1
|
Shukla C, Datta B. G-quadruplexes in long non-coding RNAs and their interactions with proteins. Int J Biol Macromol 2024; 278:134946. [PMID: 39187110 DOI: 10.1016/j.ijbiomac.2024.134946] [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: 06/07/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as crucial regulators of cellular processes, with their dysregulation linked to various disease states. Among the structural motifs in lncRNAs, RNA G-quadruplexes (rG4s) have gained increasing attention due to their diverse roles in cellular function and disease pathogenesis. This review provides an updated and comprehensive overview of rG4s in lncRNAs, elucidating their formation, interaction with proteins, and distinctive roles in cellular processes. We discuss current methodologies for experimentally probing RNA G4s, including the use of specific small molecules, biomolecular ligands and fluorescent probes. The commonly found RNA G4-interacting protein domains are summarised along with potential strategies for disrupting lncRNA G4-protein interactions from a therapeutic perspective.
Collapse
Affiliation(s)
- Chinmayee Shukla
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India
| | - Bhaskar Datta
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India; Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India.
| |
Collapse
|
2
|
Ghosh A, Pandey S, Joshi D, Rana P, Ansari A, Sundar J, Singh P, Khan Y, Ekka M, Chakraborty D, Maiti S. Identification of G-quadruplex structures in MALAT1 lncRNA that interact with nucleolin and nucleophosmin. Nucleic Acids Res 2023; 51:9415-9431. [PMID: 37558241 PMCID: PMC11314421 DOI: 10.1093/nar/gkad639] [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: 07/24/2022] [Accepted: 07/13/2023] [Indexed: 08/11/2023] Open
Abstract
Nuclear-retained long non-coding RNAs (lncRNAs) including MALAT1 have emerged as critical regulators of many molecular processes including transcription, alternative splicing and chromatin organization. Here, we report the presence of three conserved and thermodynamically stable RNA G-quadruplexes (rG4s) located in the 3' region of MALAT1. Using rG4 domain-specific RNA pull-down followed by mass spectrometry and RNA immunoprecipitation, we demonstrated that the MALAT1 rG4 structures are specifically bound by two nucleolar proteins, Nucleolin (NCL) and Nucleophosmin (NPM). Using imaging, we found that the MALAT1 rG4s facilitate the localization of both NCL and NPM to nuclear speckles, and specific G-to-A mutations that disrupt the rG4 structures compromised the localization of both NCL and NPM in speckles. In vitro biophysical studies established that a truncated version of NCL (ΔNCL) binds tightly to all three rG4s. Overall, our study revealed new rG4s within MALAT1, established that they are specifically recognized by NCL and NPM, and showed that disrupting the rG4s abolished localization of these proteins to nuclear speckles.
Collapse
Affiliation(s)
- Arpita Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Satya Prakash Pandey
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Dheeraj Chandra Joshi
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Priya Rana
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Asgar Hussain Ansari
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | | | - Praveen Singh
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Yasmeen Khan
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune
411 008, India
| |
Collapse
|
3
|
Tonello F, Massimino ML, Peggion C. Nucleolin: a cell portal for viruses, bacteria, and toxins. Cell Mol Life Sci 2022; 79:271. [PMID: 35503380 PMCID: PMC9064852 DOI: 10.1007/s00018-022-04300-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 12/18/2022]
Abstract
The main localization of nucleolin is the nucleolus, but this protein is present in multiple subcellular sites, and it is unconventionally secreted. On the cell surface, nucleolin acts as a receptor for various viruses, some bacteria, and some toxins. Aim of this review is to discuss the characteristics that make nucleolin able to act as receptor or co-receptor of so many and different pathogens. The important features that emerge are its multivalence, and its role as a bridge between the cell surface and the nucleus. Multiple domains, short linear motifs and post-translational modifications confer and modulate nucleolin ability to interact with nucleic acids, with proteins, but also with carbohydrates and lipids. This modular multivalence allows nucleolin to participate in different types of biomolecular condensates and to move to various subcellular locations, where it can act as a kind of molecular glue. It moves from the nucleus to the cell surface and can accompany particles in the reverse direction, from the cell surface into the nucleus, which is the destination of several pathogens to manipulate the cell in their favour.
Collapse
Affiliation(s)
- Fiorella Tonello
- CNR of Italy, Neuroscience Institute, viale G. Colombo 3, 35131, Padua, Italy.
| | | | - Caterina Peggion
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi, 58/B, 35131, Padua, Italy
| |
Collapse
|
4
|
Ghosh A, Pandey SP, Ansari AH, Sundar J, Singh P, Khan Y, Ekka MK, Chakraborty D, Maiti S. Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA. Nucleic Acids Res 2022; 50:378-396. [PMID: 34761272 PMCID: PMC8754661 DOI: 10.1093/nar/gkab1066] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
MALAT1, an abundant lncRNA specifically localized to nuclear speckles, regulates alternative-splicing (AS). The molecular basis of its role in AS remains poorly understood. Here, we report three conserved, thermodynamically stable, parallel RNA-G-quadruplexes (rG4s) present in the 3' region of MALAT1 which regulates this function. Using rG4 domain-specific RNA-pull-down followed by mass-spectrometry, RNA-immuno-precipitation, and imaging, we demonstrate the rG4 dependent localization of Nucleolin (NCL) and Nucleophosmin (NPM) to nuclear speckles. Specific G-to-A mutations that abolish rG4 structures, result in the localization loss of both the proteins from speckles. Functionally, disruption of rG4 in MALAT1 phenocopies NCL knockdown resulting in altered pre-mRNA splicing of endogenous genes. These results reveal a central role of rG4s within the 3' region of MALAT1 orchestrating AS.
Collapse
Affiliation(s)
- Arpita Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Satya Prakash Pandey
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Asgar Hussain Ansari
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | | | - Praveen Singh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Yasmeen Khan
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| |
Collapse
|
5
|
Shefer K, Boulos A, Gotea V, Arafat M, Ben Chaim Y, Muharram A, Isaac S, Eden A, Sperling J, Elnitski L, Sperling R. A novel role for nucleolin in splice site selection. RNA Biol 2021; 19:333-352. [PMID: 35220879 PMCID: PMC8890436 DOI: 10.1080/15476286.2021.2020455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 12/10/2021] [Indexed: 01/12/2023] Open
Abstract
Latent 5' splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and specifically with initiator-tRNA in the nucleus, but not in the cytoplasm. Next, we show the association of ini-tRNA and NCL with pre-mRNA. We further show that recovery of suppression of latent splicing by initiator-tRNA complementation is NCL dependent. Finally, upon nucleolin knockdown we show activation of latent splicing in hundreds of coding transcripts having important cellular functions. We thus propose nucleolin, a component of the endogenous spliceosome, through its direct binding to initiator-tRNA and its effect on latent splicing, as the first protein of a nuclear quality control mechanism regulating splice site selection to protect cells from latent splicing that can generate defective mRNAs.
Collapse
Affiliation(s)
- Kinneret Shefer
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Ayub Boulos
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Maram Arafat
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Yair Ben Chaim
- Department of Natural Sciences, The Open University, RaananaIsrael
| | - Aya Muharram
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Sara Isaac
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Amir Eden
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, RehovotIsrael
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| |
Collapse
|