Research Fund (SCRF/0037, SCRF/0040, SCRF0070) to C.K.K.; City University of Hong Kong projects (9678302 and 6000827) to C.K.K.; the Hong Kong Institute for Advanced Study, City University of Hong Kong [9360157] to C.K.K..
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Affiliation(s)
- Yuwei Zhang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Jieyu Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, SAR, China
| | - Xiaona Chen
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong, SAR, China
| | - Yulong Qiao
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong, SAR, China
| | - Jinjin Kang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xiaofan Guo
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong, SAR, China
| | - Feng Yang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, SAR, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Hao Sun
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China.
| | - Chun-Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, SAR, China.
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, SAR, China.
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong, SAR, China.
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7
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Gómez-Del Arco P, Isern J, Jimenez-Carretero D, López-Maderuelo D, Piñeiro-Sabarís R, El Abdellaoui-Soussi F, Torroja C, Vera-Pedrosa ML, Grima-Terrén M, Benguria A, Simón-Chica A, Queiro-Palou A, Dopazo A, Sánchez-Cabo F, Jalife J, de la Pompa JL, Filgueiras-Rama D, Muñoz-Cánoves P, Redondo JM. The G4 resolvase Dhx36 modulates cardiomyocyte differentiation and ventricular conduction system development. Nat Commun 2024; 15:8602. [PMID: 39366945 PMCID: PMC11452623 DOI: 10.1038/s41467-024-52809-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/19/2024] [Indexed: 10/06/2024] Open
Abstract
Extensive genetic studies have elucidated cardiomyocyte differentiation and associated gene networks using single-cell RNA-seq, yet the intricate transcriptional mechanisms governing cardiac conduction system (CCS) development and working cardiomyocyte differentiation remain largely unexplored. Here we show that mice deleted for Dhx36 (encoding the Dhx36 helicase) in the embryonic or neonatal heart develop overt dilated cardiomyopathy, surface ECG alterations related to cardiac impulse propagation, and (in the embryonic heart) a lack of a ventricular conduction system (VCS). Heart snRNA-seq and snATAC-seq reveal the role of Dhx36 in CCS development and in the differentiation of working cardiomyocytes. Dhx36 deficiency directly influences cardiomyocyte gene networks by disrupting the resolution of promoter G-quadruplexes in key cardiac genes, impacting cardiomyocyte differentiation and CCS morphogenesis, and ultimately leading to dilated cardiomyopathy and atrioventricular block. These findings further identify crucial genes and pathways that regulate the development and function of the VCS/Purkinje fiber (PF) network.
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Affiliation(s)
- Pablo Gómez-Del Arco
- Institute for Rare Diseases Research, Instituto de Salud Carlos III (ISCIII). Majadahonda, Madrid, Spain.
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
| | - Joan Isern
- Altos Labs, Inc., San Diego Institute of Science, San Diego, CA, USA
- Tissue Regeneration Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Daniel Jimenez-Carretero
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Dolores López-Maderuelo
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Rebeca Piñeiro-Sabarís
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Fadoua El Abdellaoui-Soussi
- Institute for Rare Diseases Research, Instituto de Salud Carlos III (ISCIII). Majadahonda, Madrid, Spain
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Center for Stem Cells and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carlos Torroja
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - María Linarejos Vera-Pedrosa
- Cardiac Arrhythmia Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Mercedes Grima-Terrén
- Altos Labs, Inc., San Diego Institute of Science, San Diego, CA, USA
- Tissue Regeneration Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Alberto Benguria
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Ana Simón-Chica
- Novel Arrhythmogenic Mechanisms Program, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Antonio Queiro-Palou
- Institute for Rare Diseases Research, Instituto de Salud Carlos III (ISCIII). Majadahonda, Madrid, Spain
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - José Jalife
- Cardiac Arrhythmia Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- University of Michigan, Ann Arbor, MI, USA
| | - José Luis de la Pompa
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - David Filgueiras-Rama
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Novel Arrhythmogenic Mechanisms Program, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Cardiovascular Institute, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Pura Muñoz-Cánoves
- Altos Labs, Inc., San Diego Institute of Science, San Diego, CA, USA.
- Tissue Regeneration Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
- Department of Experimental & Health Sciences, University Pompeu Fabra (UPF)/CIBERNED, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Juan Miguel Redondo
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
- Cell-Cell Communication & Inflammation Unit, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain.
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8
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Jia K, Cheng H, Ma W, Zhuang L, Li H, Li Z, Wang Z, Sun H, Cui Y, Zhang H, Xie H, Yi L, Chen Z, Sano M, Fukuda K, Lu L, Pu J, Zhang Y, Gao L, Zhang R, Yan X. RNA Helicase DDX5 Maintains Cardiac Function by Regulating CamkIIδ Alternative Splicing. Circulation 2024; 150:1121-1139. [PMID: 39056171 DOI: 10.1161/circulationaha.123.064774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/19/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND Heart failure (HF) is a leading cause of morbidity and mortality worldwide. RNA-binding proteins are identified as regulators of cardiac disease; DDX5 (dead-box helicase 5) is a master regulator of many RNA processes, although its function in heart physiology remains unclear. METHODS We assessed DDX5 expression in human failing hearts and a mouse HF model. To study the function of DDX5 in heart, we engineered cardiomyocyte-specific Ddx5 knockout mice. We overexpressed DDX5 in cardiomyocytes using adeno-associated virus serotype 9 and performed transverse aortic constriction to establish the murine HF model. The mechanisms underlined were subsequently investigated using immunoprecipitation-mass spectrometry, RNA-sequencing, alternative splicing analysis, and RNA immunoprecipitation sequencing. RESULTS We screened transcriptome databases of murine HF and human dilated cardiomyopathy samples and found that DDX5 was significantly downregulated in both. Cardiomyocyte-specific deletion of Ddx5 resulted in HF with reduced cardiac function, an enlarged heart chamber, and increased fibrosis in mice. DDX5 overexpression improved cardiac function and protected against adverse cardiac remodeling in mice with transverse aortic constriction-induced HF. Furthermore, proteomics revealed that DDX5 is involved in RNA splicing in cardiomyocytes. We found that DDX5 regulated the aberrant splicing of Ca2+/calmodulin-dependent protein kinase IIδ (CamkIIδ), thus preventing the production of CaMKIIδA, which phosphorylates L-type calcium channel by serine residues of Cacna1c, leading to impaired Ca2+ homeostasis. In line with this, we found increased intracellular Ca2+ transients and increased sarcoplasmic reticulum Ca2+ content in DDX5-depleted cardiomyocytes. Using adeno-associated virus serotype 9 knockdown of CaMKIIδA partially rescued the cardiac dysfunction and HF in Ddx5 knockout mice. CONCLUSIONS These findings reveal a role for DDX5 in maintaining calcium homeostasis and cardiac function by regulating alternative splicing in cardiomyocytes, identifying the DDX5 as a potential target for therapeutic intervention in HF.
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Affiliation(s)
- Kangni Jia
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Haomai Cheng
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Wenqi Ma
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Lingfang Zhuang
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Hao Li
- Translational Medical Center for Stem Cell Therapy & Institutes for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, China (H.L., L.G.)
| | - Zhigang Li
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Ziyang Wang
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Hang Sun
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Yuke Cui
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Hang Zhang
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Hongyang Xie
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Lei Yi
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Zhiyong Chen
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Motoaki Sano
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan (M.S., K.F.)
| | - Keiichi Fukuda
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan (M.S., K.F.)
| | - Lin Lu
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Jun Pu
- Department of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital (J.P.), School of Medicine, Shanghai Jiao Tong University, China
| | - Yan Zhang
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing, China (Y.Z.)
| | - Ling Gao
- Translational Medical Center for Stem Cell Therapy & Institutes for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, China (H.L., L.G.)
| | - Ruiyan Zhang
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
- Institute of Cardiovascular Diseases (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.C., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
| | - Xiaoxiang Yan
- Department of Cardiovascular Medicine, Ruijin Hospital (K.J., H.C., W.M., L.Z., Z.L., Z.W., H.S., Y.C., H.Z., H.X., L.Y., Z.C., L.L., R.Z., X.Y.), School of Medicine, Shanghai Jiao Tong University, China
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9
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Fu L, Wu Q, Fu J. Exploring the biological roles of DHX36, a DNA/RNA G-quadruplex helicase, highlights functions in male infertility: A comprehensive review. Int J Biol Macromol 2024; 268:131811. [PMID: 38677694 DOI: 10.1016/j.ijbiomac.2024.131811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/29/2024]
Abstract
It is estimated that 15 % of couples at reproductive age worldwide suffer from infertility, approximately 50 % of cases are caused by male factors. Significant progress has been made in the diagnosis and treatment of male infertility through assisted reproductive technology and molecular genetics methods. However, there is still inadequate research on the underlying mechanisms of gene regulation in the process of spermatogenesis. Guanine-quadruplexes (G4s) are a class of non-canonical secondary structures of nucleic acid commonly found in genomes and RNAs that play important roles in various biological processes. Interestingly, the DEAH-box helicase 36 (DHX36) displays high specificity for the G4s which can unwind both DNA G4s and RNA G4s enzymatically and is highly expressed in testis, thereby regulating multiple cellular functions including transcription, pre-mRNA splicing, translation, telomere maintenance, genomic stability, and RNA metabolism in development and male infertility. This review provides an overview of the roles of G4s and DHX36 in reproduction and development. We mainly focus on the potential role of DHX36 in male infertility. We also discuss possible future research directions regarding the mechanism of spermatogenesis mediated by DHX36 through G4s in spermatogenesis-related genes and provide new targets for gene therapy of male infertility.
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Affiliation(s)
- Li Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China; Department of Reproductive Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China; Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Junjiang Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China.
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10
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Paquette AR, Boddy CN. Double Stranded DNA Binding Stapled Peptides: An Emerging Tool for Transcriptional Regulation. Chembiochem 2023; 24:e202300594. [PMID: 37750576 DOI: 10.1002/cbic.202300594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
Stapled peptides have rapidly established themselves as a powerful technique to mimic α-helical interactions with a short peptide sequence. There are many examples of stapled peptides that successfully disrupt α-helix-mediated protein-protein interactions, with an example currently in clinical trials. DNA-protein interactions are also often mediated by α-helices and are involved in all transcriptional regulation processes. Unlike DNA-binding small molecules, which typically lack DNA sequence selectivity, DNA-binding proteins bind with high affinity and high selectivity. These are ideal candidates for the design DNA-binding stapled peptides. Despite the parallel to protein-protein interaction disrupting stapled peptides and the need for sequence specific DNA binders, there are very few DNA-binding stapled peptides. In this review we examine all the known DNA-binding stapled peptides. Their design concepts are compared to stapled peptides that disrupt protein-protein interactions and based on the few examples in the literature, DNA-binding stapled peptide trends are discussed.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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11
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Cao C, Li L, Zhang Q, Li H, Wang Z, Wang A, Liu J. Nkx2.5: a crucial regulator of cardiac development, regeneration and diseases. Front Cardiovasc Med 2023; 10:1270951. [PMID: 38124890 PMCID: PMC10732152 DOI: 10.3389/fcvm.2023.1270951] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Cardiomyocytes fail to regenerate after birth and respond to mitotic signals through cellular hypertrophy rather than cellular proliferation. Necrotic cardiomyocytes in the infarcted ventricular tissue are eventually replaced by fibroblasts, generating scar tissue. Cardiomyocyte loss causes localized systolic dysfunction. Therefore, achieving the regeneration of cardiomyocytes is of great significance for cardiac function and development. Heart development is a complex biological process. An integral cardiac developmental network plays a decisive role in the regeneration of cardiomyocytes. During this process, genetic epigenetic factors, transcription factors, signaling pathways and small RNAs are involved in regulating the developmental process of the heart. Cardiomyocyte-specific genes largely promote myocardial regeneration, among which the Nkx2.5 transcription factor is one of the earliest markers of cardiac progenitor cells, and the loss or overexpression of Nkx2.5 affects cardiac development and is a promising candidate factor. Nkx2.5 affects the development and function of the heart through its multiple functional domains. However, until now, the specific mechanism of Nkx2.5 in cardiac development and regeneration is not been fully understood. Therefore, this article will review the molecular structure, function and interaction regulation of Nkx2.5 to provide a new direction for cardiac development and the treatment of heart regeneration.
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Affiliation(s)
- Ce Cao
- Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing Key Laboratory of Chinese Materia Pharmacology, National Clinical Research Center of Traditional Chinese Medicine for Cardiovascular Diseases, Beijing, China
- Institute of Chinese Medicine Sciences, Guangdong Pharmaceutical University, Guangzhou, China
| | - Lei Li
- Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing Key Laboratory of Chinese Materia Pharmacology, National Clinical Research Center of Traditional Chinese Medicine for Cardiovascular Diseases, Beijing, China
| | - Qian Zhang
- Institute of Chinese Medicine Sciences, Guangdong Pharmaceutical University, Guangzhou, China
| | - Haoran Li
- Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing Key Laboratory of Chinese Materia Pharmacology, National Clinical Research Center of Traditional Chinese Medicine for Cardiovascular Diseases, Beijing, China
- Institute of Chinese Medicine Sciences, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ziyan Wang
- Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing Key Laboratory of Chinese Materia Pharmacology, National Clinical Research Center of Traditional Chinese Medicine for Cardiovascular Diseases, Beijing, China
| | - Aoao Wang
- Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing Key Laboratory of Chinese Materia Pharmacology, National Clinical Research Center of Traditional Chinese Medicine for Cardiovascular Diseases, Beijing, China
| | - Jianxun Liu
- Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing Key Laboratory of Chinese Materia Pharmacology, National Clinical Research Center of Traditional Chinese Medicine for Cardiovascular Diseases, Beijing, China
- Institute of Chinese Medicine Sciences, Guangdong Pharmaceutical University, Guangzhou, China
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12
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Shi DL. RNA-Binding Proteins as Critical Post-Transcriptional Regulators of Cardiac Regeneration. Int J Mol Sci 2023; 24:12004. [PMID: 37569379 PMCID: PMC10418649 DOI: 10.3390/ijms241512004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Myocardial injury causes death to cardiomyocytes and leads to heart failure. The adult mammalian heart has very limited regenerative capacity. However, the heart from early postnatal mammals and from adult lower vertebrates can fully regenerate after apical resection or myocardial infarction. Thus, it is of particular interest to decipher the mechanism underlying cardiac regeneration that preserves heart structure and function. RNA-binding proteins, as key regulators of post-transcriptional gene expression to coordinate cell differentiation and maintain tissue homeostasis, display dynamic expression in fetal and adult hearts. Accumulating evidence has demonstrated their importance for the survival and proliferation of cardiomyocytes following neonatal and postnatal cardiac injury. Functional studies suggest that RNA-binding proteins relay damage-stimulated cell extrinsic or intrinsic signals to regulate heart regenerative capacity by reprogramming multiple molecular and cellular processes, such as global protein synthesis, metabolic changes, hypertrophic growth, and cellular plasticity. Since manipulating the activity of RNA-binding proteins can improve the formation of new cardiomyocytes and extend the window of the cardiac regenerative capacity in mammals, they are potential targets of therapeutic interventions for cardiovascular disease. This review discusses our evolving understanding of RNA-binding proteins in regulating cardiac repair and regeneration, with the aim to identify important open questions that merit further investigations.
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Affiliation(s)
- De-Li Shi
- Department of Medical Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
- Laboratory of Developmental Biology (CNRS-UMR7622), Institute de Biologie Paris-Seine (IBPS), Sorbonne University, 75005 Paris, France
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13
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Wang Q, Chen P, Wang X, Wu Y, Xia K, Mu X, Xuan Q, Xiao J, He Y, Liu W, Song X, Sun F. piR-36249 and DHX36 together inhibit testicular cancer cells progression by upregulating OAS2. Noncoding RNA Res 2023; 8:174-186. [PMID: 36710986 PMCID: PMC9851840 DOI: 10.1016/j.ncrna.2022.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023] Open
Abstract
Background PIWI-interacting RNAs (piRNAs) are a class of noncoding RNAs originally reported in the reproductive system of mammals and later found to be aberrantly expressed in tumors. However, the function and mechanism of piRNAs in testicular cancer are not very clear. Methods The expression level and distribution of piR-36249 were detected by RT-qPCR and immunofluorescence staining assay. Testicular cancer cell (NT2) progression was measured by CCK8 assay, colony formation assay and wound healing assay. Cell apoptosis was assessed by flow cytometry and western blot. RNA sequencing and dual-luciferase reporter assay were conducted to identify the potential targets of piR-36249. The relationship between piR-36249 and OAS2 or DHX36 was confirmed using overexpression assay, knockdown assay, pull-down assay and RIP assay. Results piR-36249 is significantly downregulated in testicular cancer tissues compared to tumor-adjacent tissues. Functional studies demonstrate that piR-36249 inhibits testicular cancer cell proliferation, migration and activates the cell apoptosis pathway. Mechanically, we identify that piR-36249 binds to the 3'UTR of 2'-5'-oligoadenylate synthetase 2 (OAS2) mRNA. OAS2 has been shown in the literature to be a tumor suppressor modulating the occurrence and development of some tumors. Here, we show that OAS2 knockdown also promotes testicular cancer cell proliferation and migration. Furthermore, piR-36249 interacts with DHX36, which has been reported to promote translation. DHX36 can also bind to OAS2 mRNA, and knockdown of DHX36 increases OAS2 mRNA but downregulates its protein, indicating the enhancing effect of DHX36 on OAS2 protein expression. Conclusion All these data suggest that piR-36249, together with DHX36, functions in inhibiting the malignant phenotype of testicular cancer cells by upregulating OAS2 protein and that piR-36249 may be used as a suppressor factor to regulate the development of testicular cancer.
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Affiliation(s)
- Qianqian Wang
- Department of Urology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Peize Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xiaorong Wang
- Center for Reproductive Medicine, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, Jiangsu, 226018, China
| | - Yueming Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Kaiguo Xia
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Xiangyu Mu
- Department of Urology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Qiang Xuan
- Department of Urology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Jun Xiao
- Department of Urology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Yaohui He
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, 361102, China
| | - Wen Liu
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xiaoyuan Song
- Department of Urology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Fei Sun
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
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14
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Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
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Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
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15
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Lyu K, Chen SB, Chow EYC, Zhao H, Yuan JH, Cai M, Shi J, Chan TF, Tan JH, Kwok CK. An RNA G-Quadruplex Structure within the ADAR 5'UTR Interacts with DHX36 Helicase to Regulate Translation. Angew Chem Int Ed Engl 2022; 61:e202203553. [PMID: 36300875 DOI: 10.1002/anie.202203553] [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: 03/08/2022] [Indexed: 11/25/2022]
Abstract
RNA G-quadruplex (rG4) structures in the 5' untranslated region (5'UTR) play crucial roles in fundamental cellular processes. ADAR is an important enzyme that binds to double-strand RNA and accounts for the conversion of Adenosine to Inosine in RNA editing. However, so far there is no report on the formation and regulatory role of rG4 on ADAR expression. Here, we identify and characterize a thermostable rG4 structure within the 5'UTR of the ADAR1 mRNA and demonstrate its formation and inhibitory role on translation in reporter gene and native gene constructs. We reveal rG4-specific helicase DHX36 interacts with this rG4 in vitro and in cells under knockdown and knockout conditions by GTFH (G-quadruplex-triggered fluorogenic hybridization) probes and modulates translation in an rG4-dependent manner. Our results further substantiate the rG4 structure-DHX36 protein interaction in cells and highlight rG4 to be a key player in controlling ADAR1 translation.
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Affiliation(s)
- Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, 510006, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Haizhou Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Jia-Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, 510006, China
| | - Meng Cai
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, Tung Biomedical Sciences Center, City University of Hong Kong, Hong Kong SAR, China
| | - Jiahai Shi
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, Tung Biomedical Sciences Center, City University of Hong Kong, Hong Kong SAR, China.,Department of Biochemistry, Synthetic Biology Translational Research Programmes, Yong Loo Lin School of Medicine, National University of, Singapore, Singapore
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, 510006, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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16
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Wang G, Ye H, Wang X, Liu B. Polycomb repressive complex 2 controls cardiac cell fate decision via interacting with RNA: Promiscuously or well-ordered. Front Genet 2022; 13:1011228. [PMID: 36313464 PMCID: PMC9614146 DOI: 10.3389/fgene.2022.1011228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
The epigenetic landscape determines cell fate during heart development. Polycomb repressive complex 2 (PRC2) mediates histone methyltransferase activity during cardiac cell differentiation. The PRC2 complex contains the proteins embryonic ectoderm development (EED), suppressor of zeste (SUZ12), the chromatin assembly factor 1 (CAF1) histone-binding proteins RBBP4 and RBBP7, and the histone methyltransferase called enhancer of zeste (EZH2 or EZH1), which incorporates the Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain. Cardiac PRC2-deficient mice display lethal congenital heart malformations. The dynamic process of cardiac cell fate decisions is controlled by PRC2 and the PRC2-mediated epigenetic landscape. Although specific individual long noncoding RNAs (lncRNAs) including Braveheart were widely reported to regulate the recruitments of PRC2 to their specific targets, a promiscuous RNA binding profile by PRC2 was also identified to play an essential role in cardiac cell fate decision. In this review, we focus on RNA-mediated PRC2 recruitment machinery in the process of cardiac cell fate decisions. The roles of individual lncRNAs which recruit PRC2, as well as promiscuous RNA binding by PRC2 in heart development are summarized. Since the binding priority of RNAs with different primary and secondary structures differs in its affinity to PRC2, the competitive relationship between individual lncRNAs binding and promiscuous RNA binding by PRC2 may be important for understanding the machinery by which biding of individual lncRNA and promiscuous RNA by PRC2 coordinately control the well-ordered dynamic cardiac cell lineage differentiation process.
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Affiliation(s)
- Gang Wang
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Heng Ye
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
| | - Xuchao Wang
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
| | - Binbin Liu
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
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17
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Yang C, Yao J, Yi H, Huang X, Zhao W, Yang Z. To unwind the biological knots: The DNA/RNA G-quadruplex resolvase RHAU (DHX36) in development and disease. Animal Model Exp Med 2022; 5:542-549. [PMID: 35789129 PMCID: PMC9773310 DOI: 10.1002/ame2.12251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 12/30/2022] Open
Abstract
The G-quadruplex (G4) sequences are short fragments of 4-interval triple guanine (G) with frequent and ubiquitous distribution in the genome and RNA transcripts. The G4 sequences are usually folded into secondary "knot" structure via Hoogsteen hydrogen bond to exert negative regulation on a variety of biological processes, including DNA replication and transcription, mRNA translation, and telomere maintenance. Recent structural biological and mouse genetics studies have demonstrated that RHAU (DHX36) can bind and unwind the G4 "knots" to modulate embryonic development and postnatal organ function. Deficiency of RHAU gives rise to embryonic lethality, impaired organogenesis, and organ dysfunction. These studies uncovered the pivotal G4 resolvase function of RHAU to release the G4 barrier, which plays fundamental roles in development and physiological homeostasis. This review discusses the latest advancements and findings in deciphering RHAU functions using animal models.
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Affiliation(s)
- Chensi Yang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Jie Yao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Huijuan Yi
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Xinyi Huang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Wukui Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
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18
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Cagirici HB, Budak H, Sen TZ. G4Boost: a machine learning-based tool for quadruplex identification and stability prediction. BMC Bioinformatics 2022; 23:240. [PMID: 35717172 PMCID: PMC9206279 DOI: 10.1186/s12859-022-04782-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, and accurate energy-based methods are needed to assess their structural stability. Here, we present a decision tree-based prediction tool, G4Boost, to identify G4 motifs and predict their secondary structure folding probability and thermodynamic stability based on their sequences, nucleotide compositions, and estimated structural topologies.
Results G4Boost predicted the quadruplex folding state with an accuracy greater then 93% and an F1-score of 0.96, and the folding energy with an RMSE of 4.28 and R2 of 0.95 only by the means of sequence intrinsic feature. G4Boost was successfully applied and validated to predict the stability of experimentally-determined G4 structures, including for plants and humans. Conclusion G4Boost outperformed the three machine-learning based prediction tools, DeepG4, Quadron, and G4RNA Screener, in terms of both accuracy and F1-score, and can be highly useful for G4 prediction to understand gene regulation across species including plants and humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04782-z.
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Affiliation(s)
- H Busra Cagirici
- US Department of Agriculture - Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA
| | | | - Taner Z Sen
- US Department of Agriculture - Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA.
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19
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Lockd promotes myoblast proliferation and muscle regeneration via binding with DHX36 to facilitate 5' UTR rG4 unwinding and Anp32e translation. Cell Rep 2022; 39:110927. [PMID: 35675771 DOI: 10.1016/j.celrep.2022.110927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/10/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
Adult muscle stem cells, also known as satellite cells (SCs), play pivotal roles in muscle regeneration, and long non-coding RNA (lncRNA) functions in SCs remain largely unknown. Here, we identify a lncRNA, Lockd, which is induced in activated SCs upon acute muscle injury. We demonstrate that Lockd promotes SC proliferation; deletion of Lockd leads to cell-cycle arrest, and in vivo repression of Lockd in mouse muscles hinders regeneration process. Mechanistically, we show that Lockd directly interacts with RNA helicase DHX36 and the 5'end of Lockd possesses the strongest binding with DHX36. Furthermore, we demonstrate that Lockd stabilizes the interaction between DHX36 and EIF3B proteins; synergistically, this complex unwinds the RNA G-quadruplex (rG4) structure formed at Anp32e mRNA 5' UTR and promotes the translation of ANP32E protein, which is required for myoblast proliferation. Altogether, our findings identify a regulatory Lockd/DHX36/Anp32e axis that promotes myoblast proliferation and acute-injury-induced muscle regeneration.
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20
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Georgakopoulos-Soares I, Parada GE, Hemberg M. Secondary structures in RNA synthesis, splicing and translation. Comput Struct Biotechnol J 2022; 20:2871-2884. [PMID: 35765654 PMCID: PMC9198270 DOI: 10.1016/j.csbj.2022.05.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
Even though the functional role of mRNA molecules is primarily decided by the nucleotide sequence, several properties are determined by secondary structure conformations. Examples of secondary structures include long range interactions, hairpins, R-loops and G-quadruplexes and they are formed through interactions of non-adjacent nucleotides. Here, we discuss advances in our understanding of how secondary structures can impact RNA synthesis, splicing, translation and mRNA half-life. During RNA synthesis, secondary structures determine RNA polymerase II (RNAPII) speed, thereby influencing splicing. Splicing is also determined by RNA binding proteins and their binding rates are modulated by secondary structures. For the initiation of translation, secondary structures can control the choice of translation start site. Here, we highlight the mechanisms by which secondary structures modulate these processes, discuss advances in technologies to detect and study them systematically, and consider the roles of RNA secondary structures in disease.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Guillermo E. Parada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5A 1A8, Canada
| | - Martin Hemberg
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
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21
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Sun J, Wu G, Pastor F, Rahman N, Wang WH, Zhang Z, Merle P, Hui L, Salvetti A, Durantel D, Yang D, Andrisani O. RNA helicase DDX5 enables STAT1 mRNA translation and interferon signalling in hepatitis B virus replicating hepatocytes. Gut 2022; 71:991-1005. [PMID: 34021034 PMCID: PMC8606016 DOI: 10.1136/gutjnl-2020-323126] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 05/09/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE RNA helicase DDX5 is downregulated during HBV replication and poor prognosis HBV-related hepatocellular carcinoma (HCC). The objective of this study is to investigate the role of DDX5 in interferon (IFN) signalling. We provide evidence of a novel mechanism involving DDX5 that enables translation of transcription factor STAT1 mediating the IFN response. DESIGN AND RESULTS Molecular, pharmacological and biophysical assays were used together with cellular models of HBV replication, HCC cell lines and liver tumours. We demonstrate that DDX5 regulates STAT1 mRNA translation by resolving a G-quadruplex (rG4) RNA structure, proximal to the 5' end of STAT1 5'UTR. We employed luciferase reporter assays comparing wild type (WT) versus mutant rG4 sequence, rG4-stabilising compounds, CRISPR/Cas9 editing of the STAT1-rG4 sequence and circular dichroism determination of the rG4 structure. STAT1-rG4 edited cell lines were resistant to the effect of rG4-stabilising compounds in response to IFN-α, while HCC cell lines expressing low DDX5 exhibited reduced IFN response. Ribonucleoprotein and electrophoretic mobility assays demonstrated direct and selective binding of RNA helicase-active DDX5 to the WT STAT1-rG4 sequence. Immunohistochemistry of normal liver and liver tumours demonstrated that absence of DDX5 corresponded to absence of STAT1. Significantly, knockdown of DDX5 in HBV infected HepaRG cells reduced the anti-viral effect of IFN-α. CONCLUSION RNA helicase DDX5 resolves a G-quadruplex structure in 5'UTR of STAT1 mRNA, enabling STAT1 translation. We propose that DDX5 is a key regulator of the dynamic range of IFN response during innate immunity and adjuvant IFN-α therapy.
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Affiliation(s)
- Jiazeng Sun
- Basic Medical Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Guanhui Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Florentin Pastor
- International Center for Infectiology Research (CIRI), INSERM U1111-CNRS UMR5308, Lyon, France
| | - Naimur Rahman
- Basic Medical Sciences, Purdue University System, West Lafayette, Indiana, USA
| | - Wen-Hung Wang
- Gene Editing Core, Bindley Biosciences Center, Purdue University, West Lafayette, Indiana, USA
| | - Zhengtao Zhang
- Department of Biochemistry and Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Philippe Merle
- Service d'Hépatologie, Hôpital de La Croix-Rousse Centre Livet, Lyon, Rhône-Alpes, France
| | - Lijian Hui
- Department of Biochemistry and Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Anna Salvetti
- International Center for Infectiology Research (CIRI), INSERM U1111-CNRS UMR5308, Lyon, France
| | - David Durantel
- INSERM U1111-CNRS UMR5308 International Center for Infectiology Research (CIRI), Lyon, France
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Ourania Andrisani
- Basic Medical Sciences, Purdue University, West Lafayette, Indiana, USA
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22
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Ghafouri-Fard S, Abak A, Baniahmad A, Hussen BM, Taheri M, Jamali E, Dinger ME. Interaction between non-coding RNAs, mRNAs and G-quadruplexes. Cancer Cell Int 2022; 22:171. [PMID: 35488342 PMCID: PMC9052686 DOI: 10.1186/s12935-022-02601-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022] Open
Abstract
G-quadruplexes are secondary helical configurations established between guanine-rich nucleic acids. The structure is seen in the promoter regions of numerous genes under certain situations. Predicted G-quadruplex-forming sequences are distributed across the genome in a non-random way. These structures are formed in telomeric regions of the human genome and oncogenic promoter G-rich regions. Identification of mechanisms of regulation of stability of G-quadruplexes has practical significance for understanding the molecular basis of genetic diseases such as cancer. A number of non-coding RNAs such as H19, XIST, FLJ39051 (GSEC), BC200 (BCYRN1), TERRA, pre-miRNA-1229, pre-miRNA-149 and miR-1587 have been found to contain G-quadraplex-forming regions or affect configuration of these structures in target genes. In the current review, we outline the recent research on the interaction between G-quadruplexes and non-coding RNAs, other RNA transcripts and DNA molecules.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atefe Abak
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, 07740, Jena, Germany
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, 07740, Jena, Germany.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakin Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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23
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Feng Y, Tao S, Zhang P, Sperti FR, Liu G, Cheng X, Zhang T, Yu H, Wang XE, Chen C, Monchaud D, Zhang W. Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription. PLANT PHYSIOLOGY 2022; 188:1632-1648. [PMID: 34893906 PMCID: PMC8896617 DOI: 10.1093/plphys/kiab566] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/04/2021] [Indexed: 06/01/2023]
Abstract
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
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Affiliation(s)
- Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Pengyue Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Francesco Rota Sperti
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Guanqing Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
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24
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Castelli LM, Benson BC, Huang WP, Lin YH, Hautbergue GM. RNA Helicases in Microsatellite Repeat Expansion Disorders and Neurodegeneration. Front Genet 2022; 13:886563. [PMID: 35646086 PMCID: PMC9133428 DOI: 10.3389/fgene.2022.886563] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Short repeated sequences of 3-6 nucleotides are causing a growing number of over 50 microsatellite expansion disorders, which mainly present with neurodegenerative features. Although considered rare diseases in relation to the relatively low number of cases, these primarily adult-onset conditions, often debilitating and fatal in absence of a cure, collectively pose a large burden on healthcare systems in an ageing world population. The pathological mechanisms driving disease onset are complex implicating several non-exclusive mechanisms of neuronal injury linked to RNA and protein toxic gain- and loss- of functions. Adding to the complexity of pathogenesis, microsatellite repeat expansions are polymorphic and found in coding as well as in non-coding regions of genes. They form secondary and tertiary structures involving G-quadruplexes and atypical helices in repeated GC-rich sequences. Unwinding of these structures by RNA helicases plays multiple roles in the expression of genes including repeat-associated non-AUG (RAN) translation of polymeric-repeat proteins with aggregating and cytotoxic properties. Here, we will briefly review the pathogenic mechanisms mediated by microsatellite repeat expansions prior to focus on the RNA helicases eIF4A, DDX3X and DHX36 which act as modifiers of RAN translation in C9ORF72-linked amyotrophic lateral sclerosis/frontotemporal dementia (C9ORF72-ALS/FTD) and Fragile X-associated tremor/ataxia syndrome (FXTAS). We will further review the RNA helicases DDX5/17, DHX9, Dicer and UPF1 which play additional roles in the dysregulation of RNA metabolism in repeat expansion disorders. In addition, we will contrast these with the roles of other RNA helicases such as DDX19/20, senataxin and others which have been associated with neurodegeneration independently of microsatellite repeat expansions. Finally, we will discuss the challenges and potential opportunities that are associated with the targeting of RNA helicases for the development of future therapeutic approaches.
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Affiliation(s)
- Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Bridget C Benson
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Wan-Ping Huang
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.,Healthy Lifespan Institute (HELSI), University of Sheffield, Sheffield, United Kingdom
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25
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Antcliff A, McCullough LD, Tsvetkov AS. G-Quadruplexes and the DNA/RNA helicase DHX36 in health, disease, and aging. Aging (Albany NY) 2021; 13:25578-25587. [PMID: 34862880 PMCID: PMC8714159 DOI: 10.18632/aging.203738] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/19/2021] [Indexed: 12/20/2022]
Abstract
G-Quadruplex (G4) DNA (G4 DNA) and RNA (G4 RNA) are secondary nucleic acid structures that have multiple roles in vital cellular processes. G4 DNA- and RNA-binding proteins and unwinding helicases associate with and regulate G4s during virtually all processes that involve DNA and RNA. DEAH-Box helicase 36 (DHX36), a member of the large DExD/H box helicase family, enzymatically unwinds both G4 DNA and G4 RNA. By exerting its G4 helicase function, DHX36 regulates transcription, genomic stability, telomere maintenance, translation and RNA metabolism. This review will provide an overview of G4s and DHX36, including DHX36's potential role in neuronal development and neurodegeneration. We conclude with a discussion of the possible functions of G4s and DHX36 in the aging brain.
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Affiliation(s)
- Aaron Antcliff
- Department of Neurology, The University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Louise D. McCullough
- Department of Neurology, The University of Texas McGovern Medical School, Houston, TX 77030, USA
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Andrey S. Tsvetkov
- Department of Neurology, The University of Texas McGovern Medical School, Houston, TX 77030, USA
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX 77030, USA
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26
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Huang X, Zhao K, Jiang M, Qiu D, Zhou J, Yang Z. The G4 resolvase RHAU regulates ventricular trabeculation and compaction through transcriptional and post-transcriptional mechanisms. J Biol Chem 2021; 298:101449. [PMID: 34838591 PMCID: PMC8689214 DOI: 10.1016/j.jbc.2021.101449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/27/2022] Open
Abstract
The G-quadruplex (G4) resolvase RNA helicase associated with AU-rich element (RHAU) possesses the ability to unwind G4 structures in both DNA and RNA molecules. Previously, we revealed that RHAU plays a critical role in embryonic heart development and postnatal heart function through modulating mRNA translation and stability. However, whether RHAU functions to resolve DNA G4 in the regulation of cardiac physiology is still elusive. Here, we identified a phenotype of noncompaction cardiomyopathy in cardiomyocyte-specific Rhau deletion mice, including such symptoms as spongiform cardiomyopathy, heart dilation, and death at young ages. We also observed reduced cardiomyocyte proliferation and advanced sarcomere maturation in Rhau mutant mice. Further studies demonstrated that RHAU regulates the expression levels of several genes associated with ventricular trabeculation and compaction, including the Nkx2-5 and Hey2 that encode cardiac transcription factors of NKX2-5 and Hey2, and the myosin heavy chain 7 (Myh7) whose protein product is MYH7. While RHAU modulates Nkx2-5 mRNA and Hey2 mRNA at the post-transcriptional level, we uncovered that RHAU facilitates the transcription of Myh7 through unwinding of the G4 structures in its promoter. These findings demonstrated that RHAU regulates ventricular chamber development through both transcriptional and post-transcriptional mechanisms. These results contribute to a knowledge base that will help to understand the pathogenesis of diseases such as noncompaction cardiomyopathy.
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Affiliation(s)
- Xinyi Huang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing, China
| | - Ke Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing, China
| | - Mingyang Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing, China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, China
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing, China.
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27
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Varshney D, Cuesta SM, Herdy B, Abdullah UB, Tannahill D, Balasubramanian S. RNA G-quadruplex structures control ribosomal protein production. Sci Rep 2021; 11:22735. [PMID: 34815422 PMCID: PMC8611094 DOI: 10.1038/s41598-021-01847-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Four-stranded G-quadruplex (G4) structures form from guanine-rich tracts, but the extent of their formation in cellular RNA and details of their role in RNA biology remain poorly defined. Herein, we first delineate the presence of endogenous RNA G4s in the human cytoplasmic transcriptome via the binding sites of G4-interacting proteins, DDX3X (previously published), DHX36 and GRSF1. We demonstrate that a sub-population of these RNA G4s are reliably detected as folded structures in cross-linked cellular lysates using the G4 structure-specific antibody BG4. The 5' UTRs of protein coding mRNAs show significant enrichment in folded RNA G4s, particularly those for ribosomal proteins. Mutational disruption of G4s in ribosomal protein UTRs alleviates translation in vitro, whereas in cells, depletion of G4-resolving helicases or treatment with G4-stabilising small molecules inhibit the translation of ribosomal protein mRNAs. Our findings point to a common mode for translational co-regulation mediated by G4 structures. The results reveal a potential avenue for therapeutic intervention in diseases with dysregulated translation, such as cancer.
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Affiliation(s)
- Dhaval Varshney
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Sergio Martinez Cuesta
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, UK
| | - Barbara Herdy
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ummi Binti Abdullah
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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28
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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29
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Translational control by DHX36 binding to 5'UTR G-quadruplex is essential for muscle stem-cell regenerative functions. Nat Commun 2021; 12:5043. [PMID: 34413292 PMCID: PMC8377060 DOI: 10.1038/s41467-021-25170-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 06/06/2021] [Indexed: 12/30/2022] Open
Abstract
Skeletal muscle has a remarkable ability to regenerate owing to its resident stem cells (also called satellite cells, SCs). SCs are normally quiescent; when stimulated by damage, they activate and expand to form new fibers. The mechanisms underlying SC proliferative progression remain poorly understood. Here we show that DHX36, a helicase that unwinds RNA G-quadruplex (rG4) structures, is essential for muscle regeneration by regulating SC expansion. DHX36 (initially named RHAU) is barely expressed at quiescence but is highly induced during SC activation and proliferation. Inducible deletion of Dhx36 in adult SCs causes defective proliferation and muscle regeneration after damage. System-wide mapping in proliferating SCs reveals DHX36 binding predominantly to rG4 structures at various regions of mRNAs, while integrated polysome profiling shows that DHX36 promotes mRNA translation via 5′-untranslated region (UTR) rG4 binding. Furthermore, we demonstrate that DHX36 specifically regulates the translation of Gnai2 mRNA by unwinding its 5′ UTR rG4 structures and identify GNAI2 as a downstream effector of DHX36 for SC expansion. Altogether, our findings uncover DHX36 as an indispensable post-transcriptional regulator of SC function and muscle regeneration acting through binding and unwinding rG4 structures at 5′ UTR of target mRNAs. Skeletal muscle stem cells (or satellite cells, SCs) are normally quiescent but activate and expand in response to injury. Here the authors show that induction of DHX36 helicase during SC activation promotes mRNA translation by binding to 5′UTR mRNA G-quadruplexes (rG4) in targets including Gnai2 and unwinding them.
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Tseng YJ, Sandwith SN, Green KM, Chambers AE, Krans A, Raimer HM, Sharlow ME, Reisinger MA, Richardson AE, Routh ED, Smaldino MA, Wang YH, Vaughn JP, Todd PK, Smaldino PJ. The RNA helicase DHX36-G4R1 modulates C9orf72 GGGGCC hexanucleotide repeat-associated translation. J Biol Chem 2021; 297:100914. [PMID: 34174288 PMCID: PMC8326427 DOI: 10.1016/j.jbc.2021.100914] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/02/2021] [Accepted: 06/22/2021] [Indexed: 12/26/2022] Open
Abstract
GGGGCC (G4C2) hexanucleotide repeat expansions in the endosomal trafficking gene C9orf72 are the most common genetic cause of ALS and frontotemporal dementia. Repeat-associated non-AUG (RAN) translation of this expansion through near-cognate initiation codon usage and internal ribosomal entry generates toxic proteins that accumulate in patients' brains and contribute to disease pathogenesis. The helicase protein DEAH-box helicase 36 (DHX36–G4R1) plays active roles in RNA and DNA G-quadruplex (G4) resolution in cells. As G4C2 repeats are known to form G4 structures in vitro, we sought to determine the impact of manipulating DHX36 expression on repeat transcription and RAN translation. Using a series of luciferase reporter assays both in cells and in vitro, we found that DHX36 depletion suppresses RAN translation in a repeat length–dependent manner, whereas overexpression of DHX36 enhances RAN translation from G4C2 reporter RNAs. Moreover, upregulation of RAN translation that is typically triggered by integrated stress response activation is prevented by loss of DHX36. These results suggest that DHX36 is active in regulating G4C2 repeat translation, providing potential implications for therapeutic development in nucleotide repeat expansion disorders.
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Affiliation(s)
- Yi-Ju Tseng
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA; Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Siara N Sandwith
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | - Katelyn M Green
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Heather M Raimer
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | | | | | | | - Eric D Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - James P Vaughn
- Division of Cancer Biology, NanoMedica LLC, Winston-Salem, North Carolina, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA; Department of Neurology, Ann Arbor VA Medical Center, Ann Arbor, Michigan, USA.
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Doll CF, Pereira NJ, Hashimi MS, Grindrod TJ, Alkassis FF, Cai LX, Milovanovic U, Sandino AI, Kasahara H. Gestational intermittent hyperoxia rescues murine genetic congenital heart disease in part. Sci Rep 2021; 11:6608. [PMID: 33758249 PMCID: PMC7988122 DOI: 10.1038/s41598-021-85569-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 02/22/2021] [Indexed: 11/09/2022] Open
Abstract
Cardiac development is a dynamic process, temporally and spatially. When disturbed, it leads to congenital cardiac anomalies that affect approximately 1% of live births. Genetic variants in several loci lead to anomalies, with the transcription factor NKX2-5 being one of the largest. However, there are also non-genetic factors that influence cardiac malformations. We examined the hypothesis that hyperoxia may be beneficial and can rescue genetic cardiac anomalies induced by an Nkx2-5 mutation. Intermittent mild hyperoxia (40% PO2) was applied for 10 h per day to normal wild-type female mice mated with heterozygous Nkx2-5 mutant males from gestational day 8.5 to birth. Hyperoxia therapy reduced excessive trabeculation in Nkx2-5 mutant mice compared to normoxic conditions (ratio of trabecular layer relative to compact layer area, normoxia 1.84 ± 0.07 vs. hyperoxia 1.51 ± 0.04) and frequency of muscular ventricular septal defects per heart (1.53 ± 0.32 vs. 0.68 ± 0.15); however, the incidence of membranous ventricular septal defects in Nkx2-5 mutant hearts was not changed. Nkx2-5 mutant embryonic hearts showed defective coronary vessel organization, which was improved by intermittent mild hyperoxia. The results of our study showed that mild gestational hyperoxia therapy rescued genetic cardiac malformation induced by Nkx2-5 mutation in part.
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Affiliation(s)
- Cassandra F Doll
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1600 SW Archer Rd. M543, Gainesville, FL, 32610-0274, USA
| | - Natalia J Pereira
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1600 SW Archer Rd. M543, Gainesville, FL, 32610-0274, USA
| | - Mustafa S Hashimi
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1600 SW Archer Rd. M543, Gainesville, FL, 32610-0274, USA
| | - Tabor J Grindrod
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1600 SW Archer Rd. M543, Gainesville, FL, 32610-0274, USA
| | - Fariz F Alkassis
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1600 SW Archer Rd. M543, Gainesville, FL, 32610-0274, USA
| | - Lawrence X Cai
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1600 SW Archer Rd. M543, Gainesville, FL, 32610-0274, USA
| | - Una Milovanovic
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1600 SW Archer Rd. M543, Gainesville, FL, 32610-0274, USA
| | - Adriana I Sandino
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1600 SW Archer Rd. M543, Gainesville, FL, 32610-0274, USA
| | - Hideko Kasahara
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1600 SW Archer Rd. M543, Gainesville, FL, 32610-0274, USA. .,International University of Health and Welfare, School of Medicine, 852 Hatakeda, Narita, Chiba, Japan.
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Jiang M, Hu H, Zhao K, Di R, Huang X, Shi Y, Yue Y, Nie J, Yu S, Wang W, Yang Z. The G4 resolvase RHAU modulates mRNA translation and stability to sustain postnatal heart function and regeneration. J Biol Chem 2021; 296:100080. [PMID: 33199370 PMCID: PMC7948451 DOI: 10.1074/jbc.ra120.014948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/07/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022] Open
Abstract
Post-transcriptional regulation of mRNA translation and stability is primarily achieved by RNA-binding proteins, which are of increasing importance for heart function. Furthermore, G-quadruplex (G4) and G4 resolvase activity are involved in a variety of biological processes. However, the role of G4 resolvase activity in heart function remains unknown. The present study aims to investigate the role of RNA helicase associated with adenylate- and uridylate-rich element (RHAU), an RNA-binding protein with G4 resolvase activity in postnatal heart function through deletion of Rhau in the cardiomyocytes of postnatal mice. RHAU-deficient mice displayed progressive pathological remodeling leading to heart failure and mortality and impaired neonatal heart regeneration. RHAU ablation reduced the protein levels but enhanced mRNA levels of Yap1 and Hexim1 that are important regulators for heart development and postnatal heart function. Furthermore, RHAU was found to associate with both the 5' and 3' UTRs of these genes to destabilize mRNA and enhance translation. Thus, we have demonstrated the important functions of RHAU in the dual regulation of mRNA translation and stability, which is vital for heart physiology.
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Affiliation(s)
- Mingyang Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Han Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ke Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Ruomin Di
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Xinyi Huang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Yingchao Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Yunyun Yue
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Junwei Nie
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Shan Yu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Wengong Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China.
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Dumas L, Herviou P, Dassi E, Cammas A, Millevoi S. G-Quadruplexes in RNA Biology: Recent Advances and Future Directions. Trends Biochem Sci 2020; 46:270-283. [PMID: 33303320 DOI: 10.1016/j.tibs.2020.11.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
RNA G-quadruplexes (RG4s) are four-stranded structures known to control gene expression mechanisms, from transcription to protein synthesis, and DNA-related processes. Their potential impact on RNA biology allows these structures to shape cellular processes relevant to disease development, making their targeting for therapeutic purposes an attractive option. We review here the current knowledge on RG4s, focusing on the latest breakthroughs supporting the notion of transient structures that fluctuate dynamically in cellulo, their interplay with RNA modifications, their role in cell compartmentalization, and their deregulation impacting the host immune response. We emphasize RG4-binding proteins as determinants of their transient conformation and effectors of their biological functions.
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Affiliation(s)
- Leïla Dumas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III - Paul Sabatier, 31330 Toulouse, France
| | - Pauline Herviou
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III - Paul Sabatier, 31330 Toulouse, France
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, (TN), Italy
| | - Anne Cammas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III - Paul Sabatier, 31330 Toulouse, France
| | - Stefania Millevoi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III - Paul Sabatier, 31330 Toulouse, France.
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Belviso I, Angelini F, Di Meglio F, Picchio V, Sacco AM, Nocella C, Romano V, Nurzynska D, Frati G, Maiello C, Messina E, Montagnani S, Pagano F, Castaldo C, Chimenti I. The Microenvironment of Decellularized Extracellular Matrix from Heart Failure Myocardium Alters the Balance between Angiogenic and Fibrotic Signals from Stromal Primitive Cells. Int J Mol Sci 2020; 21:7903. [PMID: 33114386 PMCID: PMC7662394 DOI: 10.3390/ijms21217903] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 01/20/2023] Open
Abstract
Cardiac adverse remodeling is characterized by biological changes that affect the composition and architecture of the extracellular matrix (ECM). The consequently disrupted signaling can interfere with the balance between cardiogenic and pro-fibrotic phenotype of resident cardiac stromal primitive cells (CPCs). The latter are important players in cardiac homeostasis and can be exploited as therapeutic cells in regenerative medicine. Our aim was to compare the effects of human decellularized native ECM from normal (dECM-NH) or failing hearts (dECM-PH) on human CPCs. CPCs were cultured on dECM sections and characterized for gene expression, immunofluorescence, and paracrine profiles. When cultured on dECM-NH, CPCs significantly upregulated cardiac commitment markers (CX43, NKX2.5), cardioprotective cytokines (bFGF, HGF), and the angiogenesis mediator, NO. When seeded on dECM-PH, instead, CPCs upregulated pro-remodeling cytokines (IGF-2, PDGF-AA, TGF-β) and the oxidative stress molecule H2O2. Interestingly, culture on dECM-PH was associated with impaired paracrine support to angiogenesis, and increased expression of the vascular endothelial growth factor (VEGF)-sequestering decoy isoform of the KDR/VEGFR2 receptor. Our results suggest that resident CPCs exposed to the pathological microenvironment of remodeling ECM partially lose their paracrine angiogenic properties and release more pro-fibrotic cytokines. These observations shed novel insights on the crosstalk between ECM and stromal CPCs, suggesting also a cautious use of non-healthy decellularized myocardium for cardiac tissue engineering approaches.
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Affiliation(s)
- Immacolata Belviso
- Department of Public Health, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (I.B.); (F.D.M.); (A.M.S.); (V.R.); (D.N.); (S.M.); (C.C.)
| | - Francesco Angelini
- Experimental and Clinical Pharmacology Unit, CRO-National Cancer Institute, 33081 Aviano (PN), Italy;
| | - Franca Di Meglio
- Department of Public Health, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (I.B.); (F.D.M.); (A.M.S.); (V.R.); (D.N.); (S.M.); (C.C.)
| | - Vittorio Picchio
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University, Corso della Repubblica 79, 04100 Latina, Italy; (V.P.); (G.F.)
| | - Anna Maria Sacco
- Department of Public Health, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (I.B.); (F.D.M.); (A.M.S.); (V.R.); (D.N.); (S.M.); (C.C.)
| | - Cristina Nocella
- Department of Clinical, Internal Medicine, Anesthesiology and Cardiovascular Sciences, Sapienza University, 00161 Rome, Italy;
| | - Veronica Romano
- Department of Public Health, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (I.B.); (F.D.M.); (A.M.S.); (V.R.); (D.N.); (S.M.); (C.C.)
| | - Daria Nurzynska
- Department of Public Health, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (I.B.); (F.D.M.); (A.M.S.); (V.R.); (D.N.); (S.M.); (C.C.)
| | - Giacomo Frati
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University, Corso della Repubblica 79, 04100 Latina, Italy; (V.P.); (G.F.)
- Department of AngioCardioNeurology, IRCCS Neuromed, 86077 Pozzilli, Italy
| | - Ciro Maiello
- Department of Cardiovascular Surgery and Transplant, Monaldi Hospital, 80131 Naples, Italy;
| | - Elisa Messina
- Department of Maternal Infantile and Urological Sciences, “Umberto I” Hospital, 00161 Rome, Italy;
| | - Stefania Montagnani
- Department of Public Health, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (I.B.); (F.D.M.); (A.M.S.); (V.R.); (D.N.); (S.M.); (C.C.)
| | - Francesca Pagano
- Institute of Biochemistry and Cell Biology, National Council of Research (IBBC-CNR), 00015 Monterotondo (RM), Italy;
| | - Clotilde Castaldo
- Department of Public Health, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (I.B.); (F.D.M.); (A.M.S.); (V.R.); (D.N.); (S.M.); (C.C.)
| | - Isotta Chimenti
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University, Corso della Repubblica 79, 04100 Latina, Italy; (V.P.); (G.F.)
- Mediterranea Cardiocentro, 80122 Napoli, Italy
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35
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Ricciardi L, Giurato G, Memoli D, Pietrafesa M, Dal Col J, Salvato I, Nigro A, Vatrella A, Caramori G, Casolaro V, Stellato C. Posttranscriptional Gene Regulatory Networks in Chronic Airway Inflammatory Diseases: In silico Mapping of RNA-Binding Protein Expression in Airway Epithelium. Front Immunol 2020; 11:579889. [PMID: 33178205 PMCID: PMC7596416 DOI: 10.3389/fimmu.2020.579889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Posttranscriptional gene regulation (PTGR) contributes to inflammation through alterations in messenger RNA (mRNA) turnover and translation rates. RNA-binding proteins (RBPs) coordinate these processes but their role in lung inflammatory diseases is ill-defined. We evaluated the expression of a curated list of mRNA-binding RBPs (mRBPs) in selected Gene Expression Omnibus (GEO) transcriptomic databases of airway epithelium isolated from chronic obstructive pulmonary disease (COPD), severe asthma (SA) and matched control subjects, hypothesizing that global changes in mRBPs expression could be used to infer their pathogenetic roles and identify novel disease-related regulatory networks. Methods: A published list of 692 mRBPs [Nat Rev Genet 2014] was searched in GEO datasets originated from bronchial brushings of stable COPD patients (C), smokers (S), non-smokers (NS) controls with normal lung function (n = 6/12/12) (GEO ID: GSE5058) and of (SA) and healthy control (HC) (n = 6/12) (GSE63142). Fluorescence intensity data were extracted and normalized on the medians for fold change (FC) comparisons. FCs were set at ≥ |1.5| with a false discovery rate (FDR) of ≤ 0.05. Pearson correlation maps and heatmaps were generated using tMEV tools v4_9_0.45. DNA sequence motifs were searched using PScan-ChIP. Gene Ontology (GO) was performed with Ingenuity Pathway Analysis (IPA) tool. Results: Significant mRBP expression changes were detected for S/NS, COPD/NS and COPD/S (n = 41, 391, 382, respectively). Of those, 32% of genes changed by FC ≥ |1.5| in S/NS but more than 60% in COPD/NS and COPD/S (n = 13, 267, 257, respectively). Genes were predominantly downregulated in COPD/NS (n = 194, 73%) and COPD/S (n = 202, 79%), less so in S/NS (n = 4, 31%). Unsupervised cluster analysis identified in 4 out of 12 S the same mRBP pattern seen in C, postulating subclinical COPD. Significant DNA motifs enrichment for transcriptional regulation was found for downregulated RBPs. Correlation analysis identified five clusters of co-expressed mRBPs. GO analysis revealed significant enrichments in canonical pathways both specific and shared among comparisons. Unexpectedly, no significant mRBPs modulation was found in SA compared to controls. Conclusions: Airway epithelial mRBPs profiling reveals a COPD-specific global downregulation of RBPs shared by a subset of control smokers, the potential of functional cooperation by coexpressed RBPs and significant impact on relevant pathogenetic pathways in COPD. Elucidation of PTGR in COPD could identify disease biomarkers or pathways for therapeutic targeting.
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Affiliation(s)
- Luca Ricciardi
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Mariagrazia Pietrafesa
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Ilaria Salvato
- Pulmonology, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Gaetano Caramori
- Pulmonology, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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36
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Schult P, Paeschke K. The DEAH helicase DHX36 and its role in G-quadruplex-dependent processes. Biol Chem 2020; 402:581-591. [PMID: 33021960 DOI: 10.1515/hsz-2020-0292] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023]
Abstract
DHX36 is a member of the DExD/H box helicase family, which comprises a large number of proteins involved in various cellular functions. Recently, the function of DHX36 in the regulation of G-quadruplexes (G4s) was demonstrated. G4s are alternative nucleic acid structures, which influence many cellular pathways on a transcriptional and post-transcriptional level. In this review we provide an overview of the current knowledge about DHX36 structure, substrate specificity, and mechanism of action based on the available models and crystal structures. Moreover, we outline its multiple functions in cellular homeostasis, immunity, and disease. Finally, we discuss the open questions and provide potential directions for future research.
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Affiliation(s)
- Philipp Schult
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
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37
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Richardson A, Zentz ZA, Chambers AE, Sandwith SN, Reisinger MA, Saunders DW, Tompkins JD, Riggs AD, Routh ED, Rubenstein EM, Smaldino MA, Vaughn JP, Haney RA, Smaldino PJ. G-Quadruplex Helicase DHX36/G4R1 Engages Nuclear Lamina Proteins in Quiescent Breast Cancer Cells. ACS OMEGA 2020; 5:24916-24926. [PMID: 33015511 PMCID: PMC7528498 DOI: 10.1021/acsomega.0c03723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
G-quadruplexes (G4s) are nucleic acid structures found enriched within gene regulatory sequences. G4s control fundamental cellular processes, including replication, transcription, and translation. Proto-oncogenes are enriched with G4 sequences, while tumor-suppressor genes are depleted, suggesting roles for G4s in cell survival and proliferation. Specialized helicases participate in G4-mediated gene regulation via enzymatic unwinding activity. One such enzyme, DHX36/G4R1, is the major G4-helicase and is a master regulator of G4-DNAs and mRNAs. G4-resolution promotes the expression of proproliferative genes; as such, DHX36/G4R1 promotes cell proliferation. Little is known about how DHX36/G4R1 itself is regulated in nondividing cells. We hypothesized that DHX36/G4R1 protein binding partners are altered when a cell transitions from a dividing to a quiescent state. We found that DHX36/G4R1 co-purifies with a distinct set of proteins under quiescent conditions, which may represent a novel complex that regulates DHX36/G4R1 during cell cycle transitions and have implications for development and cancer.
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Affiliation(s)
- Adam.
E. Richardson
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Zachary. A. Zentz
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Antonio E. Chambers
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Siara N. Sandwith
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Michael A. Reisinger
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Destinee W. Saunders
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Joshua D. Tompkins
- Department
of Diabetes Complications and Metabolism, City of Hope, Duarte, California 91010, United States
| | - Arthur D. Riggs
- Department
of Diabetes Complications and Metabolism, City of Hope, Duarte, California 91010, United States
| | - Eric D. Routh
- Lineberger
Comprehensive Cancer Center, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eric M. Rubenstein
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Melissa A. Smaldino
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - James P. Vaughn
- NanoMedica
LLC, Winston-Salem, North Carolina 27101, United States
| | - Robert A. Haney
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Philip J. Smaldino
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
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38
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Zuccotti P, Peroni D, Potrich V, Quattrone A, Dassi E. Hyperconserved Elements in Human 5'UTRs Shape Essential Post-transcriptional Regulatory Networks. Front Mol Biosci 2020; 7:220. [PMID: 33005630 PMCID: PMC7484617 DOI: 10.3389/fmolb.2020.00220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 08/05/2020] [Indexed: 01/03/2023] Open
Abstract
Post-transcriptional regulation (PTR) of gene expression is a powerful determinant of cellular phenotypes. The 5′ and 3′ untranslated regions of the mRNA (UTRs) mediate this role through sequence and secondary structure elements bound by RNA-binding proteins (RBPs) and non-coding RNAs. While functional regions in the 3′UTRs have been extensively studied, the 5′UTRs are still relatively uncharacterized. To fill this gap, we used a computational approach exploiting phylogenetic conservation to identify hyperconserved elements in human 5′UTRs (5′HCEs). Our assumption was that 5′HCEs would represent evolutionarily stable and hence important PTR sites. We identified over 5000 5′HCEs occurring in 10% of human protein-coding genes. These sequence elements are rather short and mostly found in narrowly-spaced clusters. 5′HCEs-containing genes are enriched in essential cellular functions and include 20% of all homeotic genes. Homeotic genes are essential transcriptional regulators, driving body plan and neuromuscular development. However, the role of PTR in their expression is mostly unknown. By integrating computational and experimental approaches we identified RBMX as the initiator RBP of a post-transcriptional cascade regulating many homeotic genes. This work thus establishes 5′HCEs as mediators of essential post-transcriptional regulatory networks.
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Affiliation(s)
- Paola Zuccotti
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Daniele Peroni
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Valentina Potrich
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
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39
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General and Target-Specific DExD/H RNA Helicases in Eukaryotic Translation Initiation. Int J Mol Sci 2020; 21:ijms21124402. [PMID: 32575790 PMCID: PMC7352612 DOI: 10.3390/ijms21124402] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
DExD (DDX)- and DExH (DHX)-box RNA helicases, named after their Asp-Glu-x-Asp/His motifs, are integral to almost all RNA metabolic processes in eukaryotic cells. They play myriad roles in processes ranging from transcription and mRNA-protein complex remodeling, to RNA decay and translation. This last facet, translation, is an intricate process that involves DDX/DHX helicases and presents a regulatory node that is highly targetable. Studies aimed at better understanding this family of conserved proteins have revealed insights into their structures, catalytic mechanisms, and biological roles. They have also led to the development of chemical modulators that seek to exploit their essential roles in diseases. Herein, we review the most recent insights on several general and target-specific DDX/DHX helicases in eukaryotic translation initiation.
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40
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Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles. G3-GENES GENOMES GENETICS 2020; 10:2021-2032. [PMID: 32295768 PMCID: PMC7263691 DOI: 10.1534/g3.120.401288] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world's most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and sorghum). We identified close to 1 million G4 motifs with a density of 76 G4s/Mb across the whole genome and 93 G4s/Mb over genic regions. Remarkably, G4s were enriched around three regions, two located on the antisense and one on the sense strand at the following positions: 1) the transcription start site (TSS) (antisense), 2) the first coding domain sequence (CDS) (antisense), and 3) the start codon (sense). Functional enrichment analysis revealed that the gene models containing G4 motifs within these peaks were associated with specific gene ontology (GO) terms, such as developmental process, localization, and cellular component organization or biogenesis. We investigated genes encoding MADS-box transcription factors and showed examples of G4 motifs within critical regulatory regions in the VRN-1 genes in wheat. Furthermore, comparison with other plants showed that monocots share a similar distribution of G4s, but Arabidopsis shows a unique G4 distribution. Our study shows for the first time the prevalence and possible functional roles of G4s in wheat.
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41
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Martone J, Mariani D, Santini T, Setti A, Shamloo S, Colantoni A, Capparelli F, Paiardini A, Dimartino D, Morlando M, Bozzoni I. SMaRT lncRNA controls translation of a G-quadruplex-containing mRNA antagonizing the DHX36 helicase. EMBO Rep 2020; 21:e49942. [PMID: 32337838 PMCID: PMC7271651 DOI: 10.15252/embr.201949942] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/11/2022] Open
Abstract
Guanine‐quadruplexes (G4) included in RNA molecules exert several functions in controlling gene expression at post‐transcriptional level; however, the molecular mechanisms of G4‐mediated regulation are still poorly understood. Here, we describe a regulatory circuitry operating in the early phases of murine muscle differentiation in which a long non‐coding RNA (SMaRT) base pairs with a G4‐containing mRNA (Mlx‐γ) and represses its translation by counteracting the activity of the DHX36 RNA helicase. The time‐restricted, specific effect of lnc‐SMaRT on the translation of Mlx‐γ isoform modulates the general subcellular localization of total MLX proteins, impacting on their transcriptional output and promoting proper myogenesis and mature myotube formation. Therefore, the circuitry made of lnc‐SMaRT, Mlx‐γ, and DHX36 not only plays an important role in the control of myogenesis but also unravels a molecular mechanism where G4 structures and G4 unwinding activities are regulated in living cells.
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Affiliation(s)
- Julie Martone
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Davide Mariani
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Sama Shamloo
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Francesca Capparelli
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | | | - Dacia Dimartino
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy.,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
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42
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Srinivasan S, Liu Z, Chuenchor W, Xiao TS, Jankowsky E. Function of Auxiliary Domains of the DEAH/RHA Helicase DHX36 in RNA Remodeling. J Mol Biol 2020; 432:2217-2231. [PMID: 32087197 DOI: 10.1016/j.jmb.2020.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 01/06/2023]
Abstract
The DEAH/RHA helicase DHX36 has been linked to cellular RNA and DNA quadruplex structures and to AU-rich RNA elements. In vitro, DHX36 remodels DNA and RNA quadruplex structures and unwinds DNA duplexes in an ATP-dependent manner. DHX36 contains the superfamily 2 helicase core and several auxiliary domains that are conserved in orthologs of the enzyme. The role of these auxiliary domains for the enzymatic function of DHX36 is not well understood. Here, we combine structural and biochemical studies to define the function of three auxiliary domains that contact nucleic acid. We first report the crystal structure of mouse DHX36 bound to ADP. The structure reveals an overall architecture of mouse DHX36 that is similar to previously reported architectures of fly and bovine DHX36. In addition, our structure shows conformational changes that accompany stages of the ATP-binding and hydrolysis cycle. We then examine the roles of the DHX36-specific motif (DSM), the OB-fold, and a conserved β-hairpin (β-HP) in mouse DHX36 in the remodeling of RNA structures. We demonstrate and characterize RNA duplex unwinding for DHX36 and examine the remodeling of inter- and intramolecular RNA quadruplex structures. We find that the DSM not only functions as a quadruplex binding adaptor but also promotes the remodeling of RNA duplex and quadruplex structures. The OB-fold and the β-HP contribute to RNA binding. Both domains are also essential for remodeling RNA quadruplex and duplex structures. Our data reveal roles of auxiliary domains for multiple steps of the nucleic acid remodeling reactions.
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Affiliation(s)
| | - Zhonghua Liu
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Tsan Sam Xiao
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, USA; Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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43
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Heddi B, Cheong VV, Schmitt E, Mechulam Y, Phan AT. Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3′-end tetrad of a DNA G-quadruplex. J Struct Biol 2020; 209:107399. [DOI: 10.1016/j.jsb.2019.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022]
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44
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Sauer M, Juranek SA, Marks J, De Magis A, Kazemier HG, Hilbig D, Benhalevy D, Wang X, Hafner M, Paeschke K. DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions. Nat Commun 2019; 10:2421. [PMID: 31160600 PMCID: PMC6547686 DOI: 10.1038/s41467-019-10432-5] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/07/2019] [Indexed: 11/08/2022] Open
Abstract
Translation efficiency can be affected by mRNA stability and secondary structures, including G-quadruplex structures (G4s). The highly conserved DEAH-box helicase DHX36/RHAU resolves G4s on DNA and RNA in vitro, however a systems-wide analysis of DHX36 targets and function is lacking. We map globally DHX36 binding to RNA in human cell lines and find it preferentially interacting with G-rich and G4-forming sequences on more than 4500 mRNAs. While DHX36 knockout (KO) results in a significant increase in target mRNA abundance, ribosome occupancy and protein output from these targets decrease, suggesting that they were rendered translationally incompetent. Considering that DHX36 targets, harboring G4s, preferentially localize in stress granules, and that DHX36 KO results in increased SG formation and protein kinase R (PKR/EIF2AK2) phosphorylation, we speculate that DHX36 is involved in resolution of rG4 induced cellular stress.
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Affiliation(s)
- Markus Sauer
- Department of Biochemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - James Marks
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Alessio De Magis
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Hinke G Kazemier
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Daniel Hilbig
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Daniel Benhalevy
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Xiantao Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Katrin Paeschke
- Department of Biochemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands.
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany.
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45
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Tippana R, Chen MC, Demeshkina NA, Ferré-D'Amaré AR, Myong S. RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36. Nat Commun 2019; 10:1855. [PMID: 31015431 PMCID: PMC6478676 DOI: 10.1038/s41467-019-09802-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
DHX36 is a DEAH-box helicase that resolves parallel G-quadruplex structures formed in DNA and RNA. The recent co-crystal structure of DHX36 bound G4-DNA revealed an intimate contact, but did not address the role of ATP hydrolysis in G4 resolving activity. Here, we demonstrate that unlike on G4-DNA, DHX36 displays ATP-independent unfolding of G4-RNA followed by ATP-dependent refolding, generating a highly asymmetric pattern of activity. Interestingly, DHX36 refolds G4-RNA in several steps, reflecting the discrete steps in forming the G4 structure. We show that the ATP-dependent activity of DHX36 arises from the RNA tail rather than the G4. Mutations that perturb G4 contact result in quick dissociation of the protein from RNA upon ATP hydrolysis, while mutations that interfere with binding the RNA tail induce dysregulated activity. We propose that the ATP-dependent activity of DHX36 may be useful for dynamically resolving various G4-RNA structures in cells.
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Affiliation(s)
- Ramreddy Tippana
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Michael C Chen
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1TN, UK.,Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Natalia A Demeshkina
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL, 61801, USA.
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46
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Lerner LK, Sale JE. Replication of G Quadruplex DNA. Genes (Basel) 2019; 10:genes10020095. [PMID: 30700033 PMCID: PMC6409989 DOI: 10.3390/genes10020095] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/03/2023] Open
Abstract
A cursory look at any textbook image of DNA replication might suggest that the complex machine that is the replisome runs smoothly along the chromosomal DNA. However, many DNA sequences can adopt non-B form secondary structures and these have the potential to impede progression of the replisome. A picture is emerging in which the maintenance of processive DNA replication requires the action of a significant number of additional proteins beyond the core replisome to resolve secondary structures in the DNA template. By ensuring that DNA synthesis remains closely coupled to DNA unwinding by the replicative helicase, these factors prevent impediments to the replisome from causing genetic and epigenetic instability. This review considers the circumstances in which DNA forms secondary structures, the potential responses of the eukaryotic replisome to these impediments in the light of recent advances in our understanding of its structure and operation and the mechanisms cells deploy to remove secondary structure from the DNA. To illustrate the principles involved, we focus on one of the best understood DNA secondary structures, G quadruplexes (G4s), and on the helicases that promote their resolution.
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Affiliation(s)
- Leticia Koch Lerner
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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Developing Novel G-Quadruplex Ligands: from Interaction with Nucleic Acids to Interfering with Nucleic Acid⁻Protein Interaction. Molecules 2019; 24:molecules24030396. [PMID: 30678288 PMCID: PMC6384609 DOI: 10.3390/molecules24030396] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/10/2019] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
G-quadruplex is a special secondary structure of nucleic acids in guanine-rich sequences of genome. G-quadruplexes have been proved to be involved in the regulation of replication, DNA damage repair, and transcription and translation of oncogenes or other cancer-related genes. Therefore, targeting G-quadruplexes has become a novel promising anti-tumor strategy. Different kinds of small molecules targeting the G-quadruplexes have been designed, synthesized, and identified as potential anti-tumor agents, including molecules directly bind to the G-quadruplex and molecules interfering with the binding between the G-quadruplex structures and related binding proteins. This review will explore the feasibility of G-quadruplex ligands acting as anti-tumor drugs, from basis to application. Meanwhile, since helicase is the most well-defined G-quadruplex-related protein, the most extensive research on the relationship between helicase and G-quadruplexes, and its meaning in drug design, is emphasized.
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Vester K, Eravci M, Serikawa T, Schütze T, Weise C, Kurreck J. RNAi-mediated knockdown of the Rhau helicase preferentially depletes proteins with a Guanine-quadruplex motif in the 5'-UTR of their mRNA. Biochem Biophys Res Commun 2019; 508:756-761. [DOI: 10.1016/j.bbrc.2018.11.186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022]
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Tian T, Chen YQ, Wang SR, Zhou X. G-Quadruplex: A Regulator of Gene Expression and Its Chemical Targeting. Chem 2018. [DOI: 10.1016/j.chempr.2018.02.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Chen MC, Tippana R, Demeshkina NA, Murat P, Balasubramanian S, Myong S, Ferré-D'Amaré AR. Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36. Nature 2018; 558:465-469. [PMID: 29899445 PMCID: PMC6261253 DOI: 10.1038/s41586-018-0209-9] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 04/23/2018] [Indexed: 12/13/2022]
Abstract
Guanine-rich nucleic acid sequences challenge the replication, transcription, and translation machinery by spontaneously folding into G-quadruplexes, the unfolding of which requires forces greater than most polymerases can exert1,2. Eukaryotic cells contain numerous helicases that can unfold G-quadruplexes 3 . The molecular basis of the recognition and unfolding of G-quadruplexes by helicases remains poorly understood. DHX36 (also known as RHAU and G4R1), a member of the DEAH/RHA family of helicases, binds both DNA and RNA G-quadruplexes with extremely high affinity4-6, is consistently found bound to G-quadruplexes in cells7,8, and is a major source of G-quadruplex unfolding activity in HeLa cell lysates 6 . DHX36 is a multi-functional helicase that has been implicated in G-quadruplex-mediated transcriptional and post-transcriptional regulation, and is essential for heart development, haematopoiesis, and embryogenesis in mice9-12. Here we report the co-crystal structure of bovine DHX36 bound to a DNA with a G-quadruplex and a 3' single-stranded DNA segment. We show that the N-terminal DHX36-specific motif folds into a DNA-binding-induced α-helix that, together with the OB-fold-like subdomain, selectively binds parallel G-quadruplexes. Comparison with unliganded and ATP-analogue-bound DHX36 structures, together with single-molecule fluorescence resonance energy transfer (FRET) analysis, suggests that G-quadruplex binding alone induces rearrangements of the helicase core; by pulling on the single-stranded DNA tail, these rearrangements drive G-quadruplex unfolding one residue at a time.
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Affiliation(s)
- Michael C Chen
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ramreddy Tippana
- Biophysics Department, Johns Hopkins University, Baltimore, MD, USA
| | - Natalia A Demeshkina
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sua Myong
- Biophysics Department, Johns Hopkins University, Baltimore, MD, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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