1
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Celona B, Salomonsson SE, Wu H, Dang B, Kratochvil HT, Clelland CD, DeGrado WF, Black BL. Zfp106 binds to G-quadruplex RNAs and inhibits RAN translation and formation of RNA foci caused by G4C2 repeats. Proc Natl Acad Sci U S A 2024; 121:e2220020121. [PMID: 39042693 PMCID: PMC11295049 DOI: 10.1073/pnas.2220020121] [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: 12/16/2022] [Accepted: 06/14/2024] [Indexed: 07/25/2024] Open
Abstract
Expansion of intronic GGGGCC repeats in the C9orf72 gene causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Transcription of the expanded repeats results in the formation of RNA-containing nuclear foci and altered RNA metabolism. In addition, repeat-associated non-AUG (RAN) translation of the expanded GGGGCC-repeat sequence results in the production of highly toxic dipeptide-repeat (DPR) proteins. GGGGCC repeat-containing transcripts form G-quadruplexes, which are associated with formation of RNA foci and RAN translation. Zfp106, an RNA-binding protein essential for motor neuron survival in mice, suppresses neurotoxicity in a Drosophila model of C9orf72 ALS. Here, we show that Zfp106 inhibits formation of RNA foci and significantly reduces RAN translation caused by GGGGCC repeats in cultured mammalian cells, and we demonstrate that Zfp106 coexpression reduces the levels of DPRs in C9orf72 patient-derived cells. Further, we show that Zfp106 binds to RNA G-quadruplexes and causes a conformational change in the G-quadruplex structure formed by GGGGCC repeats. Together, these data demonstrate that Zfp106 suppresses the formation of RNA foci and DPRs caused by GGGGCC repeats and suggest that the G-quadruplex RNA-binding function of Zfp106 contributes to its suppression of GGGGCC repeat-mediated cytotoxicity.
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Affiliation(s)
- Barbara Celona
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
| | - Sally E. Salomonsson
- Weill Institute for Neurosciences, University of California, San Francisco, CA94143
- Memory & Aging Center, Department of Neurology, University of California, San Francisco, CA94143
| | - Haifan Wu
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Bobo Dang
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Huong T. Kratochvil
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Claire D. Clelland
- Weill Institute for Neurosciences, University of California, San Francisco, CA94143
- Memory & Aging Center, Department of Neurology, University of California, San Francisco, CA94143
| | - William F. DeGrado
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Brian L. Black
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
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2
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Geng Y, Liu C, Xu N, Suen MC, Miao H, Xie Y, Zhang B, Chen X, Song Y, Wang Z, Cai Q, Zhu G. Crystal structure of a tetrameric RNA G-quadruplex formed by hexanucleotide repeat expansions of C9orf72 in ALS/FTD. Nucleic Acids Res 2024; 52:7961-7970. [PMID: 38860430 PMCID: PMC11260476 DOI: 10.1093/nar/gkae473] [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: 12/18/2023] [Revised: 05/16/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
The abnormal GGGGCC hexanucleotide repeat expansions (HREs) in C9orf72 cause the fatal neurodegenerative diseases including amyotrophic lateral sclerosis and frontotemporal dementia. The transcribed RNA HREs, short for r(G4C2)n, can form toxic RNA foci which sequestrate RNA binding proteins and impair RNA processing, ultimately leading to neurodegeneration. Here, we determined the crystal structure of r(G4C2)2, which folds into a parallel tetrameric G-quadruplex composed of two four-layer dimeric G-quadruplex via 5'-to-5' stacking in coordination with a K+ ion. Notably, the two C bases locate at 3'- end stack on the outer G-tetrad with the assistance of two additional K+ ions. The high-resolution structure reported here lays a foundation in understanding the mechanism of neurological toxicity of RNA HREs. Furthermore, the atomic details provide a structural basis for the development of potential therapeutic agents against the fatal neurodegenerative diseases ALS/FTD.
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Affiliation(s)
- Yanyan Geng
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Changdong Liu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- HKUST Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen, Guangdong, China
| | - Naining Xu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- HKUST Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen, Guangdong, China
| | - Monica Ching Suen
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- HKUST Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen, Guangdong, China
| | - Haitao Miao
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yuanyuan Xie
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Bingchang Zhang
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xueqin Chen
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yuanjian Song
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhanxiang Wang
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qixu Cai
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Guang Zhu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- HKUST Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen, Guangdong, China
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3
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Ruan K, Bai G, Fang Y, Li D, Li T, Liu X, Lu B, Lu Q, Songyang Z, Sun S, Wang Z, Zhang X, Zhou W, Zhang H. Biomolecular condensates and disease pathogenesis. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2661-3. [PMID: 39037698 DOI: 10.1007/s11427-024-2661-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
Biomolecular condensates or membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) divide intracellular spaces into discrete compartments for specific functions. Dysregulation of LLPS or aberrant phase transition that disturbs the formation or material states of MLOs is closely correlated with neurodegeneration, tumorigenesis, and many other pathological processes. Herein, we summarize the recent progress in development of methods to monitor phase separation and we discuss the biogenesis and function of MLOs formed through phase separation. We then present emerging proof-of-concept examples regarding the disruption of phase separation homeostasis in a diverse array of clinical conditions including neurodegenerative disorders, hearing loss, cancers, and immunological diseases. Finally, we describe the emerging discovery of chemical modulators of phase separation.
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Affiliation(s)
- Ke Ruan
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Ge Bai
- Nanhu Brain-computer Interface Institute, Hangzhou, 311100, China.
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Yanshan Fang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 510000, China.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Qing Lu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Shuguo Sun
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Zheng Wang
- The Second Affiliated Hospital, School of Basic Medical Sciences, Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
| | - Xin Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China.
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Cammas A, Desprairies A, Dassi E, Millevoi S. The shaping of mRNA translation plasticity by RNA G-quadruplexes in cancer progression and therapy resistance. NAR Cancer 2024; 6:zcae025. [PMID: 38828391 PMCID: PMC11140630 DOI: 10.1093/narcan/zcae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/30/2024] [Accepted: 05/30/2024] [Indexed: 06/05/2024] Open
Abstract
Translational reprogramming in response to oncogenic signaling or microenvironmental stress factors shapes the proteome of cancer cells, enabling adaptation and phenotypic changes underlying cell plasticity, tumor progression and response to cancer therapy. Among the mechanisms regulating translation are RNA G-quadruplexes (RG4s), non-canonical four-stranded structures whose conformational modulation by small molecule ligands and RNA-binding proteins affects the expression of cancer proteins. Here, we discuss the role of RG4s in the regulation of mRNA translation by focusing on paradigmatic examples showing their contribution to adaptive mechanisms of mRNA translation in cancer.
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Affiliation(s)
- Anne Cammas
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm U1037, CNRS, 2 avenue Hubert Curien, 31037 Toulouse, France
| | - Alice Desprairies
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm U1037, CNRS, 2 avenue Hubert Curien, 31037 Toulouse, France
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Stefania Millevoi
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm U1037, CNRS, 2 avenue Hubert Curien, 31037 Toulouse, France
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5
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Buchan JR. Stress granule and P-body clearance: Seeking coherence in acts of disappearance. Semin Cell Dev Biol 2024; 159-160:10-26. [PMID: 38278052 PMCID: PMC10939798 DOI: 10.1016/j.semcdb.2024.01.002] [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: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/28/2024]
Abstract
Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into how cells regulate biomolecular condensate formation and function, and identify therapeutic strategies in disease states where aberrant persistence of stress granules in particular is implicated. Here, I review and compare the contributions of chaperones, the cytoskeleton, post-translational modifications, RNA helicases, granulophagy and the proteasome to stress granule and P-body clearance. Additionally, I highlight the potentially vital role of RNA regulation, cellular energy, and changes in the interaction networks of stress granules and P-bodies as means of eliciting clearance. Finally, I discuss evidence for interplay of distinct clearance mechanisms, suggest future experimental directions, and suggest a simple working model of stress granule clearance.
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Affiliation(s)
- J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85716, United States.
