1
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Wang S, Sun H, Chen G, Wu C, Sun B, Lin J, Lin D, Zeng D, Lin B, Huang G, Lu X, Lin H, Liang Y. RNA-binding proteins in breast cancer: Biological implications and therapeutic opportunities. Crit Rev Oncol Hematol 2024; 195:104271. [PMID: 38272151 DOI: 10.1016/j.critrevonc.2024.104271] [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: 06/27/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) refer to a class of proteins that participate in alternative splicing, RNA stability, polyadenylation, localization and translation of RNAs, thus regulating gene expression in post-transcriptional manner. Dysregulation of RNA-RBP interaction contributes to various diseases, including cancer. In breast cancer, disorders in RBP expression and function influence the biological characteristics of tumor cells. Targeting RBPs has fostered the development of innovative therapies for breast cancer. However, the RBP-related mechanisms in breast cancer are not completely clear. In this review, we summarize the regulatory mechanisms of RBPs and their signaling crosstalk in breast cancer. Specifically, we emphasize the potential of certain RBPs as prognostic factors due to their effects on proliferation, invasion, apoptosis, and therapy resistance of breast cancer cells. Most importantly, we present a comprehensive overview of the latest RBP-related therapeutic strategies and novel therapeutic targets that have proven to be useful in the treatment of breast cancer.
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Affiliation(s)
- Shimeng Wang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Hexing Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Guanyuan Chen
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Chengyu Wu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Bingmei Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Jiajia Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Danping Lin
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - De Zeng
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - Baohang Lin
- Department of Thyroid, Breast and Vascular Surgery, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Guan Huang
- Department of Pathology, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Xiaofeng Lu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Haoyu Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
| | - Yuanke Liang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
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Tompkins VS, Xue Z, Peterson JM, Rouse WB, O’Leary CA, Moss WN. Identification of MYC intron 2 regions that modulate expression. PLoS One 2024; 19:e0296889. [PMID: 38236931 PMCID: PMC10795982 DOI: 10.1371/journal.pone.0296889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/19/2023] [Indexed: 01/22/2024] Open
Abstract
MYC pre-mRNA is spliced with high fidelity to produce the transcription factor known to regulate cellular differentiation, proliferation, apoptosis, and alternative splicing. The mechanisms underpinning the pre-mRNA splicing of MYC, however, remain mostly unexplored. In this study, we examined the interaction of heterogeneous nuclear ribonucleoprotein C (HNRNPC) with MYC intron 2. Building off published eCLIP studies, we confirmed this interaction with poly(U) regions in intron 2 of MYC and found that full binding is correlated with optimal protein production. The interaction appears to be compensatory, as mutational disruption of all three poly(U) regions was required to reduce both HNRNPC binding capacity and fidelity of either splicing or translation. Poly(U) sequences in MYC intron 2 were relatively conserved across sequences from several different species. Lastly, we identified a short sequence just upstream of an HNRNPC binding region that when removed enhances MYC translation.
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Affiliation(s)
- Van S. Tompkins
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Zheng Xue
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Jake M. Peterson
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Warren B. Rouse
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Collin A. O’Leary
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
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3
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Liu L, Trendel J, Jiang G, Liu Y, Bruckmann A, Küster B, Sprunck S, Dresselhaus T, Bleckmann A. RBPome identification in egg-cell like callus of Arabidopsis. Biol Chem 2023; 404:1137-1149. [PMID: 37768858 DOI: 10.1515/hsz-2023-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023]
Abstract
RNA binding proteins (RBPs) have multiple and essential roles in transcriptional and posttranscriptional regulation of gene expression in all living organisms. Their biochemical identification in the proteome of a given cell or tissue requires significant protein amounts, which limits studies in rare and highly specialized cells. As a consequence, we know almost nothing about the role(s) of RBPs in reproductive processes such as egg cell development, fertilization and early embryogenesis in flowering plants. To systematically identify the RBPome of egg cells in the model plant Arabidopsis, we performed RNA interactome capture (RIC) experiments using the egg cell-like RKD2-callus and were able to identify 728 proteins associated with poly(A+)-RNA. Transcripts for 97 % of identified proteins could be verified in the egg cell transcriptome. 46 % of identified proteins can be associated with the RNA life cycle. Proteins involved in mRNA binding, RNA processing and metabolism are highly enriched. Compared with the few available RBPome datasets of vegetative plant tissues, we identified 475 egg cell-enriched RBPs, which will now serve as a resource to study RBP function(s) during egg cell development, fertilization and early embryogenesis. First candidates were already identified showing an egg cell-specific expression pattern in ovules.
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Affiliation(s)
- Liping Liu
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Jakob Trendel
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Guojing Jiang
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Yanhui Liu
- College of Life Science, Longyan University, Longyan 364012, China
| | - Astrid Bruckmann
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Bernhard Küster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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4
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Dorn G, Gmeiner C, de Vries T, Dedic E, Novakovic M, Damberger FF, Maris C, Finol E, Sarnowski CP, Kohlbrecher J, Welsh TJ, Bolisetty S, Mezzenga R, Aebersold R, Leitner A, Yulikov M, Jeschke G, Allain FHT. Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility. Nat Commun 2023; 14:6429. [PMID: 37833274 PMCID: PMC10576089 DOI: 10.1038/s41467-023-42012-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.
