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Hu Y, Li Y, Xiong H, Zhang Y, Wang F, Zhuo W, Zeng Z, Zhao Y, Wang H, Hu P, Han S, Huang Y, Lv G, Zhao G. Exosomal SLC16A1-AS1-induced M2 macrophages polarization facilitates hepatocellular carcinoma progression. Int J Biol Sci 2024; 20:4341-4363. [PMID: 39247822 PMCID: PMC11379075 DOI: 10.7150/ijbs.94440] [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: 01/18/2024] [Accepted: 07/09/2024] [Indexed: 09/10/2024] Open
Abstract
Macrophages are the most abundant alternative immune cells in the tumor microenvironment (TME). The cross-talk between macrophages and tumor cells provides an important shelter for the occurrence and development of tumors. As an important information transfer medium, exosomes play an important role in intercellular communication. Nonetheless, how exosomal lncRNAs coordinate the communication between tumor cells and immune cells in hepatocellular carcinoma (HCC) is incompletely understood. We found that HCC exosomes-derived antisense RNA of SLC16A1(SLC16A1-AS1) promoted the malignant progression of HCC by regulating macrophage M2-type polarization. Mechanistically, the HCC exosomal SLC16A1-AS1 enhanced mRNA stabilization of SLC16A1 in macrophage by promoting the interaction between 3' untranslated regions (3'UTR) of SLC16A1 mRNA and heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1). As a lactate transporter, SLC16A1 accelerated lactate influx and then activated c-Raf/ERK signaling to induce M2 polarization of macrophages. Reciprocally, M2 macrophages secreted IL-6 to activate STAT3 and then induce METTL3 transcription in HCC cells, which increasing m6A methylation and stabilization of SLC16A1-AS1. In turn, the reciprocal SLC16A1-AS1/IL-6 signaling between HCC cells and M2 macrophages promoted the proliferation, invasion and glycolysis of HCC cells. Our study highlights that exosomal SLC16A1-AS1 acts as a signaling message that induces lactate-mediated M2 polarization of macrophages, and implies that SLC16A1-AS1 might be an applicable target for therapeutic treatment of HCC.
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Affiliation(s)
- Yuhang Hu
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yang Li
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hewei Xiong
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ya Zhang
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Fan Wang
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wenfeng Zhuo
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhu Zeng
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yong Zhao
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongda Wang
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ping Hu
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shengbo Han
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yan Huang
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Guozheng Lv
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Gang Zhao
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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Levengood JD, Potoyan D, Penumutchu S, Kumar A, Zhou Q, Wang Y, Hansen AL, Kutluay S, Roche J, Tolbert BS. Thermodynamic coupling of the tandem RRM domains of hnRNP A1 underlie its pleiotropic RNA binding functions. SCIENCE ADVANCES 2024; 10:eadk6580. [PMID: 38985864 PMCID: PMC11235170 DOI: 10.1126/sciadv.adk6580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
The functional properties of RNA binding proteins (RBPs) require allosteric regulation through interdomain communication. Despite the importance of allostery to biological regulation, only a few studies have been conducted to describe the biophysical nature by which interdomain communication manifests in RBPs. Here, we show for hnRNP A1 that interdomain communication is vital for the unique stability of its amino-terminal domain, which consists of two RNA recognition motifs (RRMs). These RRMs exhibit drastically different stability under pressure. RRM2 unfolds as an individual domain but remains stable when appended to RRM1. Variants that disrupt interdomain communication between the tandem RRMs show a significant decrease in stability. Carrying these mutations over to the full-length protein for in vivo experiments revealed that the mutations affected the ability of the disordered carboxyl-terminal domain to engage in protein-protein interactions and influenced the protein's RNA binding capacity. Collectively, this work reveals that thermodynamic coupling between the tandem RRMs of hnRNP A1 accounts for its allosteric regulatory functions.
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Affiliation(s)
- Jeffrey D. Levengood
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Davit Potoyan
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Srinivasa Penumutchu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Abhishek Kumar
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Qianzi Zhou
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yiqing Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alexandar L. Hansen
- CCIC and Gateway NMR Facility, The Ohio State University, Columbus, OH 43210, USA
| | - Sebla Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Blanton S. Tolbert
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Abedeera SM, Davila-Calderon J, Haddad C, Henry B, King J, Penumutchu S, Tolbert BS. The Repurposing of Cellular Proteins during Enterovirus A71 Infection. Viruses 2023; 16:75. [PMID: 38257775 PMCID: PMC10821071 DOI: 10.3390/v16010075] [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: 12/09/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Viruses pose a great threat to people's lives. Enterovirus A71 (EV-A71) infects children and infants all over the world with no FDA-approved treatment to date. Understanding the basic mechanisms of viral processes aids in selecting more efficient drug targets and designing more effective antivirals to thwart this virus. The 5'-untranslated region (5'-UTR) of the viral RNA genome is composed of a cloverleaf structure and an internal ribosome entry site (IRES). Cellular proteins that bind to the cloverleaf structure regulate viral RNA synthesis, while those that bind to the IRES also known as IRES trans-acting factors (ITAFs) regulate viral translation. In this review, we survey the cellular proteins currently known to bind the 5'-UTR and influence viral gene expression with emphasis on comparing proteins' functions and localizations pre- and post-(EV-A71) infection. A comprehensive understanding of how the host cell's machinery is hijacked and reprogrammed by the virus to facilitate its replication is crucial for developing effective antivirals.
