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Zagrovic B, Adlhart M, Kapral TH. Coding From Binding? Molecular Interactions at the Heart of Translation. Annu Rev Biophys 2023; 52:69-89. [PMID: 36626765 DOI: 10.1146/annurev-biophys-090622-102329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The mechanism and the evolution of DNA replication and transcription, the key elements of the central dogma of biology, are fundamentally well explained by the physicochemical complementarity between strands of nucleic acids. However, the determinants that have shaped the third part of the dogma-the process of biological translation and the universal genetic code-remain unclear. We review and seek parallels between different proposals that view the evolution of translation through the prism of weak, noncovalent interactions between biological macromolecules. In particular, we focus on a recent proposal that there exists a hitherto unrecognized complementarity at the heart of biology, that between messenger RNA coding regions and the proteins that they encode, especially if the two are unstructured. Reflecting the idea that the genetic code evolved from intrinsic binding propensities between nucleotides and amino acids, this proposal promises to forge a link between the distant past and the present of biological systems.
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Affiliation(s)
- Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Marlene Adlhart
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Thomas H Kapral
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
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2
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Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
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Kossinova OA, Gopanenko AV, Babaylova ES, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. Reorganization of the Landscape of Translated mRNAs in NSUN2-Deficient Cells and Specific Features of NSUN2 Target mRNAs. Int J Mol Sci 2022; 23:ijms23179740. [PMID: 36077143 PMCID: PMC9456143 DOI: 10.3390/ijms23179740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The RNA cytosine C5 methyltransferase NSUN2 has a variety of RNA substrates and plays an important role in mRNA metabolism. NSUN2 binds to specific sequences enriched in exosomal mRNAs, suggesting its possible involvement in the sorting of mRNAs into exosomes. We applied the photoactivatable.4-thiouridine-enhanced cross-linking and immunoprecipitation assay involving high-throughput RNA sequencing (RNA-seq) to HEK293T cells to determine NSUN2 mRNA targets. NSUN2 cross-linking sites were found in more than one hundred relatively abundant mRNAs with a high GC content and a pronounced secondary structure. Then, utilizing RNA-seq for the total and polysome-associated mRNA from HEK293T cells with and without the knockdown of NSUN2, we identified differentially expressed genes, as well as genes with altered translational efficiency (GATEs). It turned out that the up-regulated GATE mRNAs were much shorter on average than the down-regulated ones, and their GC content was higher; moreover, they contained motifs with C residues located in GC-rich environments. Our findings reveal the specific features of mRNAs that make them potential targets for NSUN2 and expand our understanding of the role of NSUN2 in controlling translation and, possibly, in mRNA sorting into exosomes implemented through the methylation of cytosine residues.
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4
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Liu X, Wang H, Zhao X, Luo Q, Wang Q, Tan K, Wang Z, Jiang J, Cui J, Du E, Xia L, Du W, Chen D, Xia L, Xiao S. Arginine methylation of METTL14 promotes RNA N 6-methyladenosine modification and endoderm differentiation of mouse embryonic stem cells. Nat Commun 2021; 12:3780. [PMID: 34145242 PMCID: PMC8213825 DOI: 10.1038/s41467-021-24035-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/28/2021] [Indexed: 11/08/2022] Open
Abstract
RNA N6-methyladenosine (m6A), the most abundant internal modification of mRNAs, plays key roles in human development and health. Post-translational methylation of proteins is often critical for the dynamic regulation of enzymatic activity. However, the role of methylation of the core methyltransferase METTL3/METTL14 in m6A regulation remains elusive. We find by mass spectrometry that METTL14 arginine 255 (R255) is methylated (R255me). Global mRNA m6A levels are greatly decreased in METTL14 R255K mutant mouse embryonic stem cells (mESCs). We further find that R255me greatly enhances the interaction of METTL3/METTL14 with WTAP and promotes the binding of the complex to substrate RNA. We show that protein arginine N-methyltransferases 1 (PRMT1) interacts with and methylates METTL14 at R255, and consistent with this, loss of PRMT1 reduces mRNA m6A modification globally. Lastly, we find that loss of R255me preferentially affects endoderm differentiation in mESCs. Collectively, our findings show that arginine methylation of METTL14 stabilizes the binding of the m6A methyltransferase complex to its substrate RNA, thereby promoting global m6A modification and mESC endoderm differentiation. This work highlights the crosstalk between protein methylation and RNA methylation in gene expression.
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Affiliation(s)
- Xiaona Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, P.R. China
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hailong Wang
- Kingmed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, P.R. China
| | - Xueya Zhao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Qizhi Luo
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou, P.R. China
| | - Qingwen Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Kaifen Tan
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Zihan Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Jia Jiang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Jinru Cui
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Enhui Du
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Linjian Xia
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Wenyi Du
- Sichuan MoDe Technology Co., Ltd, Chengdu, P. R. China
| | - Dahua Chen
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute of Biomedical Research, Yunnan University, Kunming, P.R. China.
| | - Laixin Xia
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China.
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, P.R. China.
| | - Shan Xiao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China.
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5
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Yang L, Zhang R, Guo G, Wang G, Wen Y, Lin Y, Zhang X, Yu X, Huang Z, Zhao D, Zhang L. Development and validation of a prediction model for lung adenocarcinoma based on RNA-binding protein. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:474. [PMID: 33850871 PMCID: PMC8039651 DOI: 10.21037/atm-21-452] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background RNA-binding proteins (RBPs) have been found to participate in the development and progression of cancer. This present study aimed to construct a RBP-based prognostic prediction model for lung adenocarcinoma (LUAD). Methods RNA sequencing data and corresponding clinical information were acquired from The Cancer Genome Atlas (TCGA) and served as a training set. The prediction model was validated using the dataset in Gene Expression Omnibus (GEO) databases. Univariate and multivariate Cox regression analyses were conducted to identify the RBPs associated with survival. R software (http://www.r-project.org) was used for analysis in this study. Results Nine hub prognostic RBPs (CIRBP, DARS2, DDX24, GAPDH, LARP6, SNRPE, WDR3, ZC3H12C, ZC3H12D) were identified by univariate Cox regression analysis and multivariate Cox regression analysis. Using a risk score based on the nine-hub RBP model, we separated the LUAD patients into a low-risk group and a high-risk group. The outcomes revealed that patients in the high-risk group had poorer survival than those in the low-risk group. This signature was validated in the GEO database. Further study revealed that the risk score can be an independent prognostic biomarker for LUAD. A nomogram based on the nine hub RBPs was built to quantitatively predict the prognosis of LUAD patients. Conclusions Our nine-gene signature model could be used as a marker to predict the prognosis of LUAD and has potential for use in treatment individualization.
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Affiliation(s)
- Longjun Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rusi Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guangran Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Gongming Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yingsheng Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yongbin Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xuewen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiangyang Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zirui Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dechang Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lanjun Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
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6
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Balobanov V, Lekontseva N, Mikhaylina A, Nikulin A. Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface. Methods Mol Biol 2021; 2113:251-262. [PMID: 32006319 DOI: 10.1007/978-1-0716-0278-2_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, studies of RNA/protein interactions occupy a prominent place in molecular biology and medicine. The structures of RNA-protein complexes may be determined by X-ray crystallography or NMR for further analyses. These methods are time-consuming and difficult due to the versatility and dynamics of the RNA structure. Furthermore, due to the need to solve the "phase problem" for each dataset in crystallography, crystallographic structures of RNA are still underrepresented. Structure determination of single ribonucleotide-protein complexes is a useful tool to identify the position of single-stranded RNA-binding sites in proteins. We describe here a structural approach that incorporates affinity measurement of a protein for various single ribonucleotides, ranking the RNA/protein complexes according to their stability. This chapter describes how to perform these measurements, including a perspective for the analysis of RNA-binding sites in protein and single-nucleotide crystal soaking.
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Affiliation(s)
- V Balobanov
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
| | - N Lekontseva
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - A Mikhaylina
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - A Nikulin
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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7
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Grillone K, Riillo C, Scionti F, Rocca R, Tradigo G, Guzzi PH, Alcaro S, Di Martino MT, Tagliaferri P, Tassone P. Non-coding RNAs in cancer: platforms and strategies for investigating the genomic "dark matter". J Exp Clin Cancer Res 2020; 39:117. [PMID: 32563270 PMCID: PMC7305591 DOI: 10.1186/s13046-020-01622-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/11/2020] [Indexed: 12/18/2022] Open
Abstract
The discovery of the role of non-coding RNAs (ncRNAs) in the onset and progression of malignancies is a promising frontier of cancer genetics. It is clear that ncRNAs are candidates for therapeutic intervention, since they may act as biomarkers or key regulators of cancer gene network. Recently, profiling and sequencing of ncRNAs disclosed deep deregulation in human cancers mostly due to aberrant mechanisms of ncRNAs biogenesis, such as amplification, deletion, abnormal epigenetic or transcriptional regulation. Although dysregulated ncRNAs may promote hallmarks of cancer as oncogenes or antagonize them as tumor suppressors, the mechanisms behind these events remain to be clarified. The development of new bioinformatic tools as well as novel molecular technologies is a challenging opportunity to disclose the role of the "dark matter" of the genome. In this review, we focus on currently available platforms, computational analyses and experimental strategies to investigate ncRNAs in cancer. We highlight the differences among experimental approaches aimed to dissect miRNAs and lncRNAs, which are the most studied ncRNAs. These two classes indeed need different investigation taking into account their intrinsic characteristics, such as length, structures and also the interacting molecules. Finally, we discuss the relevance of ncRNAs in clinical practice by considering promises and challenges behind the bench to bedside translation.
