1
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Rajagopal V, Seiler J, Nasa I, Cantarella S, Theiss J, Herget F, Kaifer B, Schneider M, Helm D, König J, Zarnack K, Diederichs S, Kettenbach AN, Caudron-Herger M. An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.25.614981. [PMID: 39386702 PMCID: PMC11463612 DOI: 10.1101/2024.09.25.614981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Ribonucleoprotein complexes are dynamic assemblies of RNA with RNA-binding proteins (RBPs), which can modulate the fate of the RNA molecules from transcription to degradation. Vice versa, RNA can regulate the interactions and functions of the associated proteins. Dysregulation of RBPs is linked to diseases such as cancer and neurological disorders. RNA and RBPs are present in mitotic structures like the centrosomes and spindle microtubules, but their influence on mitotic spindle integrity remains unknown. Thus, we applied the R-DeeP strategy for the proteome-wide identification of RNA-dependent proteins and complexes to cells synchronized in mitosis versus interphase. The resulting atlas of RNA-dependent proteins in cell division can be accessed through the R-DeeP 3.0 database (R-DeeP3.dkfz.de). It revealed key mitotic factors as RNA-dependent such as AURKA, KIFC1 and TPX2 that were linked to RNA despite their lack of canonical RNA-binding domains. KIFC1 was identified as a new interaction partner and phosphorylation substrate of AURKA at S 349 and T 359 . In addition, KIFC1 interacted with both, AURKA and TPX2, in an RNA-dependent manner. Our data suggest a riboregulation of mitotic protein-protein interactions during spindle assembly, offering new perspectives on the control of cell division processes by RNA-protein complexes. Highlights Differential R-DeeP screens in mitosis and interphase are provided as a resource in a user-friendly database at R-DeeP3.dkfz.deAn atlas of RNA-dependent proteins in cell division identifies a substantial number of unconventional RNA-binding proteins among mitotic factorsInvestigation of protein-protein interactions reveals KIFC1 as a new AURKA and TPX2 interaction partner during spindle assemblyKIFC1, AURKA and TPX2 interact with each other in an RNA-dependent manner and directly bind to RNA AURKA phosphorylates KIFC1 at residues S 349 and T 359.
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2
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Li Y, Wang Y, Tan YQ, Yue Q, Guo Y, Yan R, Meng L, Zhai H, Tong L, Yuan Z, Li W, Wang C, Han S, Ren S, Yan Y, Wang W, Gao L, Tan C, Hu T, Zhang H, Liu L, Yang P, Jiang W, Ye Y, Tan H, Wang Y, Lu C, Li X, Xie J, Yuan G, Cui Y, Shen B, Wang C, Guan Y, Li W, Shi Q, Lin G, Ni T, Sun Z, Ye L, Vourekas A, Guo X, Lin M, Zheng K. The landscape of RNA-binding proteins in mammalian spermatogenesis. Science 2024:eadj8172. [PMID: 39208083 DOI: 10.1126/science.adj8172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 04/08/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Despite continuous expansion of the RNA-binding protein (RBP) world, there is a lack of systematic understanding of RBPs in mammalian testis, which harbors one of the most complex tissue transcriptomes. We adapted RNA interactome capture to mouse male germ cells, building an RBP atlas characterized by multiple layers of dynamics along spermatogenesis. Trapping of RNA-crosslinked peptides showed that the glutamic acid-arginine (ER) patch, a residue-coevolved polyampholytic element present in coiled-coils, enhances RNA binding of its host RBPs. Deletion of this element in NONO (non-POU domain-containing octamer-binding protein) led to a defective mitosis-to-meiosis transition due to compromised NONO-RNA interactions. Whole-exome sequencing of over 1000 infertile men revealed a prominent role of RBPs in the human genetic architecture of male infertility and identified risk ER patch variants.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yuanyuan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410083, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Qiuling Yue
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Department of Andrology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University, Nanjing 210008, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ruoyu Yan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Lanlan Meng
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410083, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Huicong Zhai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Lingxiu Tong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zihan Yuan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Wu Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Cuicui Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Shenglin Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Sen Ren
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yitong Yan
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, China
| | - Weixu Wang
- Institute of Computational Biology, Helmholtz Center Munich, Munich 85764, Germany
| | - Lei Gao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chen Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410083, China
| | - Tongyao Hu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410083, China
| | - Hao Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Liya Liu
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, China