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Affiliation(s)
- Sudeshi M. Abedeera
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Jesse Davila-Calderon
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Barrington Henry
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Josephine King
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Srinivasa Penumutchu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Blanton S. Tolbert
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Wu H, Luo Q, Chen Y, Liao S, Chen H, Chen Y, Qin Y. Inhibiting mechanism of Alpiniae oxyphyllae fructus polysaccharide 3 against the replication of porcine epidemic diarrhea virus. Virology 2023; 587:109848. [PMID: 37499528 DOI: 10.1016/j.virol.2023.109848] [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: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) causes diarrhea, vomiting, and death in piglets. Our previous study has revealed the anti-PEDV activity of Alpiniae oxyphyllae fructus polysaccharide 3 (AOFP3). However, it is still unknown whether AOFP3 can inhibit the replication of PEDV. Therefore, the effect of AOFP3 on PEDV replication was investigated in the present study, along with analysis of viral RdRp activity and expression of hnRNP A1 by RNA polymerase activity assay in vitro, RIP assay, and Western blotting. The results showed that both the PEDV gene and protein levels in IPEC-J2 cells decreased with AOFP3 treatment. In addition, AOFP3 significantly reduced PEDV's replication by down-regulating the activity of PEDV RdRp and reducing the expression of hnRNP A1, whereas only the bind of RdRp to PEDV 3'UTR was inhibited in AOFP3 treated cells.
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Affiliation(s)
- Haowen Wu
- Institute of Traditional South Chinese Veterinary Pharmacology, School of Animal Science and Technology of Hainan University, Haikou, 570228, PR China
| | - Qiyuan Luo
- Institute of Traditional South Chinese Veterinary Pharmacology, School of Animal Science and Technology of Hainan University, Haikou, 570228, PR China
| | - Yijing Chen
- Institute of Traditional South Chinese Veterinary Pharmacology, School of Animal Science and Technology of Hainan University, Haikou, 570228, PR China
| | - Suya Liao
- Institute of Traditional South Chinese Veterinary Pharmacology, School of Animal Science and Technology of Hainan University, Haikou, 570228, PR China
| | - Huricha Chen
- Institute of Traditional South Chinese Veterinary Pharmacology, School of Animal Science and Technology of Hainan University, Haikou, 570228, PR China
| | - Yun Chen
- Institute of Traditional South Chinese Veterinary Pharmacology, School of Animal Science and Technology of Hainan University, Haikou, 570228, PR China.
| | - Yao Qin
- Institute of Traditional South Chinese Veterinary Pharmacology, School of Animal Science and Technology of Hainan University, Haikou, 570228, PR China.
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Li Z, Wei H, Hu D, Li X, Guo Y, Ding X, Guo H, Zhang L. Research Progress on the Structural and Functional Roles of hnRNPs in Muscle Development. Biomolecules 2023; 13:1434. [PMID: 37892116 PMCID: PMC10604023 DOI: 10.3390/biom13101434] [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: 09/04/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a superfamily of RNA-binding proteins consisting of more than 20 members. These proteins play a crucial role in various biological processes by regulating RNA splicing, transcription, and translation through their binding to RNA. In the context of muscle development and regeneration, hnRNPs are involved in a wide range of regulatory mechanisms, including alternative splicing, transcription regulation, miRNA regulation, and mRNA stability regulation. Recent studies have also suggested a potential association between hnRNPs and muscle-related diseases. In this report, we provide an overview of our current understanding of how hnRNPs regulate RNA metabolism and emphasize the significance of the key members of the hnRNP family in muscle development. Furthermore, we explore the relationship between the hnRNP family and muscle-related diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Linlin Zhang
- Key Laboratory of Animal Breeding and Healthy Livestock Farming, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China; (Z.L.); (H.W.); (D.H.); (X.L.); (Y.G.); (X.D.); (H.G.)