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Affiliation(s)
- Georg Dorn
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christoph Gmeiner
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tebbe de Vries
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Mihajlo Novakovic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Fred F Damberger
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christophe Maris
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Esteban Finol
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, Villigen, Switzerland
| | - Timothy J Welsh
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Sreenath Bolisetty
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Raffaele Mezzenga
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Frédéric H-T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
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5
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Jiang X, Gatt A, Lashley T. HnRNP Pathologies in Frontotemporal Lobar Degeneration. Cells 2023; 12:1633. [PMID: 37371103 DOI: 10.3390/cells12121633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Frontotemporal dementia (FTD) is the second most common form of young-onset (<65 years) dementia. Clinically, it primarily manifests as a disorder of behavioural, executive, and/or language functions. Pathologically, frontotemporal lobar degeneration (FTLD) is the predominant cause of FTD. FTLD is a proteinopathy, and the main pathological proteins identified so far are tau, TAR DNA-binding protein 43 (TDP-43), and fused in sarcoma (FUS). As TDP-43 and FUS are members of the heterogeneous ribonucleic acid protein (hnRNP) family, many studies in recent years have expanded the research on the relationship between other hnRNPs and FTLD pathology. Indeed, these studies provide evidence for an association between hnRNP abnormalities and FTLD. In particular, several studies have shown that multiple hnRNPs may exhibit nuclear depletion and cytoplasmic mislocalisation within neurons in FTLD cases. However, due to the diversity and complex association of hnRNPs, most studies are still at the stage of histological discovery of different hnRNP abnormalities in FTLD. We herein review the latest studies relating hnRNPs to FTLD. Together, these studies outline an important role of multiple hnRNPs in the pathogenesis of FTLD and suggest that future research into FTLD should include the whole spectrum of this protein family.
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Affiliation(s)
- Xinwa Jiang
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ariana Gatt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
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6
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Xu J, Liu X, Wu S, Zhang D, Liu X, Xia P, Ling J, Zheng K, Xu M, Shen Y, Zhang J, Yu P. RNA-binding proteins in metabolic-associated fatty liver disease (MAFLD): From mechanism to therapy. Biosci Trends 2023; 17:21-37. [PMID: 36682800 DOI: 10.5582/bst.2022.01473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Metabolic-associated fatty liver disease (MAFLD) is the most common chronic liver disease globally and seriously increases the public health burden, affecting approximately one quarter of the world population. Recently, RNA binding proteins (RBPs)-related pathogenesis of MAFLD has received increasing attention. RBPs, vividly called the gate keepers of MAFLD, play an important role in the development of MAFLD through transcription regulation, alternative splicing, alternative polyadenylation, stability and subcellular localization. In this review, we describe the mechanisms of different RBPs in the occurrence and development of MAFLD, as well as list some drugs that can improve MAFLD by targeting RBPs. Considering the important role of RBPs in the development of MAFLD, elucidating the RNA regulatory networks involved in RBPs will facilitate the design of new drugs and biomarkers discovery.
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Affiliation(s)
- Jiawei Xu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyu Liu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shuqin Wu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Deju Zhang
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiao Liu
- Department of Cardiology, The Second Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Panpan Xia
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jitao Ling
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kai Zheng
- Medical Care Strategic Customer Department, China Merchants Bank Shenzhen Branch, Shenzhen, Guangdong, Guangdong, China
| | - Minxuan Xu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yunfeng Shen
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jing Zhang
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Peng Yu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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7
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Shang QX, Kong WL, Huang WH, Xiao X, Hu WP, Yang YS, Zhang H, Yang L, Yuan Y, Chen LQ. Identification of m6a-related signature genes in esophageal squamous cell carcinoma by machine learning method. Front Genet 2023; 14:1079795. [PMID: 36733344 PMCID: PMC9886874 DOI: 10.3389/fgene.2023.1079795] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Background: We aimed to construct and validate the esophageal squamous cell carcinoma (ESCC)-related m6A regulators by means of machine leaning. Methods: We used ESCC RNA-seq data of 66 pairs of ESCC from West China Hospital of Sichuan University and the transcriptome data extracted from The Cancer Genome Atlas (TCGA)-ESCA database to find out the ESCC-related m6A regulators, during which, two machine learning approaches: RF (Random Forest) and SVM (Support Vector Machine) were employed to construct the model of ESCC-related m6A regulators. Calibration curves, clinical decision curves, and clinical impact curves (CIC) were used to evaluate the predictive ability and best-effort ability of the model. Finally, western blot and immunohistochemistry staining were used to assess the expression of prognostic ESCC-related m6A regulators. Results: 2 m6A regulators (YTHDF1 and HNRNPC) were found to be significantly increased in ESCC tissues after screening out through RF machine learning methods from our RNA-seq data and TCGA-ESCA database, respectively, and overlapping the results of the two clusters. A prognostic signature, consisting of YTHDF1 and HNRNPC, was constructed based on our RNA-seq data and validated on TCGA-ESCA database, which can serve as an independent prognostic predictor. Experimental validation including the western and immunohistochemistry staining were further successfully confirmed the results of bioinformatics analysis. Conclusion: We constructed prognostic ESCC-related m6A regulators and validated the model in clinical ESCC cohort as well as in ESCC tissues, which provides reasonable evidence and valuable resources for prognostic stratification and the study of potential targets for ESCC.