| | - Pinglan Yang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Wanyin Jiang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yiting Ye
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Huanhuan Tan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yanfeng Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chenyu Lu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Xin Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jie Xie
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Gege Yuan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Yichun Guan
- Center for Reproductive Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Qinghua Shi
- Division of Reproduction and Genetics, First Affiliated Hospital of USC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410083, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, China
| | - Zheng Sun
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Anastasios Vourekas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Mingyan Lin
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, China
- Changzhou Medical Center, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou 213000, China
- Division of Birth Cohort Study, Fujian Maternity and Child Health Hospital, Fuzhou 350014, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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Wassmer E, Koppány G, Hermes M, Diederichs S, Caudron-Herger M. Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins. Nucleic Acids Res 2024; 52:7504-7522. [PMID: 38917322 PMCID: PMC11260472 DOI: 10.1093/nar/gkae536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
From transcription to decay, RNA-binding proteins (RBPs) influence RNA metabolism. Using the RBP2GO database that combines proteome-wide RBP screens from 13 species, we investigated the RNA-binding features of 176 896 proteins. By compiling published lists of RNA-binding domains (RBDs) and RNA-related protein family (Rfam) IDs with lists from the InterPro database, we analyzed the distribution of the RBDs and Rfam IDs in RBPs and non-RBPs to select RBDs and Rfam IDs that were enriched in RBPs. We also explored proteins for their content in intrinsically disordered regions (IDRs) and low complexity regions (LCRs). We found a strong positive correlation between IDRs and RBDs and a co-occurrence of specific LCRs. Our bioinformatic analysis indicated that RBDs/Rfam IDs were strong indicators of the RNA-binding potential of proteins and helped predicting new RBP candidates, especially in less investigated species. By further analyzing RBPs without RBD, we predicted new RBDs that were validated by RNA-bound peptides. Finally, we created the RBP2GO composite score by combining the RBP2GO score with new quality factors linked to RBDs and Rfam IDs. Based on the RBP2GO composite score, we compiled a list of 2018 high-confidence human RBPs. The knowledge collected here was integrated into the RBP2GO database at https://RBP2GO-2-Beta.dkfz.de.
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Affiliation(s)
- Elsa Wassmer
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gergely Koppány
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Malte Hermes
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, and German Cancer Consortium (DKTK), partner site Freiburg, a partnership between DKFZ and University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Maïwen Caudron-Herger
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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4
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Birkholz N, Kamata K, Feussner M, Wilkinson ME, Cuba Samaniego C, Migur A, Kimanius D, Ceelen M, Went SC, Usher B, Blower TR, Brown CM, Beisel CL, Weinberg Z, Fagerlund RD, Jackson SA, Fineran PC. Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein. Nature 2024; 631:670-677. [PMID: 38987591 DOI: 10.1038/s41586-024-07644-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/31/2024] [Indexed: 07/12/2024]
Abstract
In all organisms, regulation of gene expression must be adjusted to meet cellular requirements and frequently involves helix-turn-helix (HTH) domain proteins1. For instance, in the arms race between bacteria and bacteriophages, rapid expression of phage anti-CRISPR (acr) genes upon infection enables evasion from CRISPR-Cas defence; transcription is then repressed by an HTH-domain-containing anti-CRISPR-associated (Aca) protein, probably to reduce fitness costs from excessive expression2-5. However, how a single HTH regulator adjusts anti-CRISPR production to cope with increasing phage genome copies and accumulating acr mRNA is unknown. Here we show that the HTH domain of the regulator Aca2, in addition to repressing Acr synthesis transcriptionally through DNA binding, inhibits translation of mRNAs by binding conserved RNA stem-loops and blocking ribosome access. The cryo-electron microscopy structure of the approximately 40 kDa Aca2-RNA complex demonstrates how the versatile HTH domain specifically discriminates RNA from DNA binding sites. These combined regulatory modes are widespread in the Aca2 family and facilitate CRISPR-Cas inhibition in the face of rapid phage DNA replication without toxic acr overexpression. Given the ubiquity of HTH-domain-containing proteins, it is anticipated that many more of them elicit regulatory control by dual DNA and RNA binding.