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6
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Levengood JD, Potoyan D, Penumutchu S, Kumar A, Wang Y, Hansen AL, Kutluay S, Roche J, Tolbert BS. Thermodynamic Coupling of the tandem RRM domains of hnRNP A1 underlie its Pleiotropic RNA Binding Functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553700. [PMID: 37645738 PMCID: PMC10462124 DOI: 10.1101/2023.08.17.553700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The functional properties of RNA-binding proteins (RBPs) require allosteric regulation through inter-domain communication. Despite the foundational importance of allostery to biological regulation, almost no studies have been conducted to describe the biophysical nature by which inter-domain communication manifests in RBPs. Here, we show through high-pressure studies with hnRNP A1 that inter-domain communication is vital for the unique stability of its N- terminal domain containing a tandem of RNA Recognition Motifs (RRMs). Despite high sequence similarity and nearly identical tertiary structures, the two RRMs exhibit drastically different stability under pressure. RRM2 unfolds completely under high-pressure as an individual domain, but when appended to RRM1, it remains stable. Variants in which inter-domain communication is disrupted between the tandem RRMs show a large decrease in stability under pressure. Carrying these mutations over to the full-length protein for in vivo experiments revealed that the mutations affected the ability of the disordered C-terminus to engage in protein-protein interactions and more importantly, they also influenced the RNA binding capacity. Collectively, this work reveals that thermodynamic coupling between the tandem RRMs of hnRNP A1 accounts for its allosteric regulatory functions.
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7
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Cao Z, Guan L, Yu R, Yang F, Chen J. High Expression of Heterogeneous Nuclear Ribonucleoprotein A1 Facilitates Hepatocellular Carcinoma Growth. J Hepatocell Carcinoma 2023; 10:517-530. [PMID: 37034304 PMCID: PMC10075271 DOI: 10.2147/jhc.s402247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/09/2023] [Indexed: 04/03/2023] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) represents one of the most common tumors in the world. Our study aims to explore new markers and therapeutic targets for HCC. Heterogeneous Nuclear ribonucleoprotein A1 (hnRNPA1) has recently been found to be involved in the progression of several types of cancer, but its role in HCC remains uncovered. Methods We performed bioinformatic analysis to preliminarily show the relationship between hnRNPA1 and liver cancer. Then the correlation of the hnRNPA1 gene expression with clinicopathological characteristics of HCC patients was verified by human liver cancer tissue microarrays. The functional role of this gene was evaluated by in vivo and vitro experiments. Results Results showed that the expression of hnRNPA1 was upregulated in HCC tissues and was associated with pathological stage of HCC patients. Knockdown of hnRNPA1 gene markedly inhibited tumor growth in vivo, and reversed the effects on proliferation, migration and invasion and promoted apoptosis in vitro. Furthermore, down-regulation of hnRNPA1 gene expression can inhibit the activity of the MEK/ERK pathway. Conclusion In our work, we combined bioinformatic analysis with in vivo and in vitro experiments to initially elucidate the function of hnRNPA1 in liver cancer, which may help to explore biomarkers and therapeutic targets for HCC patients.
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Affiliation(s)
- Ziyi Cao
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, People’s Republic of China
| | - Li Guan
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, People’s Republic of China
| | - Runzhi Yu
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, People’s Republic of China
| | - Fan Yang
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, 200040, People’s Republic of China
| | - Jie Chen
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, People’s Republic of China
- Correspondence: Jie Chen; Fan Yang, Email ;
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Wang L, Ji Y, Chen Y, Bai J, Gao P, Feng P. A splicing silencer in SMN2 intron 6 is critical in spinal muscular atrophy. Hum Mol Genet 2023; 32:971-983. [PMID: 36255739 DOI: 10.1093/hmg/ddac260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/14/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a fatal neuromuscular disease caused by homozygous deletions or mutations of the SMN1 gene. SMN2 is a paralogous gene of SMN1 and a modifying gene of SMA. A better understanding of how SMN2 exon 7 splicing is regulated helps discover new therapeutic targets for SMA therapy. Based on an antisense walk method to map exonic and intronic splicing silencers (ESSs and ISSs) in SMN2 exon 7 and the proximal regions of its flanking introns, we identified one ISS (ISS6-KH) at upstream of the branch point site in intron 6. By using mutagenesis-coupled RT-PCR with SMN1/2 minigenes, immunochromatography, overexpression and siRNA-knockdown, we found this ISS consists of a bipartite hnRNP A1 binding cis-element and a poly-U sequence located between the proximal hnRNP A1 binding site (UAGCUA) and the branch site. Both HuR and hnRNP C1 proteins promote exon 7 skipping through the poly-U stretch. Mutations or deletions of these motifs lead to efficient SMN2 exon 7 inclusion comparable to SMN1 gene. Furthermore, we identified an optimal antisense oligonucleotide that binds the intron six ISS and causes striking exon 7 inclusion in the SMN2 gene in patient fibroblasts and SMA mouse model. Our findings demonstrate that this novel ISS plays an important role in SMN2 exon 7 skipping and highlight a new therapeutic target for SMA therapy.