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8
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Dantsuji S, Ohno M, Taniguchi I. The hnRNP C tetramer binds to CBC on mRNA and impedes PHAX recruitment for the classification of RNA polymerase II transcripts. Nucleic Acids Res 2023; 51:1393-1408. [PMID: 36620872 PMCID: PMC9943658 DOI: 10.1093/nar/gkac1250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
In eukaryotic cells, various classes of RNAs are exported to the cytoplasm by class-specific factors. Accumulating evidence has shown that export factors affect the fate of RNA, demonstrating the importance of proper RNA classification upon export. We previously reported that RNA polymerase II transcripts were classified after synthesis depending on their length, and identified heterogeneous nuclear ribonucleoprotein (hnRNP) C as the key classification factor. HnRNP C inhibits the recruitment of PHAX, an adapter protein for spliceosomal U snRNA export, to long transcripts, navigating these RNAs to the mRNA export pathway. However, the mechanisms by which hnRNP C inhibits PHAX recruitment to mRNA remain unknown. We showed that the cap-binding complex, a bridging factor between m7G-capped RNA and PHAX, directly interacted with hnRNP C on mRNA. Additionally, we revealed that the tetramer-forming activity of hnRNP C and its strong RNA-binding activity were crucial for the inhibition of PHAX binding to longer RNAs. These results suggest that mRNA is wrapped around the hnRNP C tetramer without a gap from the cap, thereby impeding the recruitment of PHAX. The results obtained on the mode of length-specific RNA classification by the hnRNP C tetramer will provide mechanistic insights into hnRNP C-mediated RNA biogenesis.
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Affiliation(s)
- Sayaka Dantsuji
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Kyoto 606-8507, Japan
| | - Mutsuhito Ohno
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Kyoto 606-8507, Japan
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9
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Feng J, Zhou J, Lin Y, Huang W. hnRNP A1 in RNA metabolism regulation and as a potential therapeutic target. Front Pharmacol 2022; 13:986409. [PMID: 36339596 PMCID: PMC9634572 DOI: 10.3389/fphar.2022.986409] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/10/2022] [Indexed: 11/22/2022] Open
Abstract
Abnormal RNA metabolism, regulated by various RNA binding proteins, can have functional consequences for multiple diseases. Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is an important RNA binding protein, that regulates various RNA metabolic processes, including transcription, alternative splicing of pre-mRNA, translation, miRNA processing and mRNA stability. As a potent splicing factor, hnRNP A1 can regulate multiple splicing events, including itself, collaborating with other cooperative or antagonistical splicing factors by binding to splicing sites and regulatory elements in exons or introns. hnRNP A1 can modulate gene transcription by directly interacting with promoters or indirectly impacting Pol II activities. Moreover, by interacting with the internal ribosome entry site (IRES) or 3′-UTR of mRNAs, hnRNP A1 can affect mRNA translation. hnRNP A1 can alter the stability of mRNAs by binding to specific locations of 3′-UTR, miRNAs biogenesis and Nonsense-mediated mRNA decay (NMD) pathway. In this review, we conclude the selective sites where hnRNP A1 binds to RNA and DNA, and the co-regulatory factors that interact with hnRNP A1. Given the dysregulation of hnRNP A1 in diverse diseases, especially in cancers and neurodegeneration diseases, targeting hnRNP A1 for therapeutic treatment is extremely promising. Therefore, this review also provides the small-molecule drugs, biomedicines and novel strategies targeting hnRNP A1 for therapeutic purposes.
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Wang J, Sun D, Wang M, Cheng A, Zhu Y, Mao S, Ou X, Zhao X, Huang J, Gao Q, Zhang S, Yang Q, Wu Y, Zhu D, Jia R, Chen S, Liu M. Multiple functions of heterogeneous nuclear ribonucleoproteins in the positive single-stranded RNA virus life cycle. Front Immunol 2022; 13:989298. [PMID: 36119073 PMCID: PMC9478383 DOI: 10.3389/fimmu.2022.989298] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a diverse family of RNA binding proteins that are implicated in RNA metabolism, such as alternative splicing, mRNA stabilization and translational regulation. According to their different cellular localization, hnRNPs display multiple functions. Most hnRNPs were predominantly located in the nucleus, but some of them could redistribute to the cytoplasm during virus infection. HnRNPs consist of different domains and motifs that enable these proteins to recognize predetermined nucleotide sequences. In the virus-host interactions, hnRNPs specifically bind to viral RNA or proteins. And some of the viral protein-hnRNP interactions require the viral RNA or other host factors as the intermediate. Through various mechanisms, hnRNPs could regulate viral translation, viral genome replication, the switch of translation to replication and virion release. This review highlights the common features and the distinguish roles of hnRNPs in the life cycle of positive single-stranded RNA viruses.
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Affiliation(s)
- Jingming Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- *Correspondence: Anchun Cheng,
| | - Yukun Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xuming Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
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11
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Wang X, Yu Q, Yu H, Wang Y, Sun L, Yu L, Cui H, Yang H. The prognostic value and multiomic features of m6A-related risk signature in lung adenocarcinoma. Am J Transl Res 2022; 14:5379-5393. [PMID: 36105012 PMCID: PMC9452311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES N6-methyladenosine (m6A), a predominant RNA modification, has been recently linked to messenger RNA splicing, stability and expression, and its dysregulation may be important in the initiation as well as development of human cancers. The current study was proposed to investigate the clinico-pathological value and multiomic characteristics of m6A-linked genes in the diagnosis and prognosis of lung adenocarcinoma (LUAD). METHODS The expression levels and mutation types of 21 previously identified m6A regulators were analyzed using the TCGA (The Cancer Genome Atlas) database. The patients were categorized into two groups, a training group (n=392) and a testing group (n=98). Next, the prognostic score of m6A regulators was determined by the Cox survival analysis and a regression model of LASSO to develop a risk profile for patients with LUAD. Moreover, features of risk signature, including chemosensitivity, tumor immune microenvironment and genetic mutation, were also explored. RESULTS In total, 18 of 21 m6A regulators showed significantly differential expression in LUAD (P<0.05). Among them, 6 genes were observed to be associated with the Overall Survival (OS) of patients with LUAD. Three genes (IGF2BP1 and 2, and HNRNPC) were further evaluated as a prognostic signature in LUAD. Patients, grouped as high risk based on the median of risk score, had poorer OS in comparison with those in low-risk group (P<0.05). The accuracy of our prognostic signatures was high: the AUC were 0.67, 0.59, 0.64 (training set), and 0.65, 0.69, 0.64 (testing set) at survival of 1- , 3- and 5-year, respectively. The prognostic performance of IGF2BP1, IGF2BP2 and HNRNPC was successfully validated in two independent external cohorts. High-risk score was an indicator of chemoresistance, TP53 mutation and increased infiltration of immune cells, and in vitro assessment of the cellular function of HNRNPC confirmed that the gene is involved in cell proliferation and invasion. CONCLUSION The prognostic signature based on m6A regulators might provide novel insights into prognostic assessment and individualized treatment for patients with LUAD.
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Affiliation(s)
- Xiangcheng Wang
- Department of Nuclear Medicine, Shenzhen People’s HospitalShenzhen 518020, Guangdong, China
| | - Qin Yu
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
| | - Hongfang Yu
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
| | - Yuzhe Wang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
| | - Liping Sun
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
| | - Lei Yu
- Department of Pharmacy, Traditional Chinese Medicine Hospital of Inner Mongolia Autonomous RegionHohhot 010020, Inner Mongolia Autonomous Region, China
| | - Hongwei Cui
- Scientific Research Department, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- Clinical Research Center, The Affiliated Hospital of Inner Mongolia Medical UniversityHuhhot 010050, Inner Mongolia Autonomous Region, China
| | - Hao Yang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
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12
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Hu X, Zou Q, Yao L, Yang X. Survey of the binding preferences of RNA-binding proteins to RNA editing events. Genome Biol 2022; 23:169. [PMID: 35927743 PMCID: PMC9351184 DOI: 10.1186/s13059-022-02741-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/27/2022] [Indexed: 11/20/2022] Open
Abstract
Background Adenosine-to-inosine (A-to-I) editing is an important RNA posttranscriptional process related to a multitude of cellular and molecular activities. However, systematic characterizations of whether and how the events of RNA editing are associated with the binding preferences of RNA sequences to RNA-binding proteins (RBPs) are still lacking. Results With the RNA-seq and RBP eCLIP-seq datasets from the ENCODE project, we quantitatively survey the binding preferences of 150 RBPs to RNA editing events, followed by experimental validations. Such analyses of the RBP-associated RNA editing at nucleotide resolution and genome-wide scale shed light on the involvement of RBPs specifically in RNA editing-related processes, such as RNA splicing, RNA secondary structures, RNA decay, and other posttranscriptional processes. Conclusions These results highlight the relevance of RNA editing in the functions of many RBPs and therefore serve as a resource for further characterization of the functional associations between various RNA editing events and RBPs. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02741-8.
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Affiliation(s)
- Xiaolin Hu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Qin Zou
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Li Yao
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.
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13
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Mo L, Meng L, Huang Z, Yi L, Yang N, Li G. An analysis of the role of HnRNP C dysregulation in cancers. Biomark Res 2022; 10:19. [PMID: 35395937 PMCID: PMC8994388 DOI: 10.1186/s40364-022-00366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/20/2022] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins C (HnRNP C) is part of the hnRNP family of RNA-binding proteins. The relationship between hnRNP C and cancers has been extensively studied, and dysregulation of hnRNP C has been found in many cancers. According to existing public data, hnRNP C could promote the maturation of new heterogeneous nuclear RNAs (hnRNA s, also referred to as pre-mRNAs) into mRNAs and could stabilize mRNAs, controlling their translation. This paper reviews the regulation and dysregulation of hnRNP C in cancers. It interacts with some cancer genes and other biological molecules, such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and double-stranded RNAs (dsRNAs). Even directly binds to them. The effects of hnRNP C on biological processes such as alternative cleavage and polyadenylation (APA) and N6-methyladenosine (m6A) modification differ among cancers. Its main function is regulating stability and level of translation of cancer genes, and the hnRNP C is regarded as a candidate biomarker and might be valuable for prognosis evaluation.
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Affiliation(s)
- Liyi Mo
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lijuan Meng
- Department of Ultrasonography, Second Affiliated Hospital, University of South China, Hengyang, 421001, Hunan, China
| | - Zhicheng Huang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lan Yi
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Nanyang Yang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
| | - Guoqing Li
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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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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15
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Li H, Xiao W, He Y, Wen Z, Cheng S, Zhang Y, Li Y. Novel Insights Into the Multifaceted Functions of RNA n 6-Methyladenosine Modification in Degenerative Musculoskeletal Diseases. Front Cell Dev Biol 2022; 9:766020. [PMID: 35024366 PMCID: PMC8743268 DOI: 10.3389/fcell.2021.766020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) is an important modification of eukaryotic mRNA. Since the first discovery of the corresponding demethylase and the subsequent identification of m6A as a dynamic modification, the function and mechanism of m6A in mammalian gene regulation have been extensively investigated. “Writer”, “eraser” and “reader” proteins are key proteins involved in the dynamic regulation of m6A modifications, through the anchoring, removal, and interpretation of m6A modifications, respectively. Remarkably, such dynamic modifications can regulate the progression of many diseases by affecting RNA splicing, translation, export and degradation. Emerging evidence has identified the relationship between m6A modifications and degenerative musculoskeletal diseases, such as osteoarthritis, osteoporosis, sarcopenia and degenerative spinal disorders. Here, we have comprehensively summarized the evidence of the pathogenesis of m6A modifications in degenerative musculoskeletal diseases. Moreover, the potential molecular mechanisms, regulatory functions and clinical implications of m6A modifications are thoroughly discussed. Our review may provide potential prospects for addressing key issues in further studies.
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Affiliation(s)
- Hengzhen Li
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - WenFeng Xiao
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuqiong He
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zeqin Wen
- Department of Clinical Medicine, Xiangya School of Medicine of Central South University, Changsha, China
| | - Siyuan Cheng
- Department of Clinical Medicine, Xiangya School of Medicine of Central South University, Changsha, China
| | - Yi Zhang
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yusheng Li
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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16
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Influence of N6-Methyladenosine Modification Gene HNRNPC on Cell Phenotype in Parkinson's Disease. PARKINSON'S DISEASE 2021; 2021:9919129. [PMID: 34966539 PMCID: PMC8712163 DOI: 10.1155/2021/9919129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 12/20/2022]
Abstract
This study aimed to explore the N6-methyladenosine (m6A) modification genes involved in the pathogenesis of Parkinson's disease (PD) through data analysis of the two data sets GSE120306 and GSE22491 in the GEO database and further explore its influence on cell phenotype in PD. We analyzed the differentially expressed genes and function enrichment analysis of the two sets of data and found that the expression of the m6A-modification gene HNRNPC was significantly downregulated in the PD group, and it played an important role in DNA metabolism, RNA metabolism, and RNA processing and may be involved in PD. Then, we constructed the HNRNPC differential expression cell line to study the role of this gene in the pathogenesis of PD. The results showed that overexpression of HNRNPC can promote the proliferation of PC12 cells, inhibit their apoptosis, and inhibit the expression of inflammatory factors IFN-β, IL-6, and TNF-α, suggesting that HNRNPC may cause PD by inhibiting the proliferation of dopaminergic nerve cells, promoting their apoptosis, and causing immune inflammation. Our study also has certain limitations. For example, the data of the experimental group and the validation group come from different cell types, and the data of the experimental group involve individuals with G2019S LRRK2 mutations. In addition, due to the low expression of HNRNPC in PC12 cells, we used the method of overexpressing this gene to study its function. All these factors may cause our conclusions to be biased. Therefore, more research is still needed to corroborate it in the future.
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17
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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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18
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Kumar R, Poria DK, Ray PS. RNA-binding proteins La and HuR cooperatively modulate translation repression of PDCD4 mRNA. J Biol Chem 2021; 296:100154. [PMID: 33288677 PMCID: PMC7949077 DOI: 10.1074/jbc.ra120.014894] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/28/2022] Open
Abstract
Posttranscriptional regulation of gene expression plays a critical role in controlling the inflammatory response. An uncontrolled inflammatory response results in chronic inflammation, often leading to tumorigenesis. Programmed cell death 4 (PDCD4) is a proinflammatory tumor-suppressor gene which helps to prevent the transition from chronic inflammation to cancer. PDCD4 mRNA translation is regulated by an interplay between the oncogenic microRNA miR-21 and the RNA-binding protein (RBP) human antigen R (HuR) in response to lipopolysaccharide stimulation, but the role of other regulatory factors remains unknown. Here, we report that the RBP lupus antigen (La) interacts with the 3'-untranslated region of PDCD4 mRNA and prevents miR-21-mediated translation repression. While lipopolysaccharide causes nuclear-cytoplasmic translocation of HuR, it enhances cellular La expression. Remarkably, La and HuR were found to bind cooperatively to the PDCD4 mRNA and mitigate miR-21-mediated translation repression. The cooperative action of La and HuR reduced cell proliferation and enhanced apoptosis, reversing the pro-oncogenic function of miR-21. Together, these observations demonstrate a cooperative interplay between two RBPs, triggered differentially by the same stimulus, which exerts a synergistic effect on PDCD4 expression and thereby helps maintain a balance between inflammation and tumorigenesis.
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Affiliation(s)
- Ravi Kumar
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur, Nadia, West Bengal, India
| | - Dipak Kumar Poria
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur, Nadia, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur, Nadia, West Bengal, India.
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19
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Fabbiano F, Corsi J, Gurrieri E, Trevisan C, Notarangelo M, D'Agostino VG. RNA packaging into extracellular vesicles: An orchestra of RNA-binding proteins? J Extracell Vesicles 2020; 10:e12043. [PMID: 33391635 PMCID: PMC7769857 DOI: 10.1002/jev2.12043] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/17/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) are heterogeneous membranous particles released from the cells through different biogenetic and secretory mechanisms. We now conceive EVs as shuttles mediating cellular communication, carrying a variety of molecules resulting from intracellular homeostatic mechanisms. The RNA is a widely detected cargo and, impressively, a recognized functional intermediate that elects EVs as modulators of cancer cell phenotypes, determinants of disease spreading, cell surrogates in regenerative medicine, and a source for non-invasive molecular diagnostics. The mechanistic elucidation of the intracellular events responsible for the engagement of RNA into EVs will significantly improve the comprehension and possibly the prediction of EV "quality" in association with cell physiology. Interestingly, the application of multidisciplinary approaches, including biochemical as well as cell-based and computational strategies, is increasingly revealing an active RNA-packaging process implicating RNA-binding proteins (RBPs) in the sorting of coding and non-coding RNAs. In this review, we provide a comprehensive view of RBPs recently emerging as part of the EV biology, considering the scenarios where: (i) individual RBPs were detected in EVs along with their RNA substrates, (ii) RBPs were detected in EVs with inferred RNA targets, and (iii) EV-transcripts were found to harbour sequence motifs mirroring the activity of RBPs. Proteins so far identified are members of the hnRNP family (hnRNPA2B1, hnRNPC1, hnRNPG, hnRNPH1, hnRNPK, and hnRNPQ), as well as YBX1, HuR, AGO2, IGF2BP1, MEX3C, ANXA2, ALIX, NCL, FUS, TDP-43, MVP, LIN28, SRP9/14, QKI, and TERT. We describe the RBPs based on protein domain features, current knowledge on the association with human diseases, recognition of RNA consensus motifs, and the need to clarify the functional significance in different cellular contexts. We also summarize data on previously identified RBP inhibitor small molecules that could also be introduced in EV research as potential modulators of vesicular RNA sorting.
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Affiliation(s)
- Fabrizio Fabbiano
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Jessica Corsi
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Elena Gurrieri
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Caterina Trevisan
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Michela Notarangelo
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Vito G. D'Agostino
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
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20
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The role of hnRNPs in frontotemporal dementia and amyotrophic lateral sclerosis. Acta Neuropathol 2020; 140:599-623. [PMID: 32748079 PMCID: PMC7547044 DOI: 10.1007/s00401-020-02203-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022]
Abstract
Dysregulated RNA metabolism is emerging as a crucially important mechanism underpinning the pathogenesis of frontotemporal dementia (FTD) and the clinically, genetically and pathologically overlapping disorder of amyotrophic lateral sclerosis (ALS). Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RNA-binding proteins with diverse, multi-functional roles across all aspects of mRNA processing. The role of these proteins in neurodegeneration is far from understood. Here, we review some of the unifying mechanisms by which hnRNPs have been directly or indirectly linked with FTD/ALS pathogenesis, including their incorporation into pathological inclusions and their best-known roles in pre-mRNA splicing regulation. We also discuss the broader functionalities of hnRNPs including their roles in cryptic exon repression, stress granule assembly and in co-ordinating the DNA damage response, which are all emerging pathogenic themes in both diseases. We then present an integrated model that depicts how a broad-ranging network of pathogenic events can arise from declining levels of functional hnRNPs that are inadequately compensated for by autoregulatory means. Finally, we provide a comprehensive overview of the most functionally relevant cellular roles, in the context of FTD/ALS pathogenesis, for hnRNPs A1-U.
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21
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Corley M, Burns MC, Yeo GW. How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. Mol Cell 2020; 78:9-29. [PMID: 32243832 PMCID: PMC7202378 DOI: 10.1016/j.molcel.2020.03.011] [Citation(s) in RCA: 354] [Impact Index Per Article: 88.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/13/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
RNA-binding proteins (RBPs) comprise a large class of over 2,000 proteins that interact with transcripts in all manner of RNA-driven processes. The structures and mechanisms that RBPs use to bind and regulate RNA are incredibly diverse. In this review, we take a look at the components of protein-RNA interaction, from the molecular level to multi-component interaction. We first summarize what is known about protein-RNA molecular interactions based on analyses of solved structures. We additionally describe software currently available for predicting protein-RNA interaction and other resources useful for the study of RBPs. We then review the structure and function of seventeen known RNA-binding domains and analyze the hydrogen bonds adopted by protein-RNA structures on a domain-by-domain basis. We conclude with a summary of the higher-level mechanisms that regulate protein-RNA interactions.
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Affiliation(s)
- Meredith Corley
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Margaret C Burns
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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22
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Becker WR, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D. Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2. RNA (NEW YORK, N.Y.) 2019; 25:702-712. [PMID: 30914482 PMCID: PMC6521599 DOI: 10.1261/rna.068585.118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 03/14/2019] [Indexed: 05/03/2023]
Abstract
Posttranslational gene regulation requires a complex network of RNA-protein interactions. Cooperativity, which tunes response sensitivities, originates from protein-protein interactions in many systems. For RNA-binding proteins, cooperativity can also be mediated through RNA structure. RNA structural cooperativity (RSC) arises when binding of one protein induces a redistribution of RNA conformational states that enhance access (positive cooperativity) or block access (negative cooperativity) to additional binding sites. As RSC does not require direct protein-protein interactions, it allows cooperativity to be tuned for individual RNAs, via alterations in sequence that alter structural stability. Given the potential importance of this mechanism of control and our desire to quantitatively dissect features that underlie physiological regulation, we developed a statistical mechanical framework for RSC and tested this model by performing equilibrium binding measurements of the human PUF family protein PUM2. Using 68 RNAs that contain two to five PUM2-binding sites and RNA structures of varying stabilities, we observed a range of structure-dependent cooperative behaviors. To test our ability to account for this cooperativity with known physical constants, we used PUM2 affinity and nearest-neighbor RNA secondary structure predictions. Our model gave qualitative agreement for our disparate set of 68 RNAs across two temperatures, but quantitative deviations arise from overestimation of RNA structural stability. Our results demonstrate cooperativity mediated by RNA structure and underscore the power of quantitative stepwise experimental evaluation of mechanisms and computational tools.
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Affiliation(s)
- Winston R Becker
- Program in Biophysics, Stanford University, Stanford, California 94035, USA
| | - Inga Jarmoskaite
- Department of Biochemistry, Stanford University, Stanford, California 94035, USA
| | | | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94035, USA
- Department of Applied Physics, Stanford University, Stanford, California 94035, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94035, USA
- Departments of Chemical Engineering and Chemistry, Stanford University, Stanford, California 94305, USA
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23
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Attig J, Ule J. Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA-Binding Proteins: A Hypothesis. Bioessays 2019; 41:e1800132. [DOI: 10.1002/bies.201800132] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/14/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Jan Attig
- Dr. J. Attig, Prof. J. Ule; The Francis Crick Institute; 1 Midland Road London NW1 1AT UK
| | - Jernej Ule
- Dr. J. Attig, Prof. J. Ule; The Francis Crick Institute; 1 Midland Road London NW1 1AT UK
- Prof. J. Ule; Department of Molecular Neuroscience; UCL Institute of Neurology; Queen Square London WC1N 3BG UK
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24
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn 2018; 37:2837-2866. [PMID: 30052138 DOI: 10.1080/07391102.2018.1503972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
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Affiliation(s)
- Margarita I Zarudnaya
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Iryna M Kolomiets
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Andriy L Potyahaylo
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv , Ukraine
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25
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Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition. Methods 2017; 118-119:119-136. [PMID: 28315749 DOI: 10.1016/j.ymeth.2017.03.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/19/2017] [Accepted: 03/13/2017] [Indexed: 12/20/2022] Open
Abstract
Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain arrangements and dynamics. Principles of protein-RNA recognition and current approaches are reviewed and illustrated with recent studies.
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26
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Attig J, Ruiz de Los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J, Ule J. Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. eLife 2016; 5. [PMID: 27861119 PMCID: PMC5115870 DOI: 10.7554/elife.19545] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023] Open
Abstract
Alu elements are retrotransposons that frequently form new exons during primate evolution. Here, we assess the interplay of splicing repression by hnRNPC and nonsense-mediated mRNA decay (NMD) in the quality control and evolution of new Alu-exons. We identify 3100 new Alu-exons and show that NMD more efficiently recognises transcripts with Alu-exons compared to other exons with premature termination codons. However, some Alu-exons escape NMD, especially when an adjacent intron is retained, highlighting the importance of concerted repression by splicing and NMD. We show that evolutionary progression of 3' splice sites is coupled with longer repressive uridine tracts. Once the 3' splice site at ancient Alu-exons reaches a stable phase, splicing repression by hnRNPC decreases, but the exons generally remain sensitive to NMD. We conclude that repressive motifs are strongest next to cryptic exons and that gradual weakening of these motifs contributes to the evolutionary emergence of new alternative exons.
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Affiliation(s)
- Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom.,MRC-Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Igor Ruiz de Los Mozos
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | - Nejc Haberman
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | - Zhen Wang
- Institute de Biologie de l'ENS (IBENS), CNRS UMR 8197, Paris, France
| | - Warren Emmett
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom.,University College London Genetics Institute, London, United Kingdom
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom.,MRC-Laboratory of Molecular Biology, Cambridge, United Kingdom
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27
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Chang S, Zhang DW, Xu L, Wan H, Hou TJ, Kong R. Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods. RNA Biol 2016; 13:1133-1143. [PMID: 27592836 DOI: 10.1080/15476286.2016.1223007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RNA-binding protein with multiple splicing (RBPMS) is critical for axon guidance, smooth muscle plasticity, and regulation of cancer cell proliferation and migration. Recently, different states of the RNA-recognition motif (RRM) of RBPMS, one in its free form and another in complex with CAC-containing RNA, were determined by X-ray crystallography. In this article, the free RRM domain, its wild type complex and 2 mutant complex systems are studied by molecular dynamics (MD) simulations. Through comparison of free RRM domain and complex systems, it's found that the RNA binding facilitates stabilizing the RNA-binding interface of RRM domain, especially the C-terminal loop. Although both R38Q and T103A/K104A mutations reduce the binding affinity of RRM domain and RNA, the underlining mechanisms are different. Principal component analysis (PCA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) methods were used to explore the dynamical and recognition mechanisms of RRM domain and RNA. R38Q mutation is positioned on the homodimerization interface and mainly induces the large fluctuations of RRM domains. This mutation does not directly act on the RNA-binding interface, but some interfacial hydrogen bonds are weakened. In contrast, T103A/K104A mutations are located on the RNA-binding interface of RRM domain. These mutations obviously break most of high occupancy hydrogen bonds in the RNA-binding interface. Meanwhile, the key interfacial residues lose their favorable energy contributions upon RNA binding. The ranking of calculated binding energies in 3 complex systems is well consistent with that of experimental binding affinities. These results will be helpful in understanding the RNA recognition mechanisms of RRM domain.
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Affiliation(s)
- Shan Chang
- a Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou , China
| | - Da-Wei Zhang
- a Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou , China
| | - Lei Xu
- a Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou , China
| | - Hua Wan
- b College of Mathematics and Informatics, South China Agricultural University , Guangzhou , China
| | - Ting-Jun Hou
- c College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China
| | - Ren Kong
- a Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou , China
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28
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Geuens T, Bouhy D, Timmerman V. The hnRNP family: insights into their role in health and disease. Hum Genet 2016; 135:851-67. [PMID: 27215579 PMCID: PMC4947485 DOI: 10.1007/s00439-016-1683-5] [Citation(s) in RCA: 648] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/09/2016] [Indexed: 12/14/2022]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins (RBPs) that contribute to multiple aspects of nucleic acid metabolism including alternative splicing, mRNA stabilization, and transcriptional and translational regulation. Many hnRNPs share general features, but differ in domain composition and functional properties. This review will discuss the current knowledge about the different hnRNP family members, focusing on their structural and functional divergence. Additionally, we will highlight their involvement in neurodegenerative diseases and cancer, and the potential to develop RNA-based therapies.
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Affiliation(s)
- Thomas Geuens
- Peripheral Neuropathy Group, VIB Molecular Genetics Department, University of Antwerp-CDE, Parking P4, Building V, Room 1.30, Universiteitsplein 1, 2610, Antwerp, Belgium
- Neurogenetics Laboratory, Institute Born Bunge, University of Antwerp, Antwerp, Belgium
| | - Delphine Bouhy
- Peripheral Neuropathy Group, VIB Molecular Genetics Department, University of Antwerp-CDE, Parking P4, Building V, Room 1.30, Universiteitsplein 1, 2610, Antwerp, Belgium
- Neurogenetics Laboratory, Institute Born Bunge, University of Antwerp, Antwerp, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Group, VIB Molecular Genetics Department, University of Antwerp-CDE, Parking P4, Building V, Room 1.30, Universiteitsplein 1, 2610, Antwerp, Belgium.
- Neurogenetics Laboratory, Institute Born Bunge, University of Antwerp, Antwerp, Belgium.
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