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Khan FA, Fang N, Zhang W, Ji S. The multifaceted role of Fragile X-Related Protein 1 (FXR1) in cellular processes: an updated review on cancer and clinical applications. Cell Death Dis 2024; 15:72. [PMID: 38238286 PMCID: PMC10796922 DOI: 10.1038/s41419-023-06413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
RNA-binding proteins (RBPs) modulate the expression level of several target RNAs (such as mRNAs) post-transcriptionally through interactions with unique binding sites in the 3'-untranslated region. There is mounting information that suggests RBP dysregulation plays a significant role in carcinogenesis. However, the function of FMR1 autosomal homolog 1(FXR1) in malignancies is just beginning to be unveiled. Due to the diversity of their RNA-binding domains and functional adaptability, FXR1 can regulate diverse transcript processing. Changes in FXR1 interaction with RNA networks have been linked to the emergence of cancer, although the theoretical framework defining these alterations in interaction is insufficient. Alteration in FXR1 expression or localization has been linked to the mRNAs of cancer suppressor genes, cancer-causing genes, and genes involved in genomic expression stability. In particular, FXR1-mediated gene regulation involves in several cellular phenomena related to cancer growth, metastasis, epithelial-mesenchymal transition, senescence, apoptosis, and angiogenesis. FXR1 dysregulation has been implicated in diverse cancer types, suggesting its diagnostic and therapeutic potential. However, the molecular mechanisms and biological effects of FXR1 regulation in cancer have yet to be understood. This review highlights the current knowledge of FXR1 expression and function in various cancer situations, emphasizing its functional variety and complexity. We further address the challenges and opportunities of targeting FXR1 for cancer diagnosis and treatment and propose future directions for FXR1 research in oncology. This work intends to provide an in-depth review of FXR1 as an emerging oncotarget with multiple roles and implications in cancer biology and therapy.
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Affiliation(s)
- Faiz Ali Khan
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Na Fang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Weijuan Zhang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Shaoping Ji
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
- Zhengzhou Shuqing Medical College, Zhengzhou, China.
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2
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Hayek H, Gross L, Alghoul F, Martin F, Eriani G, Allmang C. Immunoprecipitation Methods to Isolate Messenger Ribonucleoprotein Complexes (mRNP). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:1-15. [PMID: 38507196 DOI: 10.1007/978-3-031-52193-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Throughout their life cycle, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Each mRNA is part of multiple successive mRNP complexes that participate in their biogenesis, cellular localization, translation and decay. The dynamic composition of mRNP complexes and their structural remodelling play crucial roles in the control of gene expression. Studying the endogenous composition of different mRNP complexes is a major challenge. In this chapter, we describe the variety of protein-centric immunoprecipitation methods available for the identification of mRNP complexes and the requirements for their experimental settings.
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Affiliation(s)
- Hassan Hayek
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Lauriane Gross
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Fatima Alghoul
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Franck Martin
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Christine Allmang
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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Jiang F, Hedaya OM, Khor E, Wu J, Auguste M, Yao P. RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression. Nucleic Acids Res 2023; 51:5831-5846. [PMID: 37125639 PMCID: PMC10287950 DOI: 10.1093/nar/gkad322] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/28/2023] [Accepted: 04/24/2023] [Indexed: 05/02/2023] Open
Abstract
Accumulating evidence suggests that posttranscriptional control of gene expression, including RNA splicing, transport, modification, translation and degradation, primarily relies on RNA binding proteins (RBPs). However, the functions of many RBPs remain understudied. Here, we characterized the function of a novel RBP, Proline-Rich Coiled-coil 2B (PRRC2B). Through photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation and sequencing (PAR-CLIP-seq), we identified transcriptome-wide CU- or GA-rich PRRC2B binding sites near the translation initiation codon on a specific cohort of mRNAs in HEK293T cells. These mRNAs, including oncogenes and cell cycle regulators such as CCND2 (cyclin D2), exhibited decreased translation upon PRRC2B knockdown as revealed by polysome-associated RNA-seq, resulting in reduced G1/S phase transition and cell proliferation. Antisense oligonucleotides blocking PRRC2B interactions with CCND2 mRNA decreased its translation, thus inhibiting G1/S transition and cell proliferation. Mechanistically, PRRC2B interactome analysis revealed RNA-independent interactions with eukaryotic translation initiation factors 3 (eIF3) and 4G2 (eIF4G2). The interaction with translation initiation factors is essential for PRRC2B function since the eIF3/eIF4G2-interacting defective mutant, unlike wild-type PRRC2B, failed to rescue the translation deficiency or cell proliferation inhibition caused by PRRC2B knockdown. Altogether, our findings reveal that PRRC2B is essential for efficiently translating specific proteins required for cell cycle progression and cell proliferation.