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Affiliation(s)
- Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yinfeng Ji
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yuqing Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jialin Bai
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Peng Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Pengchao Feng
- Nanjing Antisense Biopharmaceutical Co., Ltd, Nanjing 210046, China
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Finger DS, Williams AE, Holt VV, Ables ET. Novel roles for RNA binding proteins squid, hephaesteus, and Hrb27C in Drosophila oogenesis. Dev Dyn 2023; 252:415-428. [PMID: 36308715 PMCID: PMC9991940 DOI: 10.1002/dvdy.550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/30/2022] [Accepted: 10/16/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Reproductive capacity in many organisms is maintained by germline stem cells (GSCs). A complex regulatory network influences stem cell fate, including intrinsic factors, local signals, and hormonal and nutritional cues. Posttranscriptional regulatory mechanisms ensure proper cell fate transitions, promoting germ cell differentiation to oocytes. As essential RNA binding proteins with constitutive functions in RNA metabolism, heterogeneous nuclear ribonucleoproteins (hnRNPs) have been implicated in GSC function and axis specification during oocyte development. HnRNPs support biogenesis, localization, maturation, and translation of nascent transcripts. Whether and individual hnRNPs specifically regulate GSC function has yet to be explored. RESULTS We demonstrate that hnRNPs are expressed in distinct patterns in the Drosophila germarium. We show that three hnRNPs, squid, hephaestus, and Hrb27C are cell-autonomously required in GSCs for their maintenance. Although these hnRNPs do not impact adhesion of GSCs to adjacent cap cells, squid and hephaestus (but not Hrb27C) are necessary for proper bone morphogenetic protein signaling in GSCs. Moreover, Hrb27C promotes proper GSC proliferation, whereas hephaestus promotes cyst division. CONCLUSIONS We find that hnRNPs are independently and intrinsically required in GSCs for their maintenance in adults. Our results support the model that hnRNPs play unique roles in stem cells essential for their self-renewal and proliferation.
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Affiliation(s)
- Danielle S. Finger
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Anna E. Williams
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Vivian V. Holt
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Elizabeth T. Ables
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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Bhattarai K, Holcik M. Diverse roles of heterogeneous nuclear ribonucleoproteins in viral life cycle. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1044652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the host-virus interactions helps to decipher the viral replication strategies and pathogenesis. Viruses have limited genetic content and rely significantly on their host cell to establish a successful infection. Viruses depend on the host for a broad spectrum of cellular RNA-binding proteins (RBPs) throughout their life cycle. One of the major RBP families is the heterogeneous nuclear ribonucleoproteins (hnRNPs) family. hnRNPs are typically localized in the nucleus, where they are forming complexes with pre-mRNAs and contribute to many aspects of nucleic acid metabolism. hnRNPs contain RNA binding motifs and frequently function as RNA chaperones involved in pre-mRNA processing, RNA splicing, and export. Many hnRNPs shuttle between the nucleus and the cytoplasm and influence cytoplasmic processes such as mRNA stability, localization, and translation. The interactions between the hnRNPs and viral components are well-known. They are critical for processing viral nucleic acids and proteins and, therefore, impact the success of the viral infection. This review discusses the molecular mechanisms by which hnRNPs interact with and regulate each stage of the viral life cycle, such as replication, splicing, translation, and assembly of virus progeny. In addition, we expand on the role of hnRNPs in the antiviral response and as potential targets for antiviral drug research and development.
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Han P, Cao P, Yue J, Kong K, Hu S, Deng Y, Li L, Li F, Zhao B. Knockdown of hnRNPA1 Promotes NSCLC Metastasis and EMT by Regulating Alternative Splicing of LAS1L exon 9. Front Oncol 2022; 12:837248. [PMID: 35814393 PMCID: PMC9260696 DOI: 10.3389/fonc.2022.837248] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/09/2022] [Indexed: 12/02/2022] Open
Abstract
Tumor metastasis is still an insurmountable obstacle in tumor treatment. Lung cancer represents one of the most common malignancies with high morbidity worldwide. hnRNPA1 has been reported to be involved in the regulation of tumor metastasis, while its specific role in tumor metastasis seems to be controversial and its molecular mechanism in lung cancer metastasis remains to be further elucidated. In this study, we confirmed that knockdown of the hnRNPA1 led to enhanced migration, invasion and EMT transition in lung cancer cells. Bioinformatics analysis of the GSE34992 dataset revealed that hnRNPA1 may regulate the alternative splicing (AS) of LAS1L exon 9. Further AGE assays and RIP assays revealed that hnRNPA1 can directly bind to the LAS1L pre-mRNA to inhibit the splicing of LAS1L exon 9. The RNA pull-down assays showed that hnRNPA1 can specifically bind to the two sites (UAGGGU(WT1) and UGGGGU(WT3)) of LAS1L Intron 9. Further Transwell assays indicated that the expression ratio of LAS1L-L/LAS1L-S regulated by hnRNPA1 can further promote the migration, invasion and EMT transition in lung cancer cells. Moreover, hnRNPA1 expression showed significant heterogeneity in lung cancer tissues, which may contain new research directions and potential therapeutic targets. Our results indicate that hnRNPA1 can affect the metastasis of lung cancer cells by modulating the AS of LAS1L exon 9, highlighting the potential significance of hnRNPA1 in lung cancer metastasis.
