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Li G, Zhao B, Su X, Yang Y, Hu P, Zhou X, Hu L. Discovering Consensus Regions for Interpretable Identification of RNA N6-Methyladenosine Modification Sites via Graph Contrastive Clustering. IEEE J Biomed Health Inform 2024; 28:2362-2372. [PMID: 38265898 DOI: 10.1109/jbhi.2024.3357979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
As a pivotal post-transcriptional modification of RNA, N6-methyladenosine (m6A) has a substantial influence on gene expression modulation and cellular fate determination. Although a variety of computational models have been developed to accurately identify potential m6A modification sites, few of them are capable of interpreting the identification process with insights gained from consensus knowledge. To overcome this problem, we propose a deep learning model, namely M6A-DCR, by discovering consensus regions for interpretable identification of m6A modification sites. In particular, M6A-DCR first constructs an instance graph for each RNA sequence by integrating specific positions and types of nucleotides. The discovery of consensus regions is then formulated as a graph clustering problem in light of aggregating all instance graphs. After that, M6A-DCR adopts a motif-aware graph reconstruction optimization process to learn high-quality embeddings of input RNA sequences, thus achieving the identification of m6A modification sites in an end-to-end manner. Experimental results demonstrate the superior performance of M6A-DCR by comparing it with several state-of-the-art identification models. The consideration of consensus regions empowers our model to make interpretable predictions at the motif level. The analysis of cross validation through different species and tissues further verifies the consistency between the identification results of M6A-DCR and the evolutionary relationships among species.
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Takeiwa T, Ikeda K, Horie K, Inoue S. Role of RNA binding proteins of the Drosophila behavior and human splicing (DBHS) family in health and cancer. RNA Biol 2024; 21:1-17. [PMID: 38551131 PMCID: PMC10984136 DOI: 10.1080/15476286.2024.2332855] [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] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
RNA-binding proteins (RBPs) play crucial roles in the functions and homoeostasis of various tissues by regulating multiple events of RNA processing including RNA splicing, intracellular RNA transport, and mRNA translation. The Drosophila behavior and human splicing (DBHS) family proteins including PSF/SFPQ, NONO, and PSPC1 are ubiquitously expressed RBPs that contribute to the physiology of several tissues. In mammals, DBHS proteins have been reported to contribute to neurological diseases and play crucial roles in cancers, such as prostate, breast, and liver cancers, by regulating cancer-specific gene expression. Notably, in recent years, multiple small molecules targeting DBHS family proteins have been developed for application as cancer therapeutics. This review provides a recent overview of the functions of DBHS family in physiology and pathophysiology, and discusses the application of DBHS family proteins as promising diagnostic and therapeutic targets for cancers.
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Affiliation(s)
- Toshihiko Takeiwa
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo, Japan
| | - Kazuhiro Ikeda
- Division of Systems Medicine & Gene Therapy, Faculty of Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Kuniko Horie
- Division of Systems Medicine & Gene Therapy, Faculty of Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo, Japan
- Division of Systems Medicine & Gene Therapy, Faculty of Medicine, Saitama Medical University, Hidaka, Saitama, Japan
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Yoshimoto R, Nakayama Y, Nomura I, Yamamoto I, Nakagawa Y, Tanaka S, Kurihara M, Suzuki Y, Kobayashi T, Kozuka-Hata H, Oyama M, Mito M, Iwasaki S, Yamazaki T, Hirose T, Araki K, Nakagawa S. 4.5SH RNA counteracts deleterious exonization of SINE B1 in mice. Mol Cell 2023; 83:4479-4493.e6. [PMID: 38096826 DOI: 10.1016/j.molcel.2023.11.019] [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: 05/04/2023] [Revised: 10/09/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023]
Abstract
4.5SH RNA is a highly abundant, small rodent-specific noncoding RNA that localizes to nuclear speckles enriched in pre-mRNA-splicing regulators. To investigate the physiological functions of 4.5SH RNA, we have created mutant mice that lack the expression of 4.5SH RNA. The mutant mice exhibited embryonic lethality, suggesting that 4.5SH RNA is an essential species-specific noncoding RNA in mice. RNA-sequencing analyses revealed that 4.5SH RNA protects the transcriptome from abnormal exonizations of the antisense insertions of the retrotransposon SINE B1 (asB1), which would otherwise introduce deleterious premature stop codons or frameshift mutations. Mechanistically, 4.5SH RNA base pairs with complementary asB1-containing exons via the target recognition region and recruits effector proteins including Hnrnpm via its 5' stem loop region. The modular organization of 4.5SH RNA allows us to engineer a programmable splicing regulator to induce the skipping of target exons of interest. Our results also suggest the general existence of splicing regulatory noncoding RNAs.
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Affiliation(s)
- Rei Yoshimoto
- Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata City, Osaka 573-0101, Japan.
| | - Yuta Nakayama
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Ikuko Nomura
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Ikuko Yamamoto
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Yumeka Nakagawa
- Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata City, Osaka 573-0101, Japan
| | - Shigeyuki Tanaka
- Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata City, Osaka 573-0101, Japan
| | - Misuzu Kurihara
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Yu Suzuki
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Tomohiro Yamazaki
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuro Hirose
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan; Center for Metabolic Regulation of Healthy Aging, Kumamoto University, 1-1-1, Honjo, Kumamoto 860-8556, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan.
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Takakuwa H, Yamazaki T, Souquere S, Adachi S, Yoshino H, Fujiwara N, Yamamoto T, Natsume T, Nakagawa S, Pierron G, Hirose T. Shell protein composition specified by the lncRNA NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles. Nat Cell Biol 2023; 25:1664-1675. [PMID: 37932453 DOI: 10.1038/s41556-023-01254-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 09/12/2023] [Indexed: 11/08/2023]
Abstract
Many membraneless organelles (MLOs) formed through phase separation play crucial roles in various cellular processes. Although these MLOs co-exist in cells, how they maintain their independence without coalescence or engulfment remains largely unknown. Here, we investigated the molecular mechanism by which paraspeckles with core-shell architecture scaffolded by NEAT1_2 long noncoding RNAs exist as distinct MLOs. We identified NEAT1 deletion mutants that assemble paraspeckles that are incorporated into nuclear speckles. Several paraspeckle proteins, including SFPQ, HNRNPF and BRG1, prevent this incorporation and thus contribute to the segregation of paraspeckles from nuclear speckles. Shell localization of these proteins in the paraspeckles, which is determined by NEAT1_2 long noncoding RNA domains, is required for this segregation process. Conversely, U2-related spliceosomal proteins are involved in internalizing the paraspeckles into nuclear speckles. This study shows that the paraspeckle shell composition dictates the independence of MLOs in the nucleus, providing insights into the importance of the shell in defining features and functions of MLOs.
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Affiliation(s)
- Hiro Takakuwa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
| | | | - Shungo Adachi
- Department of Proteomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hyura Yoshino
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Naoko Fujiwara
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan
| | - Tohru Natsume
- Cellular and Molecular Biotechnology Research Institute, National Institute for Advanced Industrial Science and Technology, Tokyo, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Gerard Pierron
- Centre National de la Recherche Scientifique, UMR-9196, Gustave Roussy, Villejuif, France
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
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Zhang S, Cooper JAL, Chong YS, Naveed A, Mayoh C, Jayatilleke N, Liu T, Amos S, Kobelke S, Marshall AC, Meers O, Choi YS, Bond CS, Fox AH. NONO enhances mRNA processing of super-enhancer-associated GATA2 and HAND2 genes in neuroblastoma. EMBO Rep 2023; 24:e54977. [PMID: 36416237 PMCID: PMC9900351 DOI: 10.15252/embr.202254977] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
High-risk neuroblastoma patients have poor survival rates and require better therapeutic options. High expression of a multifunctional DNA and RNA-binding protein, NONO, in neuroblastoma is associated with poor patient outcome; however, there is little understanding of the mechanism of NONO-dependent oncogenic gene regulatory activity in neuroblastoma. Here, we used cell imaging, biochemical and genome-wide molecular analysis to reveal complex NONO-dependent regulation of gene expression. NONO forms RNA- and DNA-tethered condensates throughout the nucleus and undergoes phase separation in vitro, modulated by nucleic acid binding. CLIP analyses show that NONO mainly binds to the 5' end of pre-mRNAs and modulates pre-mRNA processing, dependent on its RNA-binding activity. NONO regulates super-enhancer-associated genes, including HAND2 and GATA2. Abrogating NONO RNA binding, or phase separation activity, results in decreased expression of HAND2 and GATA2. Thus, future development of agents that target RNA-binding activity of NONO may have therapeutic potential in this cancer context.
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Affiliation(s)
- Song Zhang
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Jack AL Cooper
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Yee Seng Chong
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Alina Naveed
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Chelsea Mayoh
- Children's Cancer Institute AustraliaRandwickNSWAustralia
- Centre for Childhood Cancer ResearchUNSW SydneyKensingtonNSWAustralia
- School of Women's and Children's HealthUNSW SydneyKensingtonNSWAustralia
| | - Nisitha Jayatilleke
- Children's Cancer Institute AustraliaRandwickNSWAustralia
- Centre for Childhood Cancer ResearchUNSW SydneyKensingtonNSWAustralia
| | - Tao Liu
- Children's Cancer Institute AustraliaRandwickNSWAustralia
- Centre for Childhood Cancer ResearchUNSW SydneyKensingtonNSWAustralia
| | - Sebastian Amos
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Simon Kobelke
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Andrew C Marshall
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Oliver Meers
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Yu Suk Choi
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Charles S Bond
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Archa H Fox
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
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Nagai T, Terada N, Fujii M, Nagata Y, Nakahara K, Mukai S, Okasho K, Kamiyama Y, Akamatsu S, Kobayashi T, Iida K, Denawa M, Hagiwara M, Inoue T, Ogawa O, Kamoto T. Identification of the α2 chain of interleukin-13 receptor as a potential biomarker for predicting castration resistance of prostate cancer using patient-derived xenograft models. Cancer Rep (Hoboken) 2023; 6:e1701. [PMID: 36806727 PMCID: PMC9939991 DOI: 10.1002/cnr2.1701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/30/2022] [Accepted: 07/31/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Several treatment strategies use upfront chemotherapy or androgen receptor axis-targeting therapies for metastatic prostate cancer. However, there are no useful biomarkers for selecting appropriate patients who urgently require these treatments. METHODS Novel patient-derived xenograft (PDX) castration-sensitive and -resistant models were established and gene expression patterns were comprehensively compared. The function of a gene highly expressed in the castration-resistant models was evaluated by its overexpression in LNCaP prostate cancer cells. Protein expression in the tumors and serum of patients was examined by immunohistochemistry and ELISA, and correlations with castration resistance were analyzed. RESULTS Expression of the α2 chain of interleukin-13 receptor (IL13Rα2) was higher in castration-resistant PDX tumors. LNCaP cells overexpressing IL13Rα2 acquired castration resistance in vitro and in vivo. In tissue samples, IL13Rα2 expression levels were significantly associated with castration-resistant progression (p < 0.05). In serum samples, IL13Rα2 levels could be measured in 5 of 28 (18%) castration-resistant prostate cancer patients. CONCLUSION IL13Rα2 was highly expressed in castration-resistant prostate cancer PDX models and was associated with the castration resistance of prostate cancer cells. It might be a potential tissue and serum biomarker for predicting castration resistance in prostate cancer patients.
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Affiliation(s)
- Takahiro Nagai
- Department of UrologyMiyazaki University Graduate School of MedicineMiyazakiJapan
| | - Naoki Terada
- Department of UrologyMiyazaki University Graduate School of MedicineMiyazakiJapan
| | - Masato Fujii
- Department of UrologyMiyazaki University Graduate School of MedicineMiyazakiJapan
| | - Yasuhisa Nagata
- Department of UrologyMiyazaki University Graduate School of MedicineMiyazakiJapan
| | - Kozue Nakahara
- Department of UrologyMiyazaki University Graduate School of MedicineMiyazakiJapan
| | - Shoichiro Mukai
- Department of UrologyMiyazaki University Graduate School of MedicineMiyazakiJapan
| | - Kosuke Okasho
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Yuki Kamiyama
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Shusuke Akamatsu
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Takashi Kobayashi
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Kei Iida
- Medical Research Support Center, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Masatsugu Denawa
- Medical Research Support Center, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Takahiro Inoue
- Department of Nephro‐Urologic Surgery and AndrologyMie University Graduate School of MedicineTsuJapan
| | - Osamu Ogawa
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Toshiyuki Kamoto
- Department of UrologyMiyazaki University Graduate School of MedicineMiyazakiJapan
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Shadrina OA, Kikhay TF, Agapkina YY, Gottikh MB. SFPQ and NONO Proteins and Long Non-Coding NEAT1 RNA: Cellular Functions and Role in the HIV-1 Life Cycle. Mol Biol 2022. [DOI: 10.1134/s0026893322020133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Stagsted LVW, O'Leary ET, Ebbesen KK, Hansen TB. The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis in mammals. eLife 2021; 10:e63088. [PMID: 33476259 PMCID: PMC7819710 DOI: 10.7554/elife.63088] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) represent an abundant and conserved entity of non-coding RNAs; however, the principles of biogenesis are currently not fully understood. Here, we identify two factors, splicing factor proline/glutamine rich (SFPQ) and non-POU domain-containing octamer-binding protein (NONO), to be enriched around circRNA loci. We observe a subclass of circRNAs, coined DALI circRNAs, with distal inverted Alu elements and long flanking introns to be highly deregulated upon SFPQ knockdown. Moreover, SFPQ depletion leads to increased intron retention with concomitant induction of cryptic splicing, premature transcription termination, and polyadenylation, particularly prevalent for long introns. Aberrant splicing in the upstream and downstream regions of circRNA producing exons are critical for shaping the circRNAome, and specifically, we identify missplicing in the immediate upstream region to be a conserved driver of circRNA biogenesis. Collectively, our data show that SFPQ plays an important role in maintaining intron integrity by ensuring accurate splicing of long introns, and disclose novel features governing Alu-independent circRNA production.
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The Emerging Role of the RNA-Binding Protein SFPQ in Neuronal Function and Neurodegeneration. Int J Mol Sci 2020; 21:ijms21197151. [PMID: 32998269 PMCID: PMC7582472 DOI: 10.3390/ijms21197151] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are a class of proteins known for their diverse roles in RNA biogenesis, from regulating transcriptional processes in the nucleus to facilitating translation in the cytoplasm. With higher demand for RNA metabolism in the nervous system, RBP misregulation has been linked to a wide range of neurological and neurodegenerative diseases. One of the emerging RBPs implicated in neuronal function and neurodegeneration is splicing factor proline- and glutamine-rich (SFPQ). SFPQ is a ubiquitous and abundant RBP that plays multiple regulatory roles in the nucleus such as paraspeckle formation, DNA damage repair, and various transcriptional regulation processes. An increasing number of studies have demonstrated the nuclear and also cytoplasmic roles of SFPQ in neurons, particularly in post-transcriptional regulation and RNA granule formation. Not surprisingly, the misregulation of SFPQ has been linked to pathological features shown by other neurodegenerative disease-associated RBPs such as aberrant RNA splicing, cytoplasmic mislocalization, and aggregation. In this review, we discuss recent findings on the roles of SFPQ with a particular focus on those in neuronal development and homeostasis as well as its implications in neurodegenerative diseases.
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