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6
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Angel M, Fleshler E, Atrash MK, Kinor N, Benichou JC, Shav-Tal Y. Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules. Nucleic Acids Res 2024; 52:5356-5375. [PMID: 38366783 PMCID: PMC11109975 DOI: 10.1093/nar/gkae119] [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: 11/07/2022] [Revised: 01/19/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
Stress granules (SGs) are cytoplasmic assemblies formed under various stress conditions as a consequence of translation arrest. SGs contain RNA-binding proteins, ribosomal subunits and messenger RNAs (mRNAs). It is well known that mRNAs contribute to SG formation; however, the connection between SG assembly and nuclear processes that involve mRNAs is not well established. Here, we examine the effects of inhibiting mRNA transcription, splicing and export on the assembly of SGs and the related cytoplasmic P body (PB). We demonstrate that inhibition of mRNA transcription, splicing and export reduces the formation of canonical SGs in a eukaryotic initiation factor 2α phosphorylation-independent manner, and alters PB size and quantity. We find that the splicing inhibitor madrasin promotes the assembly of stress-like granules. We show that the addition of synthetic mRNAs directly to the cytoplasm is sufficient for SG assembly, and that the assembly of these SGs requires the activation of stress-associated protein synthesis pathways. Moreover, we show that adding an excess of mRNA to cells that do not have active splicing, and therefore have low levels of cytoplasmic mRNAs, promotes SG formation under stress conditions. These findings emphasize the importance of the cytoplasmic abundance of newly transcribed mRNAs in the assembly of SGs.
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Affiliation(s)
- Mor Angel
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eden Fleshler
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Mohammad Khaled Atrash
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Noa Kinor
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Jennifer I C Benichou
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
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7
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Sahoo BR, Kocman V, Clark N, Myers N, Deng X, Wong EL, Yang HJ, Kotar A, Guzman BB, Dominguez D, Plavec J, Bardwell JCA. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. Nucleic Acids Res 2024; 52:4702-4722. [PMID: 38572746 PMCID: PMC11077067 DOI: 10.1093/nar/gkae229] [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: 12/06/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
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Affiliation(s)
- Bikash R Sahoo
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vojč Kocman
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Nathan Clark
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nikhil Myers
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xiexiong Deng
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ee L Wong
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Harry J Yang
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anita Kotar
- National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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8
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [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: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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9
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Litberg TJ, Horowitz S. Roles of Nucleic Acids in Protein Folding, Aggregation, and Disease. ACS Chem Biol 2024; 19:809-823. [PMID: 38477936 PMCID: PMC11149768 DOI: 10.1021/acschembio.3c00695] [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] [Indexed: 03/14/2024]
Abstract
The role of nucleic acids in protein folding and aggregation is an area of continued research, with relevance to understanding both basic biological processes and disease. In this review, we provide an overview of the trajectory of research on both nucleic acids as chaperones and their roles in several protein misfolding diseases. We highlight key questions that remain on the biophysical and biochemical specifics of how nucleic acids have large effects on multiple proteins' folding and aggregation behavior and how this pertains to multiple protein misfolding diseases.
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Affiliation(s)
- Theodore J. Litberg
- Department of Chemistry & Biochemistry and The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80208, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry and The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80208, USA
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10
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Wang Y, Wang J, Yan Z, Hou J, Wan L, Yang Y, Liu Y, Yi J, Guo P, Han D. Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS. Nucleic Acids Res 2024; 52:2698-2710. [PMID: 38266156 PMCID: PMC10954463 DOI: 10.1093/nar/gkae032] [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: 11/10/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
An expansion of AAGGG pentanucleotide repeats in the replication factor C subunit 1 (RFC1) gene is the genetic cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), and it also links to several other neurodegenerative diseases including the Parkinson's disease. However, the pathogenic mechanism of RFC1 AAGGG repeat expansion remains enigmatic. Here, we report that the pathogenic RFC1 AAGGG repeats form DNA and RNA parallel G-quadruplex (G4) structures that play a role in impairing biological processes. We determine the first high-resolution nuclear magnetic resonance (NMR) structure of a bimolecular parallel G4 formed by d(AAGGG)2AA and reveal how AAGGG repeats fold into a higher-order structure composed of three G-tetrad layers, and further demonstrate the formation of intramolecular G4s in longer DNA and RNA repeats. The pathogenic AAGGG repeats, but not the nonpathogenic AAAAG repeats, form G4 structures to stall DNA replication and reduce gene expression via impairing the translation process in a repeat-length-dependent manner. Our results provide an unprecedented structural basis for understanding the pathogenic mechanism of AAGGG repeat expansion associated with CANVAS. In addition, the high-resolution structures resolved in this study will facilitate rational design of small-molecule ligands and helicases targeting G4s formed by AAGGG repeats for therapeutic interventions.
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Affiliation(s)
- Yang Wang
- School of Materials Science and Engineering, Tianjin University, Tianjin 300350, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junyan Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhenzhen Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jianing Hou
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liqi Wan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yingquan Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jie Yi
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Da Han
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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11
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Sahoo BR, Kocman V, Clark N, Myers N, Deng X, Wong EL, Yang HJ, Kotar A, Guzman BB, Dominguez D, Plavec J, Bardwell JC. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.21.558871. [PMID: 37790366 PMCID: PMC10542165 DOI: 10.1101/2023.09.21.558871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
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Affiliation(s)
- Bikash R. Sahoo
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vojč Kocman
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Nathan Clark
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nikhil Myers
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xiexiong Deng
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ee L. Wong
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Harry J. Yang
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anita Kotar
- National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - James C.A. Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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12
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Lee KP, Liu K, Kim EY, Medina-Puche L, Dong H, Di M, Singh RM, Li M, Qi S, Meng Z, Cho J, Zhang H, Lozano-Duran R, Kim C. The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid-dependent stress responses in Arabidopsis. THE PLANT CELL 2024; 36:746-763. [PMID: 38041863 PMCID: PMC10896288 DOI: 10.1093/plcell/koad300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 12/04/2023]
Abstract
N 6-methyladenosine (m6A) is a common epitranscriptional mRNA modification in eukaryotes. Thirteen putative m6A readers, mostly annotated as EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT) proteins, have been identified in Arabidopsis (Arabidopsis thaliana), but few have been characterized. Here, we show that the Arabidopsis m6A reader ECT1 modulates salicylic acid (SA)-mediated plant stress responses. ECT1 undergoes liquid-liquid phase separation in vitro, and its N-terminal prion-like domain is critical for forming in vivo cytosolic biomolecular condensates in response to SA or bacterial pathogens. Fluorescence-activated particle sorting coupled with quantitative PCR analyses unveiled that ECT1 sequesters SA-induced m6A modification-prone mRNAs through its conserved aromatic cage to facilitate their decay in cytosolic condensates, thereby dampening SA-mediated stress responses. Consistent with this finding, ECT1 overexpression promotes bacterial multiplication in plants. Collectively, our findings unequivocally link ECT1-associated cytosolic condensates to SA-dependent plant stress responses, advancing the current understanding of m6A readers and the SA signaling network.
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Affiliation(s)
- Keun Pyo Lee
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
| | - Kaiwei Liu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Laura Medina-Puche
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
| | - Haihong Dong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
| | - Minghui Di
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Rahul Mohan Singh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
| | - Mengping Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
| | - Shan Qi
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuoling Meng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai 200032, China
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13
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Bhatter N, Dmitriev SE, Ivanov P. Cell death or survival: Insights into the role of mRNA translational control. Semin Cell Dev Biol 2024; 154:138-154. [PMID: 37357122 PMCID: PMC10695129 DOI: 10.1016/j.semcdb.2023.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Cellular stress is an intrinsic part of cell physiology that underlines cell survival or death. The ability of mammalian cells to regulate global protein synthesis (aka translational control) represents a critical, yet underappreciated, layer of regulation during the stress response. Various cellular stress response pathways monitor conditions of cell growth and subsequently reshape the cellular translatome to optimize translational outputs. On the molecular level, such translational reprogramming involves an intricate network of interactions between translation machinery, RNA-binding proteins, mRNAs, and non-protein coding RNAs. In this review, we will discuss molecular mechanisms, signaling pathways, and targets of translational control that contribute to cellular adaptation to stress and to cell survival or death.
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Affiliation(s)
- Nupur Bhatter
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA.
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14
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Kharel P, Ivanov P. RNA G-quadruplexes and stress: emerging mechanisms and functions. Trends Cell Biol 2024:S0962-8924(24)00005-9. [PMID: 38341346 DOI: 10.1016/j.tcb.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
RNA G-quadruplexes (rG4s) are noncanonical secondary structures formed by guanine-rich sequences that are found in different regions of RNA molecules. These structures have been implicated in diverse biological processes, including translation, splicing, and RNA stability. Recent studies have suggested that rG4s play a role in the cellular response to stress. This review summarizes the current knowledge on rG4s under stress, focusing on their formation, regulation, and potential functions in stress response pathways. We discuss the molecular mechanisms that regulate the formation of rG4 under different stress conditions and the impact of these structures on RNA metabolism, gene expression, and cell survival. Finally, we highlight the potential therapeutic implications of targeting rG4s for the treatment of stress-related diseases through modulating cell survival.
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Affiliation(s)
- Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; HMS Initiative for RNA Medicine, Boston, MA 02115, USA.