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Affiliation(s)
- Katia Grillone
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Caterina Riillo
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Francesca Scionti
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Roberta Rocca
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Net4science srl, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Giuseppe Tradigo
- Laboratory of Bioinformatics, Department of Medical and Surgical Sciences, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Pietro Hiram Guzzi
- Laboratory of Bioinformatics, Department of Medical and Surgical Sciences, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Net4science srl, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Department of Health Sciences, Magna Græcia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Maria Teresa Di Martino
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Pierfrancesco Tassone
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
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8
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Burdine RD, Preston CC, Leonard RJ, Bradley TA, Faustino RS. Nucleoporins in cardiovascular disease. J Mol Cell Cardiol 2020; 141:43-52. [PMID: 32209327 DOI: 10.1016/j.yjmcc.2020.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 01/01/2023]
Abstract
Cardiovascular disease is a pressing health problem with significant global health, societal, and financial burdens. Understanding the molecular basis of polygenic cardiac pathology is thus essential to devising novel approaches for management and treatment. Recent identification of uncharacterized regulatory functions for a class of nuclear envelope proteins called nucleoporins offers the opportunity to understand novel putative mechanisms of cardiac disease development and progression. Consistent reports of nucleoporin deregulation associated with ischemic and dilated cardiomyopathies, arrhythmias and valvular disorders suggests that nucleoporin impairment may be a significant but understudied variable in cardiopathologic disorders. This review discusses and converges existing literature regarding nuclear pore complex proteins and their association with cardiac pathologies, and proposes a role for nucleoporins as facilitators of cardiac disease.
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Affiliation(s)
- Ryan D Burdine
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America; School of Health Sciences, University of South Dakota, 414 E Clark St, Vermillion, SD 57069, United States of America
| | - Claudia C Preston
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Riley J Leonard
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Tyler A Bradley
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Randolph S Faustino
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America; Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, 1400 W. 22(nd) Street, Sioux Falls, SD 57105, United States of America.
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9
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Tang L, Liang Y, Xie H, Yang X, Zheng G. Long non-coding RNAs in cutaneous biology and proliferative skin diseases: Advances and perspectives. Cell Prolif 2019; 53:e12698. [PMID: 31588640 PMCID: PMC6985680 DOI: 10.1111/cpr.12698] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/26/2019] [Accepted: 09/02/2019] [Indexed: 12/12/2022] Open
Abstract
Advances in transcriptome sequencing have revealed that the genome fraction largely encodes for thousands of non‐coding RNAs. Long non‐coding RNAs (lncRNAs), which are a class of non–protein‐coding RNAs longer than approximately 200 nucleotides in length, are emerging as key epigenetic regulators of gene expression recently. Intensive studies have characterized their crucial roles in cutaneous biology and diseases. In this review, we address the promotive or suppressive effects of lncRNAs on cutaneous physiological processes. Then, we focus on the pathogenic role of dysfunctional lncRNAs in a variety of proliferative skin diseases. These evidences suggest that lncRNAs have indispensable roles in the processes of skin biology. Additionally, lncRNAs might be promising biomarkers and therapeutic targets for cutaneous disorders.
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Affiliation(s)
- Lipeng Tang
- Department of Pharmacology of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yongxin Liang
- School of Bioscience and Bio-pharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Hesong Xie
- School of Bioscience and Bio-pharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaozhi Yang
- Guangzhou Virotech Pharmaceutical Co., Ltd, Guangzhou, China
| | - Guangjuan Zheng
- Department of Pharmacology of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Pathology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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10
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Woodward L, Gangras P, Singh G. Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq). J Vis Exp 2019. [PMID: 31355789 DOI: 10.3791/59913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
RNA immunoprecipitation in tandem (RIPiT) is a method for enriching RNA footprints of a pair of proteins within an RNA:protein (RNP) complex. RIPiT employs two purification steps. First, immunoprecipitation of a tagged RNP subunit is followed by mild RNase digestion and subsequent non-denaturing affinity elution. A second immunoprecipitation of another RNP subunit allows for enrichment of a defined complex. Following a denaturing elution of RNAs and proteins, the RNA footprints are converted into high-throughput DNA sequencing libraries. Unlike the more popular ultraviolet (UV) crosslinking followed by immunoprecipitation (CLIP) approach to enrich RBP binding sites, RIPiT is UV-crosslinking independent. Hence RIPiT can be applied to numerous proteins present in the RNA interactome and beyond that are essential to RNA regulation but do not directly contact the RNA or UV-crosslink poorly to RNA. The two purification steps in RIPiT provide an additional advantage of identifying binding sites where a protein of interest acts in partnership with another cofactor. The double purification strategy also serves to enhance signal by limiting background. Here, we provide a step-wise procedure to perform RIPiT and to generate high-throughput sequencing libraries from isolated RNA footprints. We also outline RIPiT's advantages and applications and discuss some of its limitations.
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Affiliation(s)
- Lauren Woodward
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University
| | - Pooja Gangras
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University
| | - Guramrit Singh
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University;
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11
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Han Y, Branon TC, Martell JD, Boassa D, Shechner D, Ellisman MH, Ting A. Directed Evolution of Split APEX2 Peroxidase. ACS Chem Biol 2019; 14:619-635. [PMID: 30848125 PMCID: PMC6548188 DOI: 10.1021/acschembio.8b00919] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
APEX is an engineered peroxidase that catalyzes the oxidation of a wide range of substrates, facilitating its use in a variety of applications from subcellular staining for electron microscopy to proximity biotinylation for spatial proteomics and transcriptomics. To further advance the capabilities of APEX, we used directed evolution to engineer a split APEX tool (sAPEX). A total of 20 rounds of fluorescence activated cell sorting (FACS)-based selections from yeast-displayed fragment libraries, using 3 different surface display configurations, produced a 200-amino-acid N-terminal fragment (with 9 mutations relative to APEX2) called "AP" and a 50-amino-acid C-terminal fragment called "EX". AP and EX fragments were each inactive on their own but were reconstituted to give peroxidase activity when driven together by a molecular interaction. We demonstrate sAPEX reconstitution in the mammalian cytosol, on engineered RNA motifs within a non-coding RNA scaffold, and at mitochondria-endoplasmic reticulum contact sites.
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Affiliation(s)
- Yisu Han
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Tess Caroline Branon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jeffrey D. Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Daniela Boassa
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - David Shechner
- Department of Pharmacology, University of Washington, Seattle, Washington, USA
| | - Mark H. Ellisman
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - Alice Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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12
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Rahman R, Xu W, Jin H, Rosbash M. Identification of RNA-binding protein targets with HyperTRIBE. Nat Protoc 2019; 13:1829-1849. [PMID: 30013039 DOI: 10.1038/s41596-018-0020-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RNA-binding proteins (RBPs) accompany RNA from birth to death, affecting RNA biogenesis and functions. Identifying RBP-RNA interactions is essential to understanding their complex roles in different cellular processes. However, detecting in vivo RNA targets of RBPs, especially in a small number of discrete cells, has been a technically challenging task. We previously developed a novel technique called TRIBE (targets of RNA-binding proteins identified by editing) to overcome this problem. TRIBE expresses a fusion protein consisting of a queried RBP and the catalytic domain of the RNA-editing enzyme ADAR (adenosine deaminase acting on RNA) (ADARcd), which marks target RNA transcripts by converting adenosine to inosine near the RBP binding sites. These marks can be subsequently identified via high-throughput sequencing. In spite of its usefulness, TRIBE is constrained by a low editing efficiency and editing-sequence bias from the ADARcd. Therefore, we developed HyperTRIBE by incorporating a previously characterized hyperactive mutation, E488Q, into the ADARcd. This strategy increases the editing efficiency and reduces sequence bias, which markedly increases the sensitivity of this technique without sacrificing specificity. HyperTRIBE provides a more powerful strategy for identifying RNA targets of RBPs with an easy experimental and computational protocol at low cost, that can be performed not only in flies, but also in mammals. The HyperTRIBE experimental protocol described below can be carried out in cultured Drosophila S2 cells in 1 week, using tools available in a common molecular biology laboratory; the computational analysis requires 3 more days.
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Affiliation(s)
- Reazur Rahman
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA
| | - Weijin Xu
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA
| | - Hua Jin
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA.
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Schuster SL, Hsieh AC. The Untranslated Regions of mRNAs in Cancer. Trends Cancer 2019; 5:245-262. [PMID: 30961831 PMCID: PMC6465068 DOI: 10.1016/j.trecan.2019.02.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022]
Abstract
The 5' and 3' untranslated regions (UTRs) regulate crucial aspects of post-transcriptional gene regulation that are necessary for the maintenance of cellular homeostasis. When these processes go awry through mutation or misexpression of certain regulatory elements, the subsequent deregulation of oncogenic gene expression can drive or enhance cancer pathogenesis. Although the number of known cancer-related mutations in UTR regulatory elements has recently increased markedly as a result of advances in whole-genome sequencing, little is known about how the majority of these genetic aberrations contribute functionally to disease. In this review we explore the regulatory functions of UTRs, how they are co-opted in cancer, new technologies to interrogate cancerous UTRs, and potential therapeutic opportunities stemming from these regions.
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Affiliation(s)
- Samantha L Schuster
- Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Andrew C Hsieh
- Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA; School of Medicine and Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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