1
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Jiang T, Wang L, Tang L, Zeb A, Hou Y. Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators. PeerJ 2023; 11:e16103. [PMID: 37744237 PMCID: PMC10512959 DOI: 10.7717/peerj.16103] [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: 04/19/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Background Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9. Methods In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed. Results Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1. Conclusion The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.
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Affiliation(s)
- Tao Jiang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
- Department of Rehabilitation, Southwest Hospital, Third Military Medical University Army Medical University, Chongqing, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Liang Tang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Azhar Zeb
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Yanjun Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
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2
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Jiang M, Li Y, Song J, Wang Z, Zhang L, Song L, Bai B, Tu K, Lan W, Pan L. Study on Black Spot Disease Detection and Pathogenic Process Visualization on Winter Jujubes Using Hyperspectral Imaging System. Foods 2023; 12:foods12030435. [PMID: 36765962 PMCID: PMC9914266 DOI: 10.3390/foods12030435] [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: 11/22/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
In this work, the potential of a hyperspectral imaging (HSI) system for the detection of black spot disease on winter jujubes infected by Alternaria alternata during postharvest storage was investigated. The HSI images were acquired using two systems in the visible and near-infrared (Vis-NIR, 400-1000 nm) and short-wave infrared (SWIR, 1000-2000 nm) spectral regions. Meanwhile, the change of physical (peel color, weight loss) and chemical parameters (soluble solids content, chlorophyll) and the microstructure of winter jujubes during the pathogenic process were measured. The results showed the spectral reflectance of jujubes in both the Vis-NIR and SWIR wavelength ranges presented an overall downtrend during the infection. Partial least squares discriminant models (PLS-DA) based on the HSI spectra in Vis-NIR and SWIR regions of jujubes both gave satisfactory discrimination accuracy for the disease detection, with classification rates of over 92.31% and 91.03%, respectively. Principal component analysis (PCA) was carried out on the HSI images of jujubes to visualize their infected areas during the pathogenic process. The first principal component of the HSI spectra in the Vis-NIR region could highlight the diseased areas of the infected jujubes. Consequently, Vis-NIR HSI and NIR HSI techniques had the potential to detect the black spot disease on winter jujubes during the postharvest storage, and the Vis-NIR HSI spectral information could visualize the diseased areas of jujubes during the pathogenic process.
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Affiliation(s)
- Mengwei Jiang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiting Li
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin Song
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenjie Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Zhang
- College of Food Science and Technology, Hebei Normal University of Science & Technology, Qinghuangdao 066600, China
- College of Life Sciences, Tarim University, Alaer 843300, China
| | - Lijun Song
- College of Food Science and Technology, Hebei Normal University of Science & Technology, Qinghuangdao 066600, China
- College of Life Sciences, Tarim University, Alaer 843300, China
| | - Bingyao Bai
- College of Life Sciences, Tarim University, Alaer 843300, China
| | - Kang Tu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weijie Lan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (W.L.); (L.P.); Tel.: +86-25-84399016 (L.P.)
| | - Leiqing Pan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Sanya Institute of Nanjing Agricultural University, Sanya 572024, China
- Correspondence: (W.L.); (L.P.); Tel.: +86-25-84399016 (L.P.)
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3
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Liu M, Guo J, Jia R. Emerging roles of alternative RNA splicing in oral squamous cell carcinoma. Front Oncol 2022; 12:1019750. [PMID: 36505770 PMCID: PMC9732560 DOI: 10.3389/fonc.2022.1019750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Alternative RNA splicing (ARS) is an essential and tightly regulated cellular process of post-transcriptional regulation of pre-mRNA. It produces multiple isoforms and may encode proteins with different or even opposite functions. The dysregulated ARS of pre-mRNA contributes to the development of many cancer types, including oral squamous cell carcinoma (OSCC), and may serve as a biomarker for the diagnosis and prognosis of OSCC and an attractive therapeutic target. ARS is mainly regulated by splicing factors, whose expression is also often dysregulated in OSCC and involved in tumorigenesis. This review focuses on the expression and roles of splicing factors in OSCC, the alternative RNA splicing events associated with OSCC, and recent advances in therapeutic approaches that target ARS.