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MESH Headings
- Bacteriophages/chemistry
- Bacteriophages/genetics
- Bacteriophages/metabolism
- Bacteriophages/ultrastructure
- Binding Sites
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Cryoelectron Microscopy
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/ultrastructure
- Gene Expression Regulation, Viral
- Genes, Viral
- Helix-Turn-Helix Motifs
- Models, Molecular
- Nucleic Acid Conformation
- Pectobacterium carotovorum/virology
- Protein Biosynthesis/genetics
- Protein Domains
- Ribosomes/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Messenger/ultrastructure
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA, Viral/ultrastructure
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/ultrastructure
- Substrate Specificity
- Transcription, Genetic
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Viral Proteins/ultrastructure
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Affiliation(s)
- Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Kotaro Kamata
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
| | - Maximilian Feussner
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Max E Wilkinson
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Angela Migur
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | | | - Marijn Ceelen
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Sam C Went
- Department of Biosciences, Durham University, Durham, UK
| | - Ben Usher
- Department of Biosciences, Durham University, Durham, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Durham, UK
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
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5
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Mansfield KD. RNA Binding by the m6A Methyltransferases METTL16 and METTL3. BIOLOGY 2024; 13:391. [PMID: 38927271 PMCID: PMC11200852 DOI: 10.3390/biology13060391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/10/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024]
Abstract
Methyltransferases are a wide-ranging, yet well-conserved, class of molecules that have been found to modify a wide variety of substrates. Interest in RNA methylation has surged in recent years with the identification of the major eukaryotic mRNA m6A methyltransferase METTL3. METTL16 has also been identified as an RNA m6A methyltransferase; however, much less is known about its targets and actions. Interestingly, in addition to their catalytic activities, both METTL3 and METTL16 also have "methylation-independent" functions, including translational regulation, which have been discovered. However, evidence suggests that METTL16's role as an RNA-binding protein may be more significant than is currently recognized. In this review, we will introduce RNA methylation, specifically m6A, and the enzymes responsible for its deposition. We will discuss the varying roles that these enzymes perform and delve deeper into their RNA targets and possible roles as methylation-independent RNA binding proteins. Finally, we will touch upon the many open questions still remaining.
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Affiliation(s)
- Kyle D Mansfield
- Biochemistry and Molecular Biology Department, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
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Coleman JC, Tattersall L, Yianni V, Knight L, Yu H, Hallett SR, Johnson P, Caetano AJ, Cosstick C, Ridley AJ, Gartland A, Conte MR, Grigoriadis AE. The RNA binding proteins LARP4A and LARP4B promote sarcoma and carcinoma growth and metastasis. iScience 2024; 27:109288. [PMID: 38532886 PMCID: PMC10963253 DOI: 10.1016/j.isci.2024.109288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/01/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024] Open
Abstract
RNA-binding proteins (RBPs) are emerging as important regulators of cancer pathogenesis. We reveal that the RBPs LARP4A and LARP4B are differentially overexpressed in osteosarcoma and osteosarcoma lung metastases, as well as in prostate cancer. Depletion of LARP4A and LARP4B reduced tumor growth and metastatic spread in xenografts, as well as inhibiting cell proliferation, motility, and migration. Transcriptomic profiling and high-content multiparametric analyses unveiled a central role for LARP4B, but not LARP4A, in regulating cell cycle progression in osteosarcoma and prostate cancer cells, potentially through modulating key cell cycle proteins such as Cyclins B1 and E2, Aurora B, and E2F1. This first systematic comparison between LARP4A and LARP4B assigns new pro-tumorigenic functions to LARP4A and LARP4B in bone and prostate cancer, highlighting their similarities while also indicating distinct functional differences. Uncovering clear biological roles for these paralogous proteins provides new avenues for identifying tissue-specific targets and potential druggable intervention.