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Affiliation(s)
- Peng Han
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Cao
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaqi Yue
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kangle Kong
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan Hu
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Deng
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lequn Li
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Li
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Bo Zhao, ; Fan Li,
| | - Bo Zhao
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Bo Zhao, ; Fan Li,
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12
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Zhu YF, Wang SJ, Zhou J, Sun YH, Chen YM, Ma J, Huo XX, Song H. Effects of N6-Methyladenosine Modification on Cancer Progression: Molecular Mechanisms and Cancer Therapy. Front Oncol 2022; 12:897895. [PMID: 35707365 PMCID: PMC9189310 DOI: 10.3389/fonc.2022.897895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 11/20/2022] Open
Abstract
N6-methyladenosine (m6A) is a major internal epigenetic modification in eukaryotic mRNA, which is dynamic and reversible. m6A is regulated by methylases (“writers”) and demethylases (“erasers”) and is recognized and processed by m6A-binding proteins (“readers”), which further regulate RNA transport, localization, translation, and degradation. It plays a role in promoting or suppressing tumors and has the potential to become a therapeutic target for malignant tumors. In this review, we focus on the mutual regulation of m6A and coding and non-coding RNAs and introduce the molecular mechanism of m6A methylation involved in regulation and its role in cancer treatment by taking common female malignant tumors as an example.
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Affiliation(s)
- Yong-fu Zhu
- The First Department of Oncology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- The Department of Acupuncture, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Shu-Jie Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Jie Zhou
- The Department of Acupuncture, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Ye-han Sun
- The First Department of Oncology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - You-mou Chen
- The First Department of Oncology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Jia Ma
- The First Department of Oncology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Xing-xing Huo
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- *Correspondence: Hang Song, ; Xing-xing Huo,
| | - Hang Song
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
- *Correspondence: Hang Song, ; Xing-xing Huo,
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13
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Biochemical and subcellular characterization of a squid hnRNPA/B-like protein 2 in osmotic stress activated cells reflects molecular properties conserved in this protein family. Mol Biol Rep 2022; 49:4257-4268. [PMID: 35192131 DOI: 10.1007/s11033-022-07260-0] [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: 08/21/2021] [Accepted: 02/10/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND We have identified endogenous p65 to be an SDS-stable dimer protein composed of ~ 37 kDa hnRNPA/B-like subunits. We have investigated molecular properties involved in the stability of dimeric form, and their regulation in the transition between monomeric and dimeric forms of hnRNPA/B-like protein 2. We also investigated a cellular property conserved between squid hnRNPA/B-like protein 2 and human hnRNPA1 protein in a neuronal context. METHODS AND RESULTS Here we show biochemical properties of a recombinant hnRNPA/B-like protein 2 (rP2) in vitro experiments, as one of p65 subunit. We found that interaction between rP2 and RNA molecules interfered with the dynamics of rP2 dimers formation, involved in disulfide bonds and/or postranslational alterations in distinct stage of SDS-stable dimers formation. In addition, we have performed immunofluorescence in SH-SY5Y cells and observed that the pEGFP-P2 fusion protein was expressed in the nucleus, similar to what is observed for human hnRNPA1 protein. CONCLUSION Our results reinforce the idea that p65 is an SDS-stable dimer. Thus, a deeper understanding between monomeric and dimeric transition dynamic is critical into evolution of several neurodegenerative disease.
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14
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Larizza L, Calzari L, Alari V, Russo S. Genes for RNA-binding proteins involved in neural-specific functions and diseases are downregulated in Rubinstein-Taybi iNeurons. Neural Regen Res 2022; 17:5-14. [PMID: 34100419 PMCID: PMC8451555 DOI: 10.4103/1673-5374.314286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Taking advantage of the fast-growing knowledge of RNA-binding proteins (RBPs) we review the signature of downregulated genes for RBPs in the transcriptome of induced pluripotent stem cell neurons (iNeurons) modelling the neurodevelopmental Rubinstein Taybi Syndrome (RSTS) caused by mutations in the genes encoding CBP/p300 acetyltransferases. We discuss top and functionally connected downregulated genes sorted to “RNA processing” and “Ribonucleoprotein complex biogenesis” Gene Ontology clusters. The first set of downregulated RBPs includes members of hnRNHP (A1, A2B1, D, G, H2-H1, MAGOHB, PAPBC), core subunits of U small nuclear ribonucleoproteins and Serine-Arginine splicing regulators families, acting in precursor messenger RNA alternative splicing and processing. Consistent with literature findings on reduced transcript levels of serine/arginine repetitive matrix 4 (SRRM4) protein, the main regulator of the neural-specific microexons splicing program upon depletion of Ep300 and Crebbp in mouse neurons, RSTS iNeurons show downregulated genes for proteins impacting this network. We link downregulated genes to neurological disorders including the new HNRNPH1-related intellectual disability syndrome with clinical overlap to RSTS. The set of downregulated genes for Ribosome biogenesis includes several components of ribosomal subunits and nucleolar proteins, such NOP58 and fibrillarin that form complexes with snoRNAs with a central role in guiding post-transcriptional modifications needed for rRNA maturation. These nucleolar proteins are “dual” players as fibrillarin is also required for epigenetic regulation of ribosomal genes and conversely NOP58-associated snoRNA levels are under the control of NOP58 interactor BMAL1, a transcriptional regulator of the circadian rhythm. Additional downregulated genes for “dual specificity” RBPs such as RUVBL1 and METTL1 highlight the links between chromatin and the RBP-ome and the contribution of perturbations in their cross-talk to RSTS. We underline the hub position of CBP/p300 in chromatin regulation, the impact of its defect on neurons’ post-transcriptional regulation of gene expression and the potential use of epidrugs in therapeutics of RBP-caused neurodevelopmental disorders.
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Affiliation(s)
- Lidia Larizza
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Luciano Calzari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Valentina Alari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Silvia Russo
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
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15
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Gagné M, Deshaies JE, Sidibé H, Benchaar Y, Arbour D, Dubinski A, Litt G, Peyrard S, Robitaille R, Sephton CF, Vande Velde C. hnRNP A1B, a Splice Variant of HNRNPA1, Is Spatially and Temporally Regulated. Front Neurosci 2021; 15:724307. [PMID: 34630013 PMCID: PMC8498194 DOI: 10.3389/fnins.2021.724307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022] Open
Abstract
RNA binding proteins (RBPs) play a key role in cellular growth, homoeostasis and survival and are tightly regulated. A deep understanding of their spatiotemporal regulation is needed to understand their contribution to physiology and pathology. Here, we have characterized the spatiotemporal expression pattern of hnRNP A1 and its splice variant hnRNP A1B in mice. We have found that hnRNP A1B expression is more restricted to the CNS compared to hnRNP A1, and that it can form an SDS-resistant dimer in the CNS. Also, hnRNP A1B expression becomes progressively restricted to motor neurons in the ventral horn of the spinal cord, compared to hnRNP A1 which is more broadly expressed. We also demonstrate that hnRNP A1B is present in neuronal processes, while hnRNP A1 is absent. This finding supports a hypothesis that hnRNP A1B may have a cytosolic function in neurons that is not shared with hnRNP A1. Our results demonstrate that both isoforms are differentially expressed across tissues and have distinct localization profiles, suggesting that the two isoforms may have specific subcellular functions that can uniquely contribute to disease progression.
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Affiliation(s)
- Myriam Gagné
- Department of Biochemistry, Université de Montréal, Montréal, QC, Canada.,Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Jade-Emmanuelle Deshaies
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Hadjara Sidibé
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Yousri Benchaar
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Danielle Arbour
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Alicia Dubinski
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Gurleen Litt
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Sarah Peyrard
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Richard Robitaille
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Chantelle F Sephton
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Christine Vande Velde
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
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16
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Ruff KM, Pappu RV. AlphaFold and Implications for Intrinsically Disordered Proteins. J Mol Biol 2021; 433:167208. [PMID: 34418423 DOI: 10.1016/j.jmb.2021.167208] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 10/20/2022]
Abstract
Accurate predictions of the three-dimensional structures of proteins from their amino acid sequences have come of age. AlphaFold, a deep learning-based approach to protein structure prediction, shows remarkable success in independent assessments of prediction accuracy. A significant epoch in structural bioinformatics was the structural annotation of over 98% of protein sequences in the human proteome. Interestingly, many predictions feature regions of very low confidence, and these regions largely overlap with intrinsically disordered regions (IDRs). That over 30% of regions within the proteome are disordered is congruent with estimates that have been made over the past two decades, as intense efforts have been undertaken to generalize the structure-function paradigm to include the importance of conformational heterogeneity and dynamics. With structural annotations from AlphaFold in hand, there is the temptation to draw inferences regarding the "structures" of IDRs and their interactomes. Here, we offer a cautionary note regarding the misinterpretations that might ensue and highlight efforts that provide concrete understanding of sequence-ensemble-function relationships of IDRs. This perspective is intended to emphasize the importance of IDRs in sequence-function relationships (SERs) and to highlight how one might go about extracting quantitative SERs to make sense of how IDRs function.
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Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, Campus Box 1097, St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, Campus Box 1097, St. Louis, MO 63130, USA.
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17
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Luo L, Chiu LY, Sugarman A, Gupta P, Rouskin S, Tolbert BS. HnRNP A1/A2 Proteins Assemble onto 7SK snRNA via Context Dependent Interactions. J Mol Biol 2021; 433:166885. [PMID: 33684393 DOI: 10.1016/j.jmb.2021.166885] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
Abstract
7SK small nuclear RNA (snRNA) is an abundant and ubiquitously expressed noncoding RNA that functions to modulate the activity of RNA Polymerase II (RNAPII) in part by stabilizing distinct pools of 7SK-protein complexes. Prevailing models suggest that the secondary structure of 7SK is dynamically remodeled within its alternative RNA-protein pools such that its architecture differentially regulates the exchange of cognate binding partners. The nuclear hnRNP A1/A2 proteins influence the biology of 7SK snRNA via processes that require an intact stem loop (SL) 3 domain; however, the molecular details by which hnRNPs assemble onto 7SK snRNA are yet to be described. Here, we have taken an integrated approach to present a detailed description of the 7SK-hnRNP A1 complex. We show that unbound 7SK snRNA adopts at least two major conformations in solution, with significant structural differences localizing to the SL2-3 linker and the base of SL3. Phylogenetic analysis indicates that this same region is the least genetically conserved feature of 7SK snRNA. By performing DMS modifications with the presence of excess protein, we reveal that hnRNP A1 binds with selectivity to SL3 through mechanisms that increase the flexibility of the RNA adjacent to putative binding sites. Calorimetric titrations further validate that hnRNP A1-SL3 assembly is complex with the affinity of discrete binding events modulated by the surrounding RNA structure. To interpret this context-dependent binding phenomenon, we determined a 3D model of SL3 to show that it folds to position minimal hnRNP A1/A2 binding sites (5'-Y/RAG-3') within different local environments. SL3-protein complexes resolved by SEC-MALS-SAXS confirm that up to four hnRNP A1 proteins bind along the entire surface of SL3 via interactions that preserve the overall structural integrity of this domain. In sum, the collective results presented here reveal a specific role for a folded SL3 domain to scaffold hnRNP A1/A2-7SK assembly via mechanisms modulated by the surrounding RNA structure.
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Affiliation(s)
- Le Luo
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Andrew Sugarman
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Paromita Gupta
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
| | - Silvi Rouskin
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States.
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18
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Levengood JD, Peterson J, Tolbert BS, Roche J. Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins 2021; 89:781-791. [PMID: 33550645 DOI: 10.1002/prot.26058] [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: 08/31/2020] [Revised: 12/21/2020] [Accepted: 01/31/2021] [Indexed: 11/09/2022]
Abstract
We have investigated the pressure- and temperature-induced conformational changes associated with the low complexity domain of hnRNP A1, an RNA-binding protein able to phase separate in response to cellular stress. Solution NMR spectra of the hnRNP A1 low-complexity domain fused with protein-G B1 domain were collected from 1 to 2500 bar and from 268 to 290 K. While the GB1 domain shows the typical pressure-induced and cold temperature-induced unfolding expected for small globular domains, the low-complexity domain of hnRNP A1 exhibits unusual pressure and temperature dependences. We observed that the low-complexity domain is pressure sensitive, undergoing a major conformational transition within the prescribed pressure range. Remarkably, this transition has the inverse temperature dependence of a typical folding-unfolding transition. Our results suggest the presence of a low-lying extended and fully solvated state(s) of the low-complexity domain that may play a role in phase separation. This study highlights the exquisite sensitivity of solution NMR spectroscopy to observe subtle conformational changes and illustrates how pressure perturbation can be used to determine the properties of metastable conformational ensembles.
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Affiliation(s)
- Jeffrey D Levengood
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jake Peterson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
| | - Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
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19
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Maranon DG, Anderson JR, Maranon AG, Wilusz J. The interface between coronaviruses and host cell RNA biology: Novel potential insights for future therapeutic intervention. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1614. [PMID: 32638509 PMCID: PMC7361139 DOI: 10.1002/wrna.1614] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022]
Abstract
Coronaviruses, including SARS-Cov-2, are RNA-based pathogens that interface with a large variety of RNA-related cellular processes during infection. These processes include capping, polyadenylation, localization, RNA stability, translation, and regulation by RNA binding proteins or noncoding RNA effectors. The goal of this article is to provide an in-depth perspective on the current state of knowledge of how various coronaviruses interact with, usurp, and/or avoid aspects of these cellular RNA biology machineries. A thorough understanding of how coronaviruses interact with RNA-related posttranscriptional processes in the cell should allow for new insights into aspects of viral pathogenesis as well as identify new potential avenues for the development of anti-coronaviral therapeutics. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- David G. Maranon
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - John R. Anderson
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Abril G. Maranon
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
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20
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Lukasiewicz AJ, Contreras LM. Antisense probing of dynamic RNA structures. Methods 2020; 183:76-83. [PMID: 31991194 DOI: 10.1016/j.ymeth.2020.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 01/20/2023] Open
Abstract
RNA regulation is influenced by the dynamic changes in conformational accessibility on the transcript. Here we discuss the initial validation of a cell-free antisense probing method for structured RNAs, using the Tetrahymena group I intron as a control target. We observe changes in signal that qualitatively match prior traditional DMS footprinting experiments. Importantly, we have shown that application of this technique can elucidate new RNA information given its sensitivity for detecting rare intermediates that are not as readily observed by single-hit kinetics chemical probing techniques. Observing changes in RNA accessibility has broad applications in determining the effect that regulatory elements have on regional structures. We speculate that this method could be useful in quickly observing those interactions, along with other phenomena that influence RNA accessibility including RNA-RNA interactions and small molecules.
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Affiliation(s)
- Alexandra J Lukasiewicz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Lydia M Contreras
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, United States.
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21
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He Q, Long J, Yin Y, Li Y, Lei X, Li Z, Zhu W. Emerging Roles of lncRNAs in the Formation and Progression of Colorectal Cancer. Front Oncol 2020; 9:1542. [PMID: 32010629 PMCID: PMC6978842 DOI: 10.3389/fonc.2019.01542] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the primary cause of cancer-related death worldwide; however, specific and sensitive tools for the early diagnosis and targeted therapy of CRC are currently lacking. High-throughput sequencing technology revealed that gene expression of long-chain non-coding RNAs (lncRNAs) in a number of cancers directly or indirectly interferes with various biological processes. Emerging evidence suggests that lncRNAs regulate target genes and play an important role in the biological processes of malignancies, including CRC. Many carcinostatic/oncogenic lncRNAs have been identified as biomarkers for metastasis and prognosis in CRC; hence, they serve as therapeutic tools. In this article, we systematically review the literature on the disordered lncRNAs in CRC from four aspects: DNA transcription, RNA level regulation, post-translational level, and the translation of lncRNAs into polypeptides. Subsequently, we analyze the mechanism through which lncRNAs participate in the biological process of CRC. Finally, we discuss the application and prospects of these lncRNAs in CRC.
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Affiliation(s)
- Qinglian He
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Jiali Long
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Yuting Yin
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Yuling Li
- Department of Pathology, Dongguan Hospital of Southern Medical University, Dongguan, China
| | - Xue Lei
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Ziqi Li
- Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Wei Zhu
- Department of Pathology, Guangdong Medical University, Dongguan, China
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22
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Chen EB, Qin X, Peng K, Li Q, Tang C, Wei YC, Yu S, Gan L, Liu TS. HnRNPR-CCNB1/CENPF axis contributes to gastric cancer proliferation and metastasis. Aging (Albany NY) 2019; 11:7473-7491. [PMID: 31527303 PMCID: PMC6782008 DOI: 10.18632/aging.102254] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023]
Abstract
Gastric cancer (GC) is a common disease globally with high mortality rate. It is therefore necessary to develop novel therapies targeting specific events in the pathogenesis of GC. Some hnRNP family members are involved in multiple cancer biological behaviors. However, the potential function and mechanism of hnRNPR, a new molecule of hnRNP family in GC remains unknown. We found that the expression of hnRNPR was significantly overexpressed in multiple cancers compared to the normal tissues. Functionally, hnRNPR promoted cancer cell proliferation, migration, and invasion. Knockdown of hnRNPR in two type mice models, with two types of tumors models decreased the tumor aggressiveness and metastasis. Mechanistically, hnRNPR targeted oncogenic pathways by stabilizing the expression of CCNB1 and CENPF mRNA level. Knockdown of CCNB1 and CENPF abolished the hnRNPR-induced cell growth and invasion, respectively. Furthermore, the protein level of hnRNPR in the tumor was positively correlated with the expression of CCNB1 and CENPF in clinical samples. Together, these results indicate that overexpression of hnRNPR promoted the aggressiveness of GC by increasing the mRNA expression of CCNB1 and CENPF. HnRNPR-CCNB1/CENPF axis may be a potential therapeutic target for GC treatment.
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Affiliation(s)
- Er-Bao Chen
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xuan Qin
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, China
| | - Ke Peng
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qian Li
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Tang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yi-Chou Wei
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shan Yu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lu Gan
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tian-Shu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.,Center of Evidence-based Medicine, Fudan University, Shanghai, China
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23
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Ghosh M, Singh M. RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain. Nucleic Acids Res 2019; 46:10246-10261. [PMID: 30247678 PMCID: PMC6212785 DOI: 10.1093/nar/gky854] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/12/2018] [Indexed: 12/25/2022] Open
Abstract
hnRNPA1 is a member of heteronuclear ribonucleoproteins that has been shown to promote telomere elongation apart from its roles in RNA transport and alternative splicing. It is a modular protein with an N-terminal domain called UP1 that consists of two RNA Recognition Motifs (RRM1 and RRM2 domains) and a C-terminal region that harbors functional motifs such as RGG-box, a prion-like domain, and a nuclear shuttling sequence. UP1 has been reported to bind and destabilize telomeric DNA G-quadruplexes and thereby participate in DNA telomere remodeling. An RGG-box motif that consists of four RGG repeats (containing arginine and glycine residues) is located C-terminal to the UP1 domain and constitutes an additional nucleic acid and protein-binding domain. However, the precise role of the RGG-box of hnRNPA1 in telomere DNA recognition and G-quadruplex DNA unfolding remains unexplored. Here, we show that the isolated RGG-box interacts specifically with the structured telomere G-quadruplex DNA but not with the single-stranded DNA. Further the interaction of the RGG-box with the G-quadruplex DNA is dependent on the loop nucleotides of the G-quadruplex. Finally, we show that the RGG-box enhances the G-quadruplex unfolding activity of the adjacent UP1 domain. We propose that UP1 and RGG-box act synergistically to achieve complete telomere G-quadruplex DNA unfolding.
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Affiliation(s)
- Meenakshi Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India.,NMR Research Centre, Indian Institute of Science, Bengaluru 560012, India
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