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Affiliation(s)
- Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Omar M Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - EngSoon Khor
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Matthew Auguste
- Undergraduate Program in Biology and Medicine, Department of Biological Sciences: Molecular Genetics, University of Rochester, Rochester, NY 14642, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
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Uppala JK, Ghosh C, Sabat G, Dey M. Pull-down of Biotinylated RNA and Associated Proteins. Bio Protoc 2022; 12:e4331. [PMID: 35340298 PMCID: PMC8899547 DOI: 10.21769/bioprotoc.4331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/28/2021] [Accepted: 01/05/2022] [Indexed: 09/23/2023] Open
Abstract
Mapping networks of RNA-protein interactions in cells is essential for understanding the inner workings of many biological processes, including RNA processing, trafficking, and translation. Current in vivo methods for studying protein-RNA interactions rely mostly on purification of poly(A) transcripts, which represent only ~2-3% of total RNAs (Figure 1). Alternate robust methods for tagging RNA molecules with an RNA aptamer (e.g., MS2-, U1A- and biotin-RNA aptamer) and capturing the RNA-protein complex by the respective aptamer-specific partner are not extensively studied. Here, we describe a protocol (Figure 2) in which a biotin-RNA aptamer, referred to as the RNA mimic of biotin (RMB), was conjugated separately to two small RNA secondary structures that contribute to trafficking and translating HAC1 mRNA in the budding yeast Saccharomyces cerevisiae. The RMB-tagged RNA was expressed in yeast cells from a constitutive promoter. The biotinylated RNA bound to proteins was pulled down from the cell lysate by streptavidin agarose beads. RNA was detected by RT-PCR (Figure 3) and associated proteins by mass spectrometry (Figure 4). Our findings show that an RNA aptamer tag to RNA molecule is an effective method to explore the functional roles of RNA-protein networks in vivo.
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Affiliation(s)
- Jagadeesh K. Uppala
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, 3209 N Maryland Ave, WI-53211, USA
| | - Chandrima Ghosh
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, 3209 N Maryland Ave, WI-53211, USA
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Madhusudan Dey
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, 3209 N Maryland Ave, WI-53211, USA
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Balcerak A, Trebinska-Stryjewska A, Konopinski R, Wakula M, Grzybowska EA. RNA-protein interactions: disorder, moonlighting and junk contribute to eukaryotic complexity. Open Biol 2019; 9:190096. [PMID: 31213136 PMCID: PMC6597761 DOI: 10.1098/rsob.190096] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
RNA-protein interactions are crucial for most biological processes in all organisms. However, it appears that the complexity of RNA-based regulation increases with the complexity of the organism, creating additional regulatory circuits, the scope of which is only now being revealed. It is becoming apparent that previously unappreciated features, such as disordered structural regions in proteins or non-coding regions in DNA leading to higher plasticity and pliability in RNA-protein complexes, are in fact essential for complex, precise and fine-tuned regulation. This review addresses the issue of the role of RNA-protein interactions in generating eukaryotic complexity, focusing on the newly characterized disordered RNA-binding motifs, moonlighting of metabolic enzymes, RNA-binding proteins interactions with different RNA species and their participation in regulatory networks of higher order.
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Affiliation(s)
- Anna Balcerak
- 1 The Maria Sklodowska-Curie Institute-Oncology Center , Roentgena 5, 02-781 Warsaw , Poland
| | - Alicja Trebinska-Stryjewska
- 1 The Maria Sklodowska-Curie Institute-Oncology Center , Roentgena 5, 02-781 Warsaw , Poland.,2 Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology , Sylwestra Kaliskiego 2, 00-908 Warsaw , Poland
| | - Ryszard Konopinski
- 1 The Maria Sklodowska-Curie Institute-Oncology Center , Roentgena 5, 02-781 Warsaw , Poland
| | - Maciej Wakula
- 1 The Maria Sklodowska-Curie Institute-Oncology Center , Roentgena 5, 02-781 Warsaw , Poland
| | - Ewa Anna Grzybowska
- 1 The Maria Sklodowska-Curie Institute-Oncology Center , Roentgena 5, 02-781 Warsaw , Poland
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Levi O, Arava Y. mRNA association by aminoacyl tRNA synthetase occurs at a putative anticodon mimic and autoregulates translation in response to tRNA levels. PLoS Biol 2019; 17:e3000274. [PMID: 31100060 PMCID: PMC6542539 DOI: 10.1371/journal.pbio.3000274] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 05/30/2019] [Accepted: 05/02/2019] [Indexed: 12/25/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are well studied for their role in binding and charging tRNAs with cognate amino acids. Recent RNA interactome studies had suggested that these enzymes can also bind polyadenylated RNAs. Here, we explored the mRNA repertoire bound by several yeast aaRSs. RNA immunoprecipitation (RIP) followed by deep sequencing revealed unique sets of mRNAs bound by each aaRS. Interestingly, for every tested aaRSs, a preferential association with its own mRNA was observed, suggesting an autoregulatory process. Self-association of histidyl-tRNA synthetase (HisRS) was found to be mediated primarily through binding to a region predicted to fold into a tRNAHis anticodon-like structure. Introducing point mutations that are expected to disassemble this putative anticodon mimic alleviated self-association, concomitant with increased synthesis of the protein. Finally, we found that increased cellular levels of uncharged tRNAHis lead to reduced self-association and increased HisRS translation, in a manner that depends on the anticodon-like element. Together, these results reveal a novel post-transcriptional autoregulatory mechanism that exploits binding mimicry to control mRNA translation according to tRNA demands. Better known for their enzymatic role in charging tRNAs with their cognate amino acids, this study shows that tRNA synthetases also bind mRNAs, regulating translation in order to balance the production of a tRNA synthetase with the level of its cognate tRNA.
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Affiliation(s)
- Ofri Levi
- Faculty of Biology, Technion, Israel Institute of Technology, Haifa, Israel
| | - Yoav Arava
- Faculty of Biology, Technion, Israel Institute of Technology, Haifa, Israel
- * E-mail:
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Beckmann BM, Granneman S. Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and Challenges. Methods Mol Biol 2019; 2049:213-231. [PMID: 31602614 DOI: 10.1007/978-1-4939-9736-7_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA-binding proteins are important for core cellular processes such as mRNA transcription, splicing, transport, translation, and degradation. Recently, hundreds of novel RNA-binders have been identified in vivo in various organisms and cell types. We discuss the RNA interactome capture technique which enabled this boost in identifying new RNA-binding proteins in eukaryotes. A focus of this chapter, however, is the presentation of different challenges and problems that need to be addressed to be able to understand the conserved mRNA-bound proteomes from yeast to man.
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Affiliation(s)
- Benedikt M Beckmann
- Molecular Infection Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Sander Granneman
- Centre for Systems and Synthetic Biology (SynthSys), University of Edinburgh, Edinburgh, UK
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8
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Lipshitz HD, Claycomb JM, Smibert CA. Post-transcriptional regulation of gene expression. Methods 2017; 126:1-2. [DOI: 10.1016/j.ymeth.2017.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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