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Affiliation(s)
- Jennifer C. Coleman
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
| | - Luke Tattersall
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, S10 2RX UK
| | - Val Yianni
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Laura Knight
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Hongqiang Yu
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Sadie R. Hallett
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
| | - Philip Johnson
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Ana J. Caetano
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Charlie Cosstick
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Anne J. Ridley
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD UK
| | - Alison Gartland
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, S10 2RX UK
| | - Maria R. Conte
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
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7
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Wang J, Liu J, Huang R, Chu T, Tang Q, Chen X. Proteomic Profiling of Messenger Ribonucleoproteins in Mouse Tissues Based on Formaldehyde Cross-Linking. J Proteome Res 2024; 23:1370-1378. [PMID: 38472149 DOI: 10.1021/acs.jproteome.3c00856] [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: 03/14/2024]
Abstract
Messenger ribonucleoprotein particles (mRNPs) are vital for tissue-specific gene expression via mediating posttranscriptional regulations. However, proteomic profiling of proteins in mRNPs, i.e., mRNA-associated proteins (mRAPs), has been challenging at the tissue level. Herein, we report the development of formaldehyde cross-linking-based mRNA-associated protein profiling (FAXRAP), a chemical strategy that enables the identification of mRAPs in both cultured cells and intact mouse organs. Applying FAXRAP, tissue-specific mRAPs were systematically profiled in the mouse liver, kidney, heart, and brain. Furthermore, brain mRAPs in Parkinson's disease (PD) mouse model were investigated, which revealed a global decrease of mRNP assembly in the brain of mice with PD. We envision that FAXRAP will facilitate uncovering the posttranscriptional regulation networks in various biological systems.
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Affiliation(s)
- Jiankun Wang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Jialin Liu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Rongbing Huang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Tianyu Chu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
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8
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Guo JK, Blanco MR, Walkup WG, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M. Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Mol Cell 2024; 84:1271-1289.e12. [PMID: 38387462 PMCID: PMC10997485 DOI: 10.1016/j.molcel.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here, we revisit the evidence supporting RNA binding by PRC2 and show that many reported interactions may not occur in vivo. Using denaturing purification of in vivo crosslinked RNA-protein complexes in human and mouse cell lines, we observe a loss of detectable RNA binding to PRC2 and chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, and others), despite accurately mapping bona fide RNA-binding sites across others (SPEN, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.
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Affiliation(s)
- Jimmy K Guo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ward G Walkup
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant Bonesteele
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carl R Urbinati
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Parham Peyda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Enrique Amaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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9
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Luige J, Armaos A, Tartaglia GG, Ørom UAV. Predicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation. Nat Commun 2024; 15:2585. [PMID: 38519458 PMCID: PMC10959947 DOI: 10.1038/s41467-024-46731-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
RNA-binding proteins are central for many biological processes and their characterization has demonstrated a broad range of functions as well as a wide spectrum of target structures. RNA G-quadruplexes are important regulatory elements occurring in both coding and non-coding transcripts, yet our knowledge of their structure-based interactions is at present limited. Here, using theoretical predictions and experimental approaches, we show that many chromatin-binding proteins bind to RNA G-quadruplexes, and we classify them based on their RNA G-quadruplex-binding potential. Combining experimental identification of nuclear RNA G-quadruplex-binding proteins with computational approaches, we build a prediction tool that assigns probability score for a nuclear protein to bind RNA G-quadruplexes. We show that predicted G-quadruplex RNA-binding proteins exhibit a high degree of protein disorder and hydrophilicity and suggest involvement in both transcription and phase-separation into membrane-less organelles. Finally, we present the G4-Folded/UNfolded Nuclear Interaction Explorer System (G4-FUNNIES) for estimating RNA G4-binding propensities at http://service.tartaglialab.com/new_submission/G4FUNNIES .
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Affiliation(s)
- Johanna Luige
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy.
- Catalan Institution for Research and Advanced Studies ICREA Passeig Lluis Companys, 23 08010, Barcelona, Spain.
| | - Ulf Andersson Vang Ørom
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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10
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Avila-Lopez P, Lauberth SM. Exploring new roles for RNA-binding proteins in epigenetic and gene regulation. Curr Opin Genet Dev 2024; 84:102136. [PMID: 38128453 PMCID: PMC11245729 DOI: 10.1016/j.gde.2023.102136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023]
Abstract
A significant portion of the human proteome comprises RNA-binding proteins (RBPs) that play fundamental roles in numerous biological processes. In the last decade, there has been a staggering increase in RBP identification and classification, which has fueled interest in the evolving roles of RBPs and RBP-driven molecular mechanisms. Here, we focus on recent insights into RBP-dependent regulation of the epigenetic and transcriptional landscape. We describe advances in methodologies that define the RNA-protein interactome and machine-learning algorithms that are streamlining RBP discovery and predicting new RNA-binding regions. Finally, we present how RBP dysregulation leads to alterations in tumor-promoting gene expression and discuss the potential for targeting these RBPs for the development of new cancer therapeutics.