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Affiliation(s)
- Miaomiao Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China,Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China,*Correspondence: Jihua Guo, ; Rong Jia,
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China,RNA Institute, Wuhan University, Wuhan, China,*Correspondence: Jihua Guo, ; Rong Jia,
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4
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Zhang S, Mao M, Lv Y, Yang Y, He W, Song Y, Wang Y, Yang Y, Al Abo M, Freedman JA, Patierno SR, Wang Y, Wang Z. A widespread length-dependent splicing dysregulation in cancer. SCIENCE ADVANCES 2022; 8:eabn9232. [PMID: 35977015 PMCID: PMC9385142 DOI: 10.1126/sciadv.abn9232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Dysregulation of alternative splicing is a key molecular hallmark of cancer. However, the common features and underlying mechanisms remain unclear. Here, we report an intriguing length-dependent splicing regulation in cancers. By systematically analyzing the transcriptome of thousands of cancer patients, we found that short exons are more likely to be mis-spliced and preferentially excluded in cancers. Compared to other exons, cancer-associated short exons (CASEs) are more conserved and likely to encode in-frame low-complexity peptides, with functional enrichment in GTPase regulators and cell adhesion. We developed a CASE-based panel as reliable cancer stratification markers and strong predictors for survival, which is clinically useful because the detection of short exon splicing is practical. Mechanistically, mis-splicing of CASEs is regulated by elevated transcription and alteration of certain RNA binding proteins in cancers. Our findings uncover a common feature of cancer-specific splicing dysregulation with important clinical implications in cancer diagnosis and therapies.
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Affiliation(s)
- Sirui Zhang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Miaowei Mao
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuesheng Lv
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Yingqun Yang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Tech University, Shanghai 200031, China
| | - Weijing He
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yun Yang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muthana Al Abo
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer A. Freedman
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Steven R. Patierno
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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5
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Zhu L, Li W. Roles of Physicochemical and Structural Properties of RNA-Binding Proteins in Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning. Int J Mol Sci 2022; 23:ijms23084426. [PMID: 35457243 PMCID: PMC9030803 DOI: 10.3390/ijms23084426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
Trans-acting splicing factors play a pivotal role in modulating alternative splicing by specifically binding to cis-elements in pre-mRNAs. There are approximately 1500 RNA-binding proteins (RBPs) in the human genome, but the activities of these RBPs in alternative splicing are unknown. Since determining RBP activities through experimental methods is expensive and time consuming, the development of an efficient computational method for predicting the activities of RBPs in alternative splicing from their sequences is of great practical importance. Recently, a machine learning model for predicting the activities of splicing factors was built based on features of single and dual amino acid compositions. Here, we explored the role of physicochemical and structural properties in predicting their activities in alternative splicing using machine learning approaches and found that the prediction performance is significantly improved by including these properties. By combining the minimum redundancy–maximum relevance (mRMR) method and forward feature searching strategy, a promising feature subset with 24 features was obtained to predict the activities of RBPs. The feature subset consists of 16 dual amino acid compositions, 5 physicochemical features, and 3 structural features. The physicochemical and structural properties were as important as the sequence composition features for an accurate prediction of the activities of splicing factors. The hydrophobicity and distribution of coil are suggested to be the key physicochemical and structural features, respectively.
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Affiliation(s)
| | - Wenjin Li
- Correspondence: ; Tel.: +86-0755-26942336
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6
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Recent Advances in the Prediction of Protein Structural Classes: Feature Descriptors and Machine Learning Algorithms. CRYSTALS 2021. [DOI: 10.3390/cryst11040324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the postgenomic age, rapid growth in the number of sequence-known proteins has been accompanied by much slower growth in the number of structure-known proteins (as a result of experimental limitations), and a widening gap between the two is evident. Because protein function is linked to protein structure, successful prediction of protein structure is of significant importance in protein function identification. Foreknowledge of protein structural class can help improve protein structure prediction with significant medical and pharmaceutical implications. Thus, a fast, suitable, reliable, and reasonable computational method for protein structural class prediction has become pivotal in bioinformatics. Here, we review recent efforts in protein structural class prediction from protein sequence, with particular attention paid to new feature descriptors, which extract information from protein sequence, and the use of machine learning algorithms in both feature selection and the construction of new classification models. These new feature descriptors include amino acid composition, sequence order, physicochemical properties, multiprofile Bayes, and secondary structure-based features. Machine learning methods, such as artificial neural networks (ANNs), support vector machine (SVM), K-nearest neighbor (KNN), random forest, deep learning, and examples of their application are discussed in detail. We also present our view on possible future directions, challenges, and opportunities for the applications of machine learning algorithms for prediction of protein structural classes.
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7
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Nisar S, Bhat AA, Singh M, Karedath T, Rizwan A, Hashem S, Bagga P, Reddy R, Jamal F, Uddin S, Chand G, Bedognetti D, El-Rifai W, Frenneaux MP, Macha MA, Ahmed I, Haris M. Insights Into the Role of CircRNAs: Biogenesis, Characterization, Functional, and Clinical Impact in Human Malignancies. Front Cell Dev Biol 2021; 9:617281. [PMID: 33614648 PMCID: PMC7894079 DOI: 10.3389/fcell.2021.617281] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/04/2021] [Indexed: 01/17/2023] Open
Abstract
Circular RNAs (circRNAs) are an evolutionarily conserved novel class of non-coding endogenous RNAs (ncRNAs) found in the eukaryotic transcriptome, originally believed to be aberrant RNA splicing by-products with decreased functionality. However, recent advances in high-throughput genomic technology have allowed circRNAs to be characterized in detail and revealed their role in controlling various biological and molecular processes, the most essential being gene regulation. Because of the structural stability, high expression, availability of microRNA (miRNA) binding sites and tissue-specific expression, circRNAs have become hot topic of research in RNA biology. Compared to the linear RNA, circRNAs are produced differentially by backsplicing exons or lariat introns from a pre-messenger RNA (mRNA) forming a covalently closed loop structure missing 3′ poly-(A) tail or 5′ cap, rendering them immune to exonuclease-mediated degradation. Emerging research has identified multifaceted roles of circRNAs as miRNA and RNA binding protein (RBP) sponges and transcription, translation, and splicing event regulators. CircRNAs have been involved in many human illnesses, including cancer and neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease, due to their aberrant expression in different pathological conditions. The functional versatility exhibited by circRNAs enables them to serve as potential diagnostic or predictive biomarkers for various diseases. This review discusses the properties, characterization, profiling, and the diverse molecular mechanisms of circRNAs and their use as potential therapeutic targets in different human malignancies.
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Affiliation(s)
- Sabah Nisar
- Functional and Molecular Imaging Laboratory, Cancer Research Department, Sidra Medicine, Doha, Qatar
| | - Ajaz A Bhat
- Functional and Molecular Imaging Laboratory, Cancer Research Department, Sidra Medicine, Doha, Qatar
| | - Mayank Singh
- Dr. B. R. Ambedkar Institute Rotary Cancer Hospital (BRAIRCH), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | | | - Arshi Rizwan
- Department of Nephrology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sheema Hashem
- Functional and Molecular Imaging Laboratory, Cancer Research Department, Sidra Medicine, Doha, Qatar
| | - Puneet Bagga
- Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Ravinder Reddy
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Farrukh Jamal
- Dr. Rammanohar Lohia Avadh University, Ayodhya, India
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Gyan Chand
- Department of Endocrine Surgery, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Davide Bedognetti
- Laboratory of Cancer Immunogenomics, Cancer Research Department, Sidra Medicine, Doha, Qatar.,Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Wael El-Rifai
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | | | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology (IUST), Pulwama, India
| | - Ikhlak Ahmed
- Research Branch, Sidra Medicine, Doha, Qatar.,Research Branch, Sidra Medicine, Doha, Qatar
| | - Mohammad Haris
- Functional and Molecular Imaging Laboratory, Cancer Research Department, Sidra Medicine, Doha, Qatar.,Laboratory Animal Research Center, Qatar University, Doha, Qatar
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