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15
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Wang S, Xu Y. RNA structure promotes liquid-to-solid phase transition of short RNAs in neuronal dysfunction. Commun Biol 2024; 7:137. [PMID: 38287096 PMCID: PMC10824717 DOI: 10.1038/s42003-024-05828-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
In nucleotide expansion disorders, RNA foci are reportedly associated with neurodegenerative disease pathogeneses. Characteristically, these RNAs exhibit long poly-RNA repeats, such as 47 × CAG, 47 × CUG, or 29 × GGGGCC, usually becoming abnormal pathological aggregations above a critical number of nucleotide repeats. However, it remains unclear whether short, predominantly cellular RNA molecules can cause phase transitions to induce RNA foci. Herein, we demonstrated that short RNAs even with only two repeats can aggregate into a solid-like state via special RNA G-quadruplex structures. In human cells, these solid RNA foci could not dissolve even when using agents that disrupt RNA gelation. The aggregation of shorter RNAs can be clearly observed in vivo. Furthermore, we found that RNA foci induce colocalization of the RNA-binding protein Sam68, a protein commonly found in patients with fragile X-associated tremor/ataxia syndrome, suppressing cell clonogenicity and eventually causing cell death. Our results suggest that short RNA gelation promoted by specific RNA structures contribute to the neurological diseases, which disturb functional cellular processes.
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Affiliation(s)
- Shiyu Wang
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
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16
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Geng Y, Cai Q. Role of C9orf72 hexanucleotide repeat expansions in ALS/FTD pathogenesis. Front Mol Neurosci 2024; 17:1322720. [PMID: 38318532 PMCID: PMC10838790 DOI: 10.3389/fnmol.2024.1322720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are progressive neurological disorders that share neurodegenerative pathways and features. The most prevalent genetic causes of ALS/FTD is the GGGGCC hexanucleotide repeat expansions in the first intron region of the chromosome 9 open reading frame 72 (C9orf72) gene. In this review, we comprehensively summarize the accumulating evidences elucidating the pathogenic mechanism associated with hexanucleotide repeat expansions in ALS/FTD. These mechanisms encompass the structural polymorphism of DNA and transcribed RNA, the formation of RNA foci via phase separation, and the cytoplasmic accumulation and toxicities of dipeptide-repeat proteins. Additionally, the formation of G-quadruplex structures significantly impairs the expression and normal function of the C9orf72 protein. We also discuss the sequestration of specific RNA binding proteins by GGGGCC RNA, which further contributes to the toxicity of C9orf72 hexanucleotide repeat expansions. The deeper understanding of the pathogenic mechanism of hexanucleotide repeat expansions in ALS/FTD provides multiple potential drug targets for these devastating diseases.
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Affiliation(s)
- Yanyan Geng
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qixu Cai
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China
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17
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Sahayasheela VJ, Sugiyama H. RNA G-quadruplex in functional regulation of noncoding RNA: Challenges and emerging opportunities. Cell Chem Biol 2024; 31:53-70. [PMID: 37909035 DOI: 10.1016/j.chembiol.2023.08.010] [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: 04/18/2023] [Revised: 07/12/2023] [Accepted: 08/22/2023] [Indexed: 11/02/2023]
Abstract
G-quadruplexes (G4s) are stable, noncanonical structures formed in guanine (G)-rich sequences of DNA/RNA. G4 structures are reported to play a regulatory role in various cellular processes and, recently, a considerable number of studies have attributed new biological functions to these structures, especially in RNA. Noncoding RNA (ncRNA), which does not translate into a functional protein, is widely expressed and has been shown to play a key role in shaping cellular activity. There has been growing evidence of G4 formation in several ncRNA classes, and it has been identified as a key part for diverse biological functions and physio-pathological contexts in neurodegenerative diseases and cancer. This review discusses RNA G4s (rG4s) in ncRNA, focusing on the molecular mechanism underlying its function. This review also aims to highlight potential and emerging opportunities to identify and target the rG4s in ncRNA to understand its function and, ultimately, treat many diseases.
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Affiliation(s)
- Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan.
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18
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Wang Y, Cao K, Zong M, Yuan S, Zhang N, Liu Y. Mutual promotion of co-condensation of KRAS G-quadruplex and a well-folded protein HMGB1. Nucleic Acids Res 2024; 52:288-299. [PMID: 37897365 PMCID: PMC10783520 DOI: 10.1093/nar/gkad938] [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: 06/01/2023] [Revised: 09/09/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) of G-quadruplex (GQ) is involved in many crucial cellular processes, while the quadruplex-folding and their functions are typically modulated by specific DNA-binding proteins. However, the regulatory mechanism of binding proteins, particularly the well-folded proteins, on the LLPS of GQs is largely unknown. Here, we investigated the effect of HMGB1 on the condensation of a G-quadruplex of KRAS promoter (GQKRAS). The results show that these two rigid macro-biomolecules undergo co-condensation through a mutual promotion manner, while neither of them can form LLPS alone. Fluidity measurements confirm that the liquid-like droplets are highly dynamic. HMGB1 facilitates and stabilizes the quadruplex folding of GQKRAS, and this process enhances their co-condensation. The KRAS promoter DNA retains quadruplex folding in the droplets; interference with the GQ-folding disrupts the co-condensation of GQKRAS/HMGB1. Mechanistic studies reveal that electrostatic interaction is a key driving force of the interaction and co-condensation of GQKRAS/HMGB1; meanwhile, the recognition of two macro-biomolecules plays a crucial role in this process. This result indicates that the phase separation of GQs can be modulated by DNA binding proteins, and this process could also be an efficient way to recruit specific DNA binding proteins.
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Affiliation(s)
- Yu Wang
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Kaiming Cao
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Mingxi Zong
- School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Siming Yuan
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Yangzhong Liu
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230001, China
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19
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Kharel P, Ivanov P. Identification of bona fide RNA G-quadruplex binding proteins. Methods Enzymol 2023; 695:255-274. [PMID: 38521588 DOI: 10.1016/bs.mie.2023.12.001] [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] [Indexed: 03/25/2024]
Abstract
RNAs often accomplish their diverse functions through direct interactions with RNA-binding proteins (RBPs) in a sequence- and/or structure-dependent manner. RNA G-quadruplexes (rG4s) are unique secondary structures formed by guanine-rich RNA sequences which impact RNA function independently and in combination with RBPs. Efforts from several labs have identified dozens of rG4 specific RBPs (rG4BPs), although the research is still in the growing phase. Here we present methods for the systematic identification of rG4BPs using a pull-down approach that takes advantage of the chemical modification of guanine bases. This allows abolishing the rG4 structures while still maintaining the base composition intact, and hence helps in recognizing true rG4BPS (in contrast to G-rich motif binders). In combination with other biochemical assays, such an approach can be efficiently used for the identification and characterization of bona fide rG4BPs.
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Affiliation(s)
- Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States; HMS Initiative for RNA Medicine, Boston, MA, United States.
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20
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Raguseo F, Wang Y, Li J, Petrić Howe M, Balendra R, Huyghebaert A, Vadukul DM, Tanase DA, Maher TE, Malouf L, Rubio-Sánchez R, Aprile FA, Elani Y, Patani R, Di Michele L, Di Antonio M. The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes. Nat Commun 2023; 14:8272. [PMID: 38092738 PMCID: PMC10719400 DOI: 10.1038/s41467-023-43872-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative diseases that exist on a clinico-pathogenetic spectrum, designated ALS/FTD. The most common genetic cause of ALS/FTD is expansion of the intronic hexanucleotide repeat (GGGGCC)n in C9orf72. Here, we investigate the formation of nucleic acid secondary structures in these expansion repeats, and their role in generating condensates characteristic of ALS/FTD. We observe significant aggregation of the hexanucleotide sequence (GGGGCC)n, which we associate to the formation of multimolecular G-quadruplexes (mG4s) by using a range of biophysical techniques. Exposing the condensates to G4-unfolding conditions leads to prompt disassembly, highlighting the key role of mG4-formation in the condensation process. We further validate the biological relevance of our findings by detecting an increased prevalence of G4-structures in C9orf72 mutant human motor neurons when compared to healthy motor neurons by staining with a G4-selective fluorescent probe, revealing signal in putative condensates. Our findings strongly suggest that RNA G-rich repetitive sequences can form protein-free condensates sustained by multimolecular G-quadruplexes, highlighting their potential relevance as therapeutic targets for C9orf72 mutation-related ALS/FTD.
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Affiliation(s)
- Federica Raguseo
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yiran Wang
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jessica Li
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Marija Petrić Howe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Rubika Balendra
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Anouk Huyghebaert
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Devkee M Vadukul
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Diana A Tanase
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Thomas E Maher
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Layla Malouf
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Roger Rubio-Sánchez
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Francesco A Aprile
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yuval Elani
- Imperial College London, Department of Chemical Engineering, South Kensington, London, SW7 2AZ, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
| | - Lorenzo Di Michele
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
| | - Marco Di Antonio
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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21
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Wadsworth GM, Zahurancik WJ, Zeng X, Pullara P, Lai LB, Sidharthan V, Pappu RV, Gopalan V, Banerjee PR. RNAs undergo phase transitions with lower critical solution temperatures. Nat Chem 2023; 15:1693-1704. [PMID: 37932412 PMCID: PMC10872781 DOI: 10.1038/s41557-023-01353-4] [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: 10/19/2022] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Co-phase separation of RNAs and RNA-binding proteins drives the biogenesis of ribonucleoprotein granules. RNAs can also undergo phase transitions in the absence of proteins. However, the physicochemical driving forces of protein-free, RNA-driven phase transitions remain unclear. Here we report that various types of RNA undergo phase separation with system-specific lower critical solution temperatures. This entropically driven phase separation is an intrinsic feature of the phosphate backbone that requires Mg2+ ions and is modulated by RNA bases. RNA-only condensates can additionally undergo enthalpically favourable percolation transitions within dense phases. This is enabled by a combination of Mg2+-dependent bridging interactions between phosphate groups and RNA-specific base stacking and base pairing. Phase separation coupled to percolation can cause dynamic arrest of RNAs within condensates and suppress the catalytic activity of an RNase P ribozyme. Our work highlights the need to incorporate RNA-driven phase transitions into models for ribonucleoprotein granule biogenesis.
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Affiliation(s)
- Gable M Wadsworth
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Walter J Zahurancik
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Xiangze Zeng
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
- Department of Physics, Hong Kong Baptist University, Hong Kong, China
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Paul Pullara
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Lien B Lai
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Vaishnavi Sidharthan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Priya R Banerjee
- Department of Physics, The State University of New York at Buffalo, Buffalo, NY, USA.
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22
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Ocharán-Mercado A, Loaeza-Loaeza J, Castro-Coronel Y, Acosta-Saavedra LC, Hernández-Kelly LC, Hernández-Sotelo D, Ortega A. RNA-Binding Proteins: A Role in Neurotoxicity? Neurotox Res 2023; 41:681-697. [PMID: 37776476 PMCID: PMC10682104 DOI: 10.1007/s12640-023-00669-w] [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: 03/15/2023] [Revised: 03/15/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023]
Abstract
Despite sustained efforts to treat neurodegenerative diseases, little is known at the molecular level to understand and generate novel therapeutic approaches for these malignancies. Therefore, it is not surprising that neurogenerative diseases are among the leading causes of death in the aged population. Neurons require sophisticated cellular mechanisms to maintain proper protein homeostasis. These cells are generally sensitive to loss of gene expression control at the post-transcriptional level. Post-translational control responds to signals that can arise from intracellular processes or environmental factors that can be regulated through RNA-binding proteins. These proteins recognize RNA through one or more RNA-binding domains and form ribonucleoproteins that are critically involved in the regulation of post-transcriptional processes from splicing to the regulation of association of the translation machinery allowing a relatively rapid and precise modulation of the transcriptome. Neurotoxicity is the result of the biological, chemical, or physical interaction of agents with an adverse effect on the structure and function of the central nervous system. The disruption of the proper levels or function of RBPs in neurons and glial cells triggers neurotoxic events that are linked to neurodegenerative diseases such as spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), fragile X syndrome (FXS), and frontotemporal dementia (FTD) among many others. The connection between RBPs and neurodegenerative diseases opens a new landscape for potentially novel therapeutic targets for the intervention of these neurodegenerative pathologies. In this contribution, a summary of the recent findings of the molecular mechanisms involved in the plausible role of RBPs in RNA processing in neurodegenerative disease is discussed.
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Affiliation(s)
- Andrea Ocharán-Mercado
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Jaqueline Loaeza-Loaeza
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Yaneth Castro-Coronel
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas 88, Chilpancingo, Guerrero, 39086, México
| | - Leonor C Acosta-Saavedra
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Luisa C Hernández-Kelly
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas 88, Chilpancingo, Guerrero, 39086, México
| | - Arturo Ortega
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México.
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23
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Yan MP, Wee CE, Yen KP, Stevens A, Wai LK. G-quadruplex ligands as therapeutic agents against cancer, neurological disorders and viral infections. Future Med Chem 2023; 15:1987-2009. [PMID: 37933551 DOI: 10.4155/fmc-2023-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
G-quadruplexes (G4s) within the human genome have undergone extensive molecular investigation, with a strong focus on telomeres, gene promoters and repetitive regulatory sequences. G4s play central roles in regulating essential biological processes, including telomere maintenance, replication, transcription and translation. Targeting these molecular processes with G4-binding ligands holds substantial therapeutic potential in anticancer treatments and has also shown promise in treating neurological, skeletal and muscular disorders. The presence of G4s in bacterial and viral genomes also suggests that G4-binding ligands could be a critical tool in fighting infections. This review provides an overview of the progress and applications of G4-binding ligands, their proposed mechanisms of action, challenges faced and prospects for their utilization in anticancer treatments, neurological disorders and antiviral activities.
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Affiliation(s)
- Mock Phooi Yan
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Chua Eng Wee
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Khor Poh Yen
- Faculty Pharmacy & Health Sciences, Universiti Kuala Lumpur, Royal College of Medicine Perak, 3, Jalan Greentown, Ipoh, Perak, 30450, Malaysia
| | - Aaron Stevens
- Department of Pathology & Molecular Medicine, University of Otago, Wellington, 6021, New Zealand
| | - Lam Kok Wai
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
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24
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Ripin N, Parker R. Formation, function, and pathology of RNP granules. Cell 2023; 186:4737-4756. [PMID: 37890457 PMCID: PMC10617657 DOI: 10.1016/j.cell.2023.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/28/2023] [Accepted: 09/07/2023] [Indexed: 10/29/2023]
Abstract
Ribonucleoprotein (RNP) granules are diverse membrane-less organelles that form through multivalent RNA-RNA, RNA-protein, and protein-protein interactions between RNPs. RNP granules are implicated in many aspects of RNA physiology, but in most cases their functions are poorly understood. RNP granules can be described through four key principles. First, RNP granules often arise because of the large size, high localized concentrations, and multivalent interactions of RNPs. Second, cells regulate RNP granule formation by multiple mechanisms including posttranslational modifications, protein chaperones, and RNA chaperones. Third, RNP granules impact cell physiology in multiple manners. Finally, dysregulation of RNP granules contributes to human diseases. Outstanding issues in the field remain, including determining the scale and molecular mechanisms of RNP granule function and how granule dysfunction contributes to human disease.
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Affiliation(s)
- Nina Ripin
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Roy Parker
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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25
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Guzman BB, Son A, Litberg TJ, Huang Z, Dominguez D, Horowitz S. Emerging roles for G-quadruplexes in proteostasis. FEBS J 2023; 290:4614-4625. [PMID: 36017725 PMCID: PMC10071977 DOI: 10.1111/febs.16608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/22/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]
Abstract
How nucleic acids interact with proteins, and how they affect protein folding, aggregation, and misfolding is a still-evolving area of research. Considerable effort is now focusing on a particular structure of RNA and DNA, G-quadruplexes, and their role in protein homeostasis and disease. In this state-of-the-art review, we track recent reports on how G-quadruplexes influence protein aggregation, proteolysis, phase separation, and protein misfolding diseases, and pose currently unanswered questions in the advance of this scientific field.
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Affiliation(s)
- Bryan B Guzman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Theodore J Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Zijue Huang
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
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26
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Danino YM, Molitor L, Rosenbaum-Cohen T, Kaiser S, Cohen Y, Porat Z, Marmor-Kollet H, Katina C, Savidor A, Rotkopf R, Ben-Isaac E, Golani O, Levin Y, Monchaud D, Hickson I, Hornstein E. BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures. Nucleic Acids Res 2023; 51:9369-9384. [PMID: 37503837 PMCID: PMC10516661 DOI: 10.1093/nar/gkad613] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
Bloom's syndrome (BLM) protein is a known nuclear helicase that is able to unwind DNA secondary structures such as G-quadruplexes (G4s). However, its role in the regulation of cytoplasmic processes that involve RNA G-quadruplexes (rG4s) has not been previously studied. Here, we demonstrate that BLM is recruited to stress granules (SGs), which are cytoplasmic biomolecular condensates composed of RNAs and RNA-binding proteins. BLM is enriched in SGs upon different stress conditions and in an rG4-dependent manner. Also, we show that BLM unwinds rG4s and acts as a negative regulator of SG formation. Altogether, our data expand the cellular activity of BLM and shed light on the function that helicases play in the dynamics of biomolecular condensates.
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Affiliation(s)
- Yehuda M Danino
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lena Molitor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Rosenbaum-Cohen
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Brain science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sebastian Kaiser
- Center for Chromosome Stability, Dept. of Cellular and Molecular Medicine, Panum Institute, Copenhagen Univ, 2200 København N., Denmark
| | - Yahel Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hagai Marmor-Kollet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- 1E therapeutics, Rehovot, Israel
| | - Corine Katina
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Rotkopf
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal Ben-Isaac
- MICC Cell Observatory Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ofra Golani
- MICC Cell Observatory Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, uB Dijon, France
| | - Ian D Hickson
- Center for Chromosome Stability, Dept. of Cellular and Molecular Medicine, Panum Institute, Copenhagen Univ, 2200 København N., Denmark
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
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27
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Liu X, Zhao X, He J, Wang S, Shen X, Liu Q, Wang S. Advances in the Structure of GGGGCC Repeat RNA Sequence and Its Interaction with Small Molecules and Protein Partners. Molecules 2023; 28:5801. [PMID: 37570771 PMCID: PMC10420822 DOI: 10.3390/molecules28155801] [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: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
The aberrant expansion of GGGGCC hexanucleotide repeats within the first intron of the C9orf72 gene represent the predominant genetic etiology underlying amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). The transcribed r(GGGGCC)n RNA repeats form RNA foci, which recruit RNA binding proteins and impede their normal cellular functions, ultimately resulting in fatal neurodegenerative disorders. Furthermore, the non-canonical translation of the r(GGGGCC)n sequence can generate dipeptide repeats, which have been postulated as pathological causes. Comprehensive structural analyses of r(GGGGCC)n have unveiled its polymorphic nature, exhibiting the propensity to adopt dimeric, hairpin, or G-quadruplex conformations, all of which possess the capacity to interact with RNA binding proteins. Small molecules capable of binding to r(GGGGCC)n have been discovered and proposed as potential lead compounds for the treatment of ALS and FTD. Some of these molecules function in preventing RNA-protein interactions or impeding the phase transition of r(GGGGCC)n. In this review, we present a comprehensive summary of the recent advancements in the structural characterization of r(GGGGCC)n, its propensity to form RNA foci, and its interactions with small molecules and proteins. Specifically, we emphasize the structural diversity of r(GGGGCC)n and its influence on partner binding. Given the crucial role of r(GGGGCC)n in the pathogenesis of ALS and FTD, the primary objective of this review is to facilitate the development of therapeutic interventions targeting r(GGGGCC)n RNA.
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Affiliation(s)
- Xiaole Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Xinyue Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Jinhan He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Sishi Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Xinfei Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Qingfeng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Shenlin Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
- Beijing NMR Center, Peking University, Beijing 100087, China
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28
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Antoniani F, Cimino M, Mediani L, Vinet J, Verde EM, Secco V, Yamoah A, Tripathi P, Aronica E, Cicardi ME, Trotti D, Sterneckert J, Goswami A, Carra S. Loss of PML nuclear bodies in familial amyotrophic lateral sclerosis-frontotemporal dementia. Cell Death Discov 2023; 9:248. [PMID: 37454169 DOI: 10.1038/s41420-023-01547-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/20/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are two neurodegenerative disorders that share genetic causes and pathogenic mechanisms. The critical genetic players of ALS and FTD are the TARDBP, FUS and C9orf72 genes, whose protein products, TDP-43, FUS and the C9orf72-dipeptide repeat proteins, accumulate in form of cytoplasmic inclusions. The majority of the studies focus on the understanding of how cells control TDP-43 and FUS aggregation in the cytoplasm, overlooking how dysfunctions occurring at the nuclear level may influence the maintenance of protein solubility outside of the nucleus. However, protein quality control (PQC) systems that maintain protein homeostasis comprise a cytoplasmic and a nuclear arm that are interconnected and share key players. It is thus conceivable that impairment of the nuclear arm of the PQC may have a negative impact on the cytoplasmic arm of the PQC, contributing to the formation of the cytoplasmic pathological inclusions. Here we focused on two stress-inducible condensates that act as transient deposition sites for misfolding-prone proteins: Promyelocytic leukemia protein (PML) nuclear bodies (PML-NBs) and cytoplasmic stress granules (SGs). Upon stress, PML-NBs compartmentalize misfolded proteins, including defective ribosomal products (DRiPs), and recruit chaperones and proteasomes to promote their nuclear clearance. SGs transiently sequester aggregation-prone RNA-binding proteins linked to ALS-FTD and mRNAs to attenuate their translation. We report that PML assembly is impaired in the human brain and spinal cord of familial C9orf72 and FUS ALS-FTD cases. We also show that defective PML-NB assembly impairs the compartmentalization of DRiPs in the nucleus, leading to their accumulation inside cytoplasmic SGs, negatively influencing SG dynamics. Although it is currently unclear what causes the decrease of PML-NBs in ALS-FTD, our data highlight the existence of a cross-talk between the cytoplasmic and nuclear PQC systems, whose alteration can contribute to SG accumulation and cytoplasmic protein aggregation in ALS-FTD.
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Affiliation(s)
- Francesco Antoniani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marco Cimino
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jonathan Vinet
- Centro Interdipartimentale Grandi Strumenti (CIGS), University of Modena and Reggio Emilia, Modena, Italy
| | - Enza M Verde
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Valentina Secco
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alfred Yamoah
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Priyanka Tripathi
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Eleonora Aronica
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, the Netherlands
| | - Maria E Cicardi
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Davide Trotti
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Dresden, Germany
- Medical Faculty Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Anand Goswami
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany.
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, 10032, New York, NY, USA.
- Department of Neurology, Eleanor and Lou Gehrig ALS Center, Columbia University, 10032, New York, NY, USA.
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy.
- Medical Faculty Carl Gustav Carus of TU Dresden, Dresden, Germany.
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29
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Arnold FJ, Nguyen AD, Bedlack RS, Bennett CL, La Spada AR. Intercellular transmission of pathogenic proteins in ALS: Exploring the pathogenic wave. Neurobiol Dis 2023:106218. [PMID: 37394036 DOI: 10.1016/j.nbd.2023.106218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023] Open
Abstract
In patients with amyotrophic lateral sclerosis (ALS), disease symptoms and pathology typically spread in a predictable spatiotemporal pattern beginning at a focal site of onset and progressing along defined neuroanatomical tracts. Like other neurodegenerative diseases, ALS is characterized by the presence of protein aggregates in postmortem patient tissue. Cytoplasmic, ubiquitin-positive aggregates of TDP-43 are observed in approximately 97% of sporadic and familial ALS patients, while SOD1 inclusions are likely specific to cases of SOD1-ALS. Additionally, the most common subtype of familial ALS, caused by a hexanucleotide repeat expansion in the first intron of the C9orf72 gene (C9-ALS), is further characterized by the presence of aggregated dipeptide repeat proteins (DPRs). As we will describe, cell-to-cell propagation of these pathological proteins tightly correlates with the contiguous spread of disease. While TDP-43 and SOD1 are capable of seeding protein misfolding and aggregation in a prion-like manner, C9orf72 DPRs appear to induce (and transmit) a 'disease state' more generally. Multiple mechanisms of intercellular transport have been described for all of these proteins, including anterograde and retrograde axonal transport, extracellular vesicle secretion, and macropinocytosis. In addition to neuron-to-neuron transmission, transmission of pathological proteins occurs between neurons and glia. Given that the spread of ALS disease pathology corresponds with the spread of symptoms in patients, the various mechanisms by which ALS-associated protein aggregates propagate through the central nervous system should be closely examined.
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Affiliation(s)
- F J Arnold
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - A D Nguyen
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - R S Bedlack
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - C L Bennett
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - A R La Spada
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; Departments of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, University of California, Irvine, Irvine, CA, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
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30
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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: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [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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31
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Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
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32
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Figueiredo AS, Loureiro JR, Macedo-Ribeiro S, Silveira I. Advances in Nucleotide Repeat Expansion Diseases: Transcription Gets in Phase. Cells 2023; 12:cells12060826. [PMID: 36980167 PMCID: PMC10047669 DOI: 10.3390/cells12060826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023] Open
Abstract
Unstable DNA repeat expansions and insertions have been found to cause more than 50 neurodevelopmental, neurodegenerative, and neuromuscular disorders. One of the main hallmarks of repeat expansion diseases is the formation of abnormal RNA or protein aggregates in the neuronal cells of affected individuals. Recent evidence indicates that alterations of the dynamic or material properties of biomolecular condensates assembled by liquid/liquid phase separation are critical for the formation of these aggregates. This is a thermodynamically-driven and reversible local phenomenon that condenses macromolecules into liquid-like compartments responsible for compartmentalizing molecules required for vital cellular processes. Disease-associated repeat expansions modulate the phase separation properties of RNAs and proteins, interfering with the composition and/or the material properties of biomolecular condensates and resulting in the formation of abnormal aggregates. Since several repeat expansions have arisen in genes encoding crucial players in transcription, this raises the hypothesis that wide gene expression dysregulation is common to multiple repeat expansion diseases. This review will cover the impact of these mutations in the formation of aberrant aggregates and how they modify gene transcription.
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Affiliation(s)
- Ana S. Figueiredo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
| | - Joana R. Loureiro
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
| | - Sandra Macedo-Ribeiro
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
| | - Isabel Silveira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-2240-8800
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33
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Asamitsu S, Yabuki Y, Matsuo K, Kawasaki M, Hirose Y, Kashiwazaki G, Chandran A, Bando T, Wang DO, Sugiyama H, Shioda N. RNA G-quadruplex organizes stress granule assembly through DNAPTP6 in neurons. SCIENCE ADVANCES 2023; 9:eade2035. [PMID: 36827365 PMCID: PMC9956113 DOI: 10.1126/sciadv.ade2035] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Consecutive guanine RNA sequences can adopt quadruple-stranded structures, termed RNA G-quadruplexes (rG4s). Although rG4-forming sequences are abundant in transcriptomes, the physiological roles of rG4s in the central nervous system remain poorly understood. In the present study, proteomics analysis of the mouse forebrain identified DNAPTP6 as an RNA binding protein with high affinity and selectivity for rG4s. We found that DNAPTP6 coordinates the assembly of stress granules (SGs), cellular phase-separated compartments, in an rG4-dependent manner. In neurons, the knockdown of DNAPTP6 diminishes the SG formation under oxidative stress, leading to synaptic dysfunction and neuronal cell death. rG4s recruit their mRNAs into SGs through DNAPTP6, promoting RNA self-assembly and DNAPTP6 phase separation. Together, we propose that the rG4-dependent phase separation of DNAPTP6 plays a critical role in neuronal function through SG assembly.
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Affiliation(s)
- Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Japan
| | - Yasushi Yabuki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuya Matsuo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
| | - Moe Kawasaki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Gengo Kashiwazaki
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Anandhakumar Chandran
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Dan Ohtan Wang
- Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
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34
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Guo W, Ji D, Kinghorn AB, Chen F, Pan Y, Li X, Li Q, Huck WTS, Kwok CK, Shum HC. Tuning Material States and Functionalities of G-Quadruplex-Modulated RNA-Peptide Condensates. J Am Chem Soc 2023; 145:2375-2385. [PMID: 36689740 DOI: 10.1021/jacs.2c11362] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA encodes sequence- and structure-dependent interactions to modulate the assembly and properties of biomolecular condensates. RNA G-quadruplexes (rG4s) formed by guanine-rich sequences can trigger the formation of liquid- or solid-like condensates that are involved in many aberrant phase transitions. However, exactly how rG4 motifs modulate different phase transitions and impart distinct material properties to condensates is unclear. Here, using RNA oligonucleotides and cationic peptides as model systems, we show that RNA-peptide condensates exhibit tunability in material properties over a wide spectrum via interactions arising from rG4 folding/unfolding kinetics. rG4-containing oligonucleotides formed strong pairwise attraction with peptides and tended to form solid-like condensates, while their less-structured non-G4 mutants formed liquid-like droplets. We find that the coupling between rG4 dissociation and RNA-peptide complex coacervation triggers solid-to-liquid transition of condensates prior to the complete unfolding of rG4s. This coupling points to a mechanism that material states of rG4-modulated condensates can be finely tuned from solid-like to liquid-like by the addition of less-structured RNA oligonucleotides, which have weak but dominant binding with peptides. We further show that the tunable material states of condensates can enhance RNA aptamer compartmentalization and RNA cleavage reactions. Our results suggest that condensates with complex properties can emerge from subtle changes in RNA oligonucleotides, contributing ways to treat dysfunctional condensates in diseases and insights into prebiotic compartmentalization.
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Affiliation(s)
- Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Feipeng Chen
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Yi Pan
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Xiufeng Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Qingchuan Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
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35
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Kharel P, Fay M, Manasova EV, Anderson PJ, Kurkin AV, Guo JU, Ivanov P. Stress promotes RNA G-quadruplex folding in human cells. Nat Commun 2023; 14:205. [PMID: 36639366 PMCID: PMC9839774 DOI: 10.1038/s41467-023-35811-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. In this report, we showed that the folding of putative rG4s in human cells into rG4 structures is dynamically regulated under stress. By using high-throughput dimethylsulfate (DMS) probing, we identified hundreds of endogenous stress-induced rG4s, and validated them by using an rG4 pull-down approach. Our results demonstrate that stress-induced rG4s are enriched in mRNA 3'-untranslated regions and enhance mRNA stability. Furthermore, stress-induced rG4 folding is readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in human cells and suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.
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Affiliation(s)
- Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marta Fay
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ekaterina V Manasova
- Chemistry Department of Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Paul J Anderson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Alexander V Kurkin
- Chemistry Department of Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Junjie U Guo
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06520, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, 02115, USA.
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36
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Sahayasheela VJ, Yu Z, Hidaka T, Pandian GN, Sugiyama H. Mitochondria and G-quadruplex evolution: an intertwined relationship. Trends Genet 2023; 39:15-30. [PMID: 36414480 PMCID: PMC9772288 DOI: 10.1016/j.tig.2022.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/27/2022] [Accepted: 10/27/2022] [Indexed: 11/21/2022]
Abstract
G-quadruplexes (G4s) are non-canonical structures formed in guanine (G)-rich sequences through stacked G tetrads by Hoogsteen hydrogen bonding. Several studies have demonstrated the existence of G4s in the genome of various organisms, including humans, and have proposed that G4s have a regulatory role in various cellular functions. However, little is known regarding the dissemination of G4s in mitochondria. In this review, we report the observation that the number of potential G4-forming sequences in the mitochondrial genome increases with the evolutionary complexity of different species, suggesting that G4s have a beneficial role in higher-order organisms. We also discuss the possible function of G4s in mitochondrial (mt)DNA and long noncoding (lnc)RNA and their role in various biological processes.
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Affiliation(s)
- Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Zutao Yu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Takuya Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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37
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Isiktas AU, Eshov A, Yang S, Guo JU. Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation. CELL REPORTS METHODS 2022; 2:100334. [PMID: 36452875 PMCID: PMC9701603 DOI: 10.1016/j.crmeth.2022.100334] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
A common pathological feature of RNAs containing expanded repeat sequences is their propensity to aggregate in cells. While some repeat RNA aggregates have been shown to cause toxicity by sequestering RNA-binding proteins, the molecular mechanism of aggregation remains unclear. Here, we devised an efficient method to generate long tandem repeat DNAs de novo and applied it to systematically determine the sequence features underlying RNA aggregation. Live-cell imaging of repeat RNAs indicated that aggregation was promoted by multivalent RNA-RNA interactions via either canonical or noncanonical base pairs. While multiple runs of two consecutive base pairs were sufficient, longer runs of base pairs such as those formed by GGGGCC hexanucleotide repeats further enhanced aggregation. In summary, our study provides a unifying model for the molecular basis of repeat RNA aggregation and a generalizable approach for identifying the sequence and structural determinants underlying the distinct properties of repeat DNAs and RNAs.
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Affiliation(s)
- Atagun U. Isiktas
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Aziz Eshov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Suzhou Yang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Junjie U. Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
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38
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Turner M, Danino YM, Barshai M, Yacovzada NS, Cohen Y, Olender T, Rotkopf R, Monchaud D, Hornstein E, Orenstein Y. rG4detector, a novel RNA G-quadruplex predictor, uncovers their impact on stress granule formation. Nucleic Acids Res 2022; 50:11426-11441. [PMID: 36350614 PMCID: PMC9723610 DOI: 10.1093/nar/gkac950] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/21/2022] [Accepted: 10/14/2022] [Indexed: 11/11/2022] Open
Abstract
RNA G-quadruplexes (rG4s) are RNA secondary structures, which are formed by guanine-rich sequences and have important cellular functions. Existing computational tools for rG4 prediction rely on specific sequence features and/or were trained on small datasets, without considering rG4 stability information, and are therefore sub-optimal. Here, we developed rG4detector, a convolutional neural network to identify potential rG4s in transcriptomics data. rG4detector outperforms existing methods in both predicting rG4 stability and in detecting rG4-forming sequences. To demonstrate the biological-relevance of rG4detector, we employed it to study RNAs that are bound by the RNA-binding protein G3BP1. G3BP1 is central to the induction of stress granules (SGs), which are cytoplasmic biomolecular condensates that form in response to a variety of cellular stresses. Unexpectedly, rG4detector revealed a dynamic enrichment of rG4s bound by G3BP1 in response to cellular stress. In addition, we experimentally characterized G3BP1 cross-talk with rG4s, demonstrating that G3BP1 is a bona fide rG4-binding protein and that endogenous rG4s are enriched within SGs. Furthermore, we found that reduced rG4 availability impairs SG formation. Hence, we conclude that rG4s play a direct role in SG biology via their interactions with RNA-binding proteins and that rG4detector is a novel useful tool for rG4 transcriptomics data analyses.
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Affiliation(s)
| | | | - Mira Barshai
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Be’er-Sheva 8410501, Israel
| | - Nancy S Yacovzada
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel,Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yahel Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel,Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Rotkopf
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | | | - Yaron Orenstein
- Correspondence may also be addressed to Yaron Orenstein. Tel: +972 3 531 7990;
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39
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Williams AM, Dickson TM, Lagoa-Miguel CA, Bevilacqua PC. Biological solution conditions and flanking sequence modulate LLPS of RNA G-quadruplex structures. RNA (NEW YORK, N.Y.) 2022; 28:1197-1209. [PMID: 35760522 PMCID: PMC9380743 DOI: 10.1261/rna.079196.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/13/2022] [Indexed: 05/17/2023]
Abstract
Guanine-rich regions of DNA or RNA can form structures with two or more consecutive G-quartets called G-quadruplexes (GQ). Recent studies reveal the potential for these structures to aggregate in vitro. Here, we report effects of in vivo concentrations of additives-amino acids, nucleotides, and crowding agents-on the structure and solution behavior of RNAs containing GQ-forming sequences. We found that cytosine nucleotides destabilize a model GQ structure at biological salt concentrations, while free amino acids and other nucleotides do not do so to a substantial degree. We also report that the tendency of folded GQs to form droplets or to aggregate depends on the nature of flanking sequence and the presence of additives. Notably, in the presence of biological amounts of polyamines, flanking regions on the 5'-end of the RNA drive more droplet-like phase separation, while flanking regions on the 3'-end, as well as both the 5'- and 3'-ends, induce more condensed, granular structures. Finally, we provide an example of a biological sequence in the presence of polyamines and show that crowders such as PEG and dextran can selectively cause its phase separation. These findings have implications for the participation of GQS in LLPS in vivo.
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Affiliation(s)
- Allison M Williams
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Taylor M Dickson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Claudia A Lagoa-Miguel
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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40
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Conti BA, Oppikofer M. Biomolecular condensates: new opportunities for drug discovery and RNA therapeutics. Trends Pharmacol Sci 2022; 43:820-837. [PMID: 36028355 DOI: 10.1016/j.tips.2022.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 11/18/2022]
Abstract
Biomolecular condensates organize cellular functions in the absence of membranes. These membraneless organelles can form through liquid-liquid phase separation coalescing RNA and proteins into well-defined, yet dynamic, structures distinct from the surrounding cellular milieu. Numerous physiological and disease-causing processes link to biomolecular condensates, which could impact drug discovery in several ways. First, disruption of pathological condensates seeded by mutated proteins or RNAs may provide new opportunities to treat disease. Second, condensates may be leveraged to tackle difficult-to-drug targets lacking binding pockets whose function depends on phase separation. Third, condensate-resident small molecules and RNA therapeutics may display unexpected pharmacology. We discuss the potential impact of phase separation on drug discovery and RNA therapeutics, leveraging concrete examples, towards novel clinical opportunities.
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Affiliation(s)
- Brooke A Conti
- Pfizer Centers for Therapeutic Innovation, Pfizer Inc., New York, NY, USA
| | - Mariano Oppikofer
- Pfizer Centers for Therapeutic Innovation, Pfizer Inc., New York, NY, USA.
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41
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Fingerhut JM, Yamashita YM. The regulation and potential functions of intronic satellite DNA. Semin Cell Dev Biol 2022; 128:69-77. [PMID: 35469677 DOI: 10.1016/j.semcdb.2022.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022]
Abstract
Satellite DNAs are arrays of tandem repeats found in the eukaryotic genome. They are mainly found in pericentromeric heterochromatin and have been believed to be mostly inert, leading satellite DNAs to be erroneously regarded as junk. Recent studies have started to elucidate the function of satellite DNA, yet little is known about the peculiar case where satellite DNA is found within the introns of protein coding genes, resulting in incredibly large introns, a phenomenon termed intron gigantism. Studies in Drosophila demonstrated that satellite DNA-containing introns are transcribed with the gene and require specialized mechanisms to overcome the burdens imposed by the extremely long stretches of repetitive DNA. Whether intron gigantism confers any benefit or serves any functional purpose for cells and/or organisms remains elusive. Here we review our current understanding of intron gigantism: where it is found, the challenges it imposes, how it is regulated and what purpose it may serve.
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Affiliation(s)
- Jaclyn M Fingerhut
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
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42
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Xu B, Zhu Y, Cao C, Chen H, Jin Q, Li G, Ma J, Yang SL, Zhao J, Zhu J, Ding Y, Fang X, Jin Y, Kwok CK, Ren A, Wan Y, Wang Z, Xue Y, Zhang H, Zhang QC, Zhou Y. Recent advances in RNA structurome. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1285-1324. [PMID: 35717434 PMCID: PMC9206424 DOI: 10.1007/s11427-021-2116-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiongli Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangnan Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Siwy Ling Yang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Jieyu Zhao
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chun Kit Kwok
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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43
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Baud A, Derbis M, Tutak K, Sobczak K. Partners in crime: Proteins implicated in
RNA
repeat expansion diseases. WIRES RNA 2022; 13:e1709. [PMID: 35229468 PMCID: PMC9539487 DOI: 10.1002/wrna.1709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Baud
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Magdalena Derbis
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Katarzyna Tutak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Krzysztof Sobczak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
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44
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C9orf72 Hexanucleotide Repeat Expansion-Related Neuropathology Is Attenuated by Nasal Rifampicin in Mice. Biomedicines 2022; 10:biomedicines10051080. [PMID: 35625816 PMCID: PMC9138602 DOI: 10.3390/biomedicines10051080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
The non-coding GGGGCC hexanucleotide repeat expansion (HRE) in C9orf72 gene is a dominant cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). This intronic mutation elicits the formation of nuclear and cytoplasmic inclusions containing RNA, RNA-binding proteins, and HRE-derived dipeptide repeat proteins (DPRs), leading to neurodegeneration via the gain-of-toxic function or loss-of-function of relevant proteins. Using C9-500 mice harboring ~500 repeats of the GGGGCC sequence in human C9orf72 gene, we investigated the effects of rifampicin against HRE-related pathological phenotypes. Rifampicin was administered intranasally to 4.5- to 5-month-old mice for 1 month, and their cognitive function and neuropathology were assessed by the Morris water maze test and immunohistochemical staining. Rifampicin treatment reduced the formation of RNA foci and cytoplasmic inclusions containing DPRs or phosphorylated TDP-43, and furthermore, the levels of phosphorylated double-strand RNA-dependent protein kinase (PKR) that regulates repeat-associated non-ATG (RAN) translation. Synapse loss in the hippocampus and neuronal loss and microglial activation in the prefrontal and motor cortices were also attenuated, and mouse memory was significantly improved. Our findings suggest a therapeutic potential of nasal rifampicin in the prevention of C9orf72-linked neurodegenerative disorders.
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45
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Bose K, Maity A, Ngo KH, Vandana JJ, Shneider NA, Phan AT. Formation of RNA G-wires by G4C2 repeats associated with ALS and FTD. Biochem Biophys Res Commun 2022; 610:113-118. [DOI: 10.1016/j.bbrc.2022.03.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
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46
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Teng X, Dai Y, Li J. Methodological advances of bioanalysis and biochemical targeting of intracellular G-quadruplexes. EXPLORATION (BEIJING, CHINA) 2022; 2:20210214. [PMID: 37323879 PMCID: PMC10191030 DOI: 10.1002/exp.20210214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/11/2022] [Indexed: 06/17/2023]
Abstract
G-quadruplexes (G4s) are a kind of non-canonical nucleic acid secondary structures, which involve in various biological processes in living cells. The relationships between G4s and human diseases, such as tumors, neurodegenerative diseases, and viral infections, have attracted great attention in the last decade. G4s are considered as a promising new target for disease treatment. For instance, G4 ligands are reported to be potentially effective in SARS-COV-2 treatment. However, because of the lack of analytical methods with high performance for the identification of intracellular G4s, the detailed mechanisms of the biofunctions of G4s remain elusive. Meanwhile, through demonstrating the principles of how the G4s systematically modulate the cellular processes with advanced detection methods, biochemical targeting of G4s in living cells can be realized by chemical and biological tools and becomes useful in biomedicine. This review highlights recent methodological advances about intracellular G4s and provides an outlook on the improvement of the bioanalysis and biochemical targeting tools of G4s.
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Affiliation(s)
- Xucong Teng
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
| | - Yicong Dai
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
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47
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Ma Y, Li H, Gong Z, Yang S, Wang P, Tang C. Nucleobase Clustering Contributes to the Formation and Hollowing of Repeat-Expansion RNA Condensate. J Am Chem Soc 2022; 144:4716-4720. [PMID: 35179357 DOI: 10.1021/jacs.1c12085] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules with repeat expansion sequences can phase separate into gel-like condensate, which could lead to neurodegenerative diseases. Here, we report that, in the presence of Mg2+, RNA molecules containing 20× CAG repeats self-assemble into three morphologically distinct droplets. Using hyperspectral stimulated Raman microscopy, we show that RNA phase separation is accompanied by the clustering of nucleobases while forfeiting the canonical base-paired structure. As the RNA/Mg2+ ratio increases, the RNA droplets first expand and then shrink to adopt hollow vesicle-like structures. Significantly, for both large and vesicle-like RNA droplets, the nucleobase-clustered structure is more prominent at the rim, suggesting a continuously hardening process. This mechanism may be implicated in the general aging processes of RNA-containing membrane-less organelles.
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Affiliation(s)
- Yingxue Ma
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Haozheng Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Shuai Yang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ping Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Center for Computational Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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48
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Haldar S, Zhang Y, Xia Y, Islam B, Liu S, Gervasio FL, Mulholland AJ, Waller ZAE, Wei D, Haider S. Mechanistic Insights into the Ligand-Induced Unfolding of an RNA G-Quadruplex. J Am Chem Soc 2022; 144:935-950. [PMID: 34989224 DOI: 10.1021/jacs.1c11248] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The cationic porphyrin TMPyP4 is a well-established DNA G-quadruplex (G4) binding ligand that can stabilize different topologies via multiple binding modes. However, TMPyP4 can have both a stabilizing and destabilizing effect on RNA G4 structures. The structural mechanisms that mediate RNA G4 unfolding remain unknown. Here, we report on the TMPyP4-induced RNA G4 unfolding mechanism studied by well-tempered metadynamics (WT-MetaD) with supporting biophysical experiments. The simulations predict a two-state mechanism of TMPyP4 interaction via a groove-bound and a top-face-bound conformation. The dynamics of TMPyP4 stacking on the top tetrad disrupts Hoogsteen H-bonds between guanine bases, resulting in the consecutive TMPyP4 intercalation from top-to-bottom G-tetrads. The results reveal a striking correlation between computational and experimental approaches and validate WT-MetaD simulations as a powerful tool for studying RNA G4-ligand interactions.
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Affiliation(s)
- Susanta Haldar
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K
- D.E. Shaw India Private Ltd., Hyderabad, Telangana 500096, India
| | - Yashu Zhang
- State Key Laboratory of Agricultural Microbiology, College of Vetrinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Xia
- UCL School of Pharmacy, University College London, London, WC1N 1AX, U.K
| | - Barira Islam
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, U.K
| | - Sisi Liu
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Francesco L Gervasio
- Department of Chemistry, University College London, London, WC1H 0AJ, U.K
- Pharmaceutical Sciences, University of Geneva, Geneva CH-1211, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), Geneva CH-1211, Switzerland
| | | | - Zoë A E Waller
- UCL School of Pharmacy, University College London, London, WC1N 1AX, U.K
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Vetrinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London, WC1N 1AX, U.K
- UCL Centre for Advanced Research Computing, University College London, London, WC1H 9RN, U.K
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49
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Benson BC, Shaw PJ, Azzouz M, Highley JR, Hautbergue GM. Proteinopathies as Hallmarks of Impaired Gene Expression, Proteostasis and Mitochondrial Function in Amyotrophic Lateral Sclerosis. Front Neurosci 2022; 15:783624. [PMID: 35002606 PMCID: PMC8733206 DOI: 10.3389/fnins.2021.783624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/26/2021] [Indexed: 01/15/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal adult-onset neurodegenerative disease characterized by progressive degeneration of upper and lower motor neurons. As with the majority of neurodegenerative diseases, the pathological hallmarks of ALS involve proteinopathies which lead to the formation of various polyubiquitylated protein aggregates in neurons and glia. ALS is a highly heterogeneous disease, with both familial and sporadic forms arising from the convergence of multiple disease mechanisms, many of which remain elusive. There has been considerable research effort invested into exploring these disease mechanisms and in recent years dysregulation of RNA metabolism and mitochondrial function have emerged as of crucial importance to the onset and development of ALS proteinopathies. Widespread alterations of the RNA metabolism and post-translational processing of proteins lead to the disruption of multiple biological pathways. Abnormal mitochondrial structure, impaired ATP production, dysregulation of energy metabolism and calcium homeostasis as well as apoptosis have been implicated in the neurodegenerative process. Dysfunctional mitochondria further accumulate in ALS motor neurons and reflect a wider failure of cellular quality control systems, including mitophagy and other autophagic processes. Here, we review the evidence for RNA and mitochondrial dysfunction as some of the earliest critical pathophysiological events leading to the development of ALS proteinopathies, explore their relative pathological contributions and their points of convergence with other key disease mechanisms. This review will focus primarily on mutations in genes causing four major types of ALS (C9ORF72, SOD1, TARDBP/TDP-43, and FUS) and in protein homeostasis genes (SQSTM1, OPTN, VCP, and UBQLN2) as well as sporadic forms of the disease. Finally, we will look to the future of ALS research and how an improved understanding of central mechanisms underpinning proteinopathies might inform research directions and have implications for the development of novel therapeutic approaches.
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Affiliation(s)
- Bridget C Benson
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Pamela J Shaw
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Mimoun Azzouz
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.,Healthy Lifespan Institute (HELSI), University of Sheffield, Sheffield, United Kingdom
| | - J Robin Highley
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.,Healthy Lifespan Institute (HELSI), University of Sheffield, Sheffield, United Kingdom
| | - Guillaume M Hautbergue
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), 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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50
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Liano D, Monti L, Chowdhury S, Raguseo F, Di Antonio M. Long-range DNA interactions: inter-molecular G-quadruplexes and their potential biological relevance. Chem Commun (Camb) 2022; 58:12753-12762. [PMID: 36281554 PMCID: PMC9671097 DOI: 10.1039/d2cc04872h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Guanine-rich DNA sequences are known to fold into secondary structures called G-quadruplexes (G4s), which can form from either individual DNA strands (intra-molecular) or multiple DNA strands (inter-molecular, iG4s). Intra-molecular G4s have been the object of extensive biological investigation due to their enrichment in gene-promoters and telomers. On the other hand, iG4s have never been considered in biological contexts, as the interaction between distal sequences of DNA to form an iG4 in cells was always deemed as highly unlikely. In this feature article, we challenge this dogma by presenting our recent discovery of the first human protein (CSB) displaying astonishing picomolar affinity and binding selectivity for iG4s. These findings suggest potential for iG4 structures to form in cells and highlight the need of further studies to unravel the fundamental biological roles of these inter-molecular DNA structures. Furthermore, we discuss how the potential for formation of iG4s in neuronal cells, triggered by repeat expansions in the C9orf72 gene, can lead to the formation of nucleic-acids based pathological aggregates in neurodegenerative diseases like ALS and FTD. Finally, based on our recent work on short LNA-modified probes, we provide a prespective on how the rational design of G4-selective chemical tools can be leveraged to further elucidate the biological relevance of iG4 structures in the context of ageing-related diseases. Intermolecular G-quadruplex structures can form within distal region of genomic DNA, contributing to chromatin looping. Herein, we discuss recent evidence supporting formation of iG4s in living cells and their potential biological function.![]()
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Affiliation(s)
- Denise Liano
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
| | - Ludovica Monti
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Souroprobho Chowdhury
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Institute of Chemical Biology, Molecular Science Research Hub, 82 Wood Lane, W12 0BZ, London, UK
| | - Federica Raguseo
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Institute of Chemical Biology, Molecular Science Research Hub, 82 Wood Lane, W12 0BZ, London, UK
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
- The Institute of Chemical Biology, Molecular Science Research Hub, 82 Wood Lane, W12 0BZ, London, UK
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