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Affiliation(s)
- Pedro Avila-Lopez
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shannon M Lauberth
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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11
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Sun H, Fu B, Qian X, Xu P, Qin W. Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction. Nat Commun 2024; 15:852. [PMID: 38286993 PMCID: PMC10825125 DOI: 10.1038/s41467-024-44987-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation.
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Affiliation(s)
- Haofan Sun
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Bin Fu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Ping Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Weijie Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
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12
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Heindel AJ, Brulet JW, Wang X, Founds MW, Libby AH, Bai DL, Lemke MC, Leace DM, Harris TE, Hafner M, Hsu KL. Chemoproteomic capture of RNA binding activity in living cells. Nat Commun 2023; 14:6282. [PMID: 37805600 PMCID: PMC10560261 DOI: 10.1038/s41467-023-41844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023] Open
Abstract
Proteomic methods for RNA interactome capture (RIC) rely principally on crosslinking native or labeled cellular RNA to enrich and investigate RNA-binding protein (RBP) composition and function in cells. The ability to measure RBP activity at individual binding sites by RIC, however, has been more challenging due to the heterogenous nature of peptide adducts derived from the RNA-protein crosslinked site. Here, we present an orthogonal strategy that utilizes clickable electrophilic purines to directly quantify protein-RNA interactions on proteins through photoaffinity competition with 4-thiouridine (4SU)-labeled RNA in cells. Our photo-activatable-competition and chemoproteomic enrichment (PACCE) method facilitated detection of >5500 cysteine sites across ~3000 proteins displaying RNA-sensitive alterations in probe binding. Importantly, PACCE enabled functional profiling of canonical RNA-binding domains as well as discovery of moonlighting RNA binding activity in the human proteome. Collectively, we present a chemoproteomic platform for global quantification of protein-RNA binding activity in living cells.
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Affiliation(s)
- Andrew J Heindel
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jeffrey W Brulet
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Xiantao Wang
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Michael W Founds
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Adam H Libby
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22903, USA
| | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Michael C Lemke
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David M Leace
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Ku-Lung Hsu
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22903, USA.
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
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13
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Jin W, Brannan KW, Kapeli K, Park SS, Tan HQ, Gosztyla ML, Mujumdar M, Ahdout J, Henroid B, Rothamel K, Xiang JS, Wong L, Yeo GW. HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence. Mol Cell 2023; 83:2595-2611.e11. [PMID: 37421941 PMCID: PMC11098078 DOI: 10.1016/j.molcel.2023.06.019] [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: 01/03/2023] [Revised: 03/20/2023] [Accepted: 06/13/2023] [Indexed: 07/10/2023]
Abstract
RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier (HydRA), which leverages information from both intermolecular protein interactions and internal protein sequence patterns to predict RNA-binding capacity with unparalleled specificity and sensitivity using support vector machines (SVMs), convolutional neural networks (CNNs), and Transformer-based protein language models. Occlusion mapping by HydRA robustly detects known RBDs and predicts hundreds of uncharacterized RNA-binding associated domains. Enhanced CLIP (eCLIP) for HydRA-predicted RBP candidates reveals transcriptome-wide RNA targets and confirms RNA-binding activity for HydRA-predicted RNA-binding associated domains. HydRA accelerates construction of a comprehensive RBP catalog and expands the diversity of RNA-binding associated domains.
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Affiliation(s)
- Wenhao Jin
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Kristopher W Brannan
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Katannya Kapeli
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Samuel S Park
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Hui Qing Tan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Mayuresh Mujumdar
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Joshua Ahdout
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Bryce Henroid
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Katherine Rothamel
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Joy S Xiang
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Limsoon Wong
- Department of Computer Science, National University of Singapore, Singapore, Singapore
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of Califorinia, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine and UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.
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14
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Mullari M, Fossat N, Skotte NH, Asenjo-Martinez A, Humphreys DT, Bukh J, Kirkeby A, Scheel TKH, Nielsen ML. Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington's disease. Nat Commun 2023; 14:4348. [PMID: 37468457 DOI: 10.1038/s41467-023-39936-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/30/2023] [Indexed: 07/21/2023] Open
Abstract
RNA-binding proteins (RBPs) are key players regulating RNA processing and are associated with disorders ranging from cancer to neurodegeneration. Here, we present a proteomics workflow for large-scale identification of RBPs and their RNA-binding regions in the mammalian brain identifying 526 RBPs. Analysing brain tissue from males of the Huntington's disease (HD) R6/2 mouse model uncovered differential RNA-binding of the alternative splicing regulator RBM5. Combining several omics workflows, we show that RBM5 binds differentially to transcripts enriched in pathways of neurodegeneration in R6/2 brain tissue. We further find these transcripts to undergo changes in splicing and demonstrate that RBM5 directly regulates these changes in human neurons derived from embryonic stem cells. Finally, we reveal that RBM5 interacts differently with several known huntingtin interactors and components of huntingtin aggregates. Collectively, we demonstrate the applicability of our method for capturing RNA interactor dynamics in the contexts of tissue and disease.
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Affiliation(s)
- Meeli Mullari
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Nicolas Fossat
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- CO-HEP, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Niels H Skotte
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Asenjo-Martinez
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - David T Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- CO-HEP, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Agnete Kirkeby
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
- Wallenberg Center for Molecular Medicine (WCMM) and Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- CO-HEP, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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15
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García-Martínez J, Singh A, Medina D, Chávez S, Pérez-Ortín JE. Enhanced gene regulation by cooperation between mRNA decay and gene transcription. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194910. [PMID: 36731791 PMCID: PMC10663100 DOI: 10.1016/j.bbagrm.2023.194910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
It has become increasingly clear in the last few years that gene expression in eukaryotes is not a linear process from mRNA synthesis in the nucleus to translation and degradation in the cytoplasm, but works as a circular one where the mRNA level is controlled by crosstalk between nuclear transcription and cytoplasmic decay pathways. One of the consequences of this crosstalk is the approximately constant level of mRNA. This is called mRNA buffering and happens when transcription and mRNA degradation act at compensatory rates. However, if transcription and mRNA degradation act additively, enhanced gene expression regulation occurs. In this work, we analyzed new and previously published genomic datasets obtained for several yeast mutants related to either transcription or mRNA decay that are not known to play any role in the other process. We show that some, which were presumed only transcription factors (Sfp1) or only decay factors (Puf3, Upf2/3), may represent examples of RNA-binding proteins (RBPs) that make specific crosstalk to enhance the control of the mRNA levels of their target genes by combining additive effects on transcription and mRNA stability. These results were mathematically modeled to see the effects of RBPs when they have positive or negative effects on mRNA synthesis and decay rates. We found that RBPs can be an efficient way to buffer or enhance gene expression responses depending on their respective effects on transcription and mRNA stability.
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Affiliation(s)
- José García-Martínez
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Daniel Medina
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain; Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, Doña Berenguela s/n, planta 3ª C.P. 14006, Córdoba, Spain
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain.
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16
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Zhao R, Fang X, Mai Z, Chen X, Mo J, Lin Y, Xiao R, Bao X, Weng X, Zhou X. Transcriptome-wide identification of single-stranded RNA binding proteins. Chem Sci 2023; 14:4038-4047. [PMID: 37063799 PMCID: PMC10094363 DOI: 10.1039/d3sc00957b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 04/18/2023] Open
Abstract
RNA-protein interactions are precisely regulated by RNA secondary structures in various biological processes. Large-scale identification of proteins that interact with particular RNA structure is important to the RBPome. Herein, a kethoxal assisted single-stranded RNA interactome capture (KASRIC) strategy was developed to globally identify single-stranded RNA binding proteins (ssRBPs). This approach combines RNA secondary structure probing technology with the conventional method of RNA-binding proteins profiling, realizing the transcriptome-wide identification of ssRBPs. Applying KASRIC, we identified 3180 candidate RBPs and 244 candidate ssRBPs in HeLa cells. Importantly, the 244 candidate ssRBPs contained 55 previously reported ssRBPs and 189 novel ssRBPs. Function analysis of the candidate ssRBPs exhibited enrichment in cellular processes related to RNA splicing and RNA degradation. The KASRIC strategy will facilitate the investigation of RNA-protein interactions.
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Affiliation(s)
- Ruiqi Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Xin Fang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Zhibiao Mai
- Laboratory of RNA Molecular Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences Guangzhou Guangdong Province 510530 China
| | - Xi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Yingying Lin
- Laboratory of RNA Molecular Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences Guangzhou Guangdong Province 510530 China
| | - Rui Xiao
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University Wuhan Hubei 430071 China
- TaiKang Center for Life and Medical Sciences, Wuhan University Wuhan Hubei 430071 China
| | - Xichen Bao
- Laboratory of RNA Molecular Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences Guangzhou Guangdong Province 510530 China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
- TaiKang Center for Life and Medical Sciences, Wuhan University Wuhan Hubei 430071 China
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17
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Perez-Perri JI, Ferring-Appel D, Huppertz I, Schwarzl T, Sahadevan S, Stein F, Rettel M, Galy B, Hentze MW. The RNA-binding protein landscapes differ between mammalian organs and cultured cells. Nat Commun 2023; 14:2074. [PMID: 37045843 PMCID: PMC10097726 DOI: 10.1038/s41467-023-37494-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
System-wide approaches have unveiled an unexpected breadth of the RNA-bound proteomes of cultured cells. Corresponding information regarding RNA-binding proteins (RBPs) of mammalian organs is still missing, largely due to technical challenges. Here, we describe ex vivo enhanced RNA interactome capture (eRIC) to characterize the RNA-bound proteomes of three different mouse organs. The resulting organ atlases encompass more than 1300 RBPs active in brain, kidney or liver. Nearly a quarter (291) of these had formerly not been identified in cultured cells, with more than 100 being metabolic enzymes. Remarkably, RBP activity differs between organs independent of RBP abundance, suggesting organ-specific levels of control. Similarly, we identify systematic differences in RNA binding between animal organs and cultured cells. The pervasive RNA binding of enzymes of intermediary metabolism in organs points to tightly knit connections between gene expression and metabolism, and displays a particular enrichment for enzymes that use nucleotide cofactors. We describe a generically applicable refinement of the eRIC technology and provide an instructive resource of RBPs active in intact mammalian organs, including the brain.
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Affiliation(s)
- Joel I Perez-Perri
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Dunja Ferring-Appel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Ina Huppertz
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sudeep Sahadevan
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Bruno Galy
- German Cancer Research Center (DKFZ), Division of Virus-associated Carcinogenesis, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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18
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Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR. RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Sci Rep 2023; 13:5238. [PMID: 37002329 PMCID: PMC10066285 DOI: 10.1038/s41598-023-32245-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Thousands of RNA-binding proteins (RBPs) crosslink to cellular mRNA. Among these are numerous unconventional RBPs (ucRBPs)-proteins that associate with RNA but lack known RNA-binding domains (RBDs). The vast majority of ucRBPs have uncharacterized RNA-binding specificities. We analyzed 492 human ucRBPs for intrinsic RNA-binding in vitro and identified 23 that bind specific RNA sequences. Most (17/23), including 8 ribosomal proteins, were previously associated with RNA-related function. We identified the RBDs responsible for sequence-specific RNA-binding for several of these 23 ucRBPs and surveyed whether corresponding domains from homologous proteins also display RNA sequence specificity. CCHC-zf domains from seven human proteins recognized specific RNA motifs, indicating that this is a major class of RBD. For Nudix, HABP4, TPR, RanBP2-zf, and L7Ae domains, however, only isolated members or closely related homologs yielded motifs, consistent with RNA-binding as a derived function. The lack of sequence specificity for most ucRBPs is striking, and we suggest that many may function analogously to chromatin factors, which often crosslink efficiently to cellular DNA, presumably via indirect recruitment. Finally, we show that ucRBPs tend to be highly abundant proteins and suggest their identification in RNA interactome capture studies could also result from weak nonspecific interactions with RNA.
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Affiliation(s)
- Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kaitlin U Laverty
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Arttu Jolma
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kate Nie
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Reuben Samson
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Sara E Pour
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cyrus L Tam
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Niklas von Krosigk
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Mihai Albu
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Gabrielle Perron
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0C7, Canada
- McGill Genome Centre, Montréal, QC, H3A 0G1, Canada
| | - Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Hamed Najafabadi
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0C7, Canada
- McGill Genome Centre, Montréal, QC, H3A 0G1, Canada
| | - Benjamin Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jack Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Quaid Morris
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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19
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Steinmetz B, Smok I, Bikaki M, Leitner A. Protein-RNA interactions: from mass spectrometry to drug discovery. Essays Biochem 2023; 67:175-186. [PMID: 36866608 PMCID: PMC10070478 DOI: 10.1042/ebc20220177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 03/04/2023]
Abstract
Proteins and RNAs are fundamental parts of biological systems, and their interactions affect many essential cellular processes. Therefore, it is crucial to understand at a molecular and at a systems level how proteins and RNAs form complexes and mutually affect their functions. In the present mini-review, we will first provide an overview of different mass spectrometry (MS)-based methods to study the RNA-binding proteome (RBPome), most of which are based on photochemical cross-linking. As we will show, some of these methods are also able to provide higher-resolution information about binding sites, which are important for the structural characterisation of protein-RNA interactions. In addition, classical structural biology techniques such as nuclear magnetic resonance (NMR) spectroscopy and biophysical methods such as electron paramagnetic resonance (EPR) spectroscopy and fluorescence-based methods contribute to a detailed understanding of the interactions between these two classes of biomolecules. We will discuss the relevance of such interactions in the context of the formation of membrane-less organelles (MLOs) by liquid-liquid phase separation (LLPS) processes and their emerging importance as targets for drug discovery.
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Affiliation(s)
- Benjamin Steinmetz
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
- RNA Biology PhD Program, University of Zurich and ETH Zürich, Zurich, Switzerland
| | - Izabela Smok
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
- RNA Biology PhD Program, University of Zurich and ETH Zürich, Zurich, Switzerland
| | - Maria Bikaki
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
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20
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Proteome-Wide Identification of RNA-Dependent Proteins in Lung Cancer Cells. Cancers (Basel) 2022; 14:cancers14246109. [PMID: 36551595 PMCID: PMC9776756 DOI: 10.3390/cancers14246109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Following the concept of RNA dependence and exploiting its application in the R-DeeP screening approach, we have identified RNA-dependent proteins in A549 lung adenocarcinoma cells. RNA-dependent proteins are defined as proteins whose interactome depends on RNA and thus entails RNA-binding proteins (RBPs) as well as proteins in ribonucleoprotein complexes (RNPs) without direct RNA interaction. With this proteome-wide technique based on sucrose density gradient ultracentrifugation and fractionation followed by quantitative mass spectrometry and bioinformatic analysis, we have identified 1189 RNA-dependent proteins including 170 proteins which had never been linked to RNA before. R-DeeP provides quantitative information on the fraction of a protein being RNA-dependent as well as it allows the reconstruction of protein complexes based on co-segregation. The RNA dependence of three newly identified RNA-dependent proteins, DOCK5, ELMO2, also known as CED12A, and ABRAXAS1, also known as CCDC98, was validated using western blot analysis, and the direct RNA interaction was verified by iCLIP2 for the migration-related protein DOCK5 and the mitosis-related protein ABRAXAS1. The R-DeeP 2.0 database provides proteome-wide and cell line-specific information from A549 and HeLa S3 cells on proteins and their RNA dependence to contribute to understanding the functional role of RNA and RNA-binding proteins in cancer cells.
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21
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Mestre-Farràs N, Guerrero S, Bley N, Rivero E, Coll O, Borràs E, Sabidó E, Indacochea A, Casillas-Serra C, Järvelin AI, Oliva B, Castello A, Hüttelmaier S, Gebauer F. Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis. Nucleic Acids Res 2022; 50:8207-8225. [PMID: 35848924 PMCID: PMC9371929 DOI: 10.1093/nar/gkac605] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) have been relatively overlooked in cancer research despite their contribution to virtually every cancer hallmark. Here, we use RNA interactome capture (RIC) to characterize the melanoma RBPome and uncover novel RBPs involved in melanoma progression. Comparison of RIC profiles of a non-tumoral versus a metastatic cell line revealed prevalent changes in RNA-binding capacities that were not associated with changes in RBP levels. Extensive functional validation of a selected group of 24 RBPs using five different in vitro assays unveiled unanticipated roles of RBPs in melanoma malignancy. As proof-of-principle we focused on PDIA6, an ER-lumen chaperone that displayed a novel RNA-binding activity. We show that PDIA6 is involved in metastatic progression, map its RNA-binding domain, and find that RNA binding is required for PDIA6 tumorigenic properties. These results exemplify how RIC technologies can be harnessed to uncover novel vulnerabilities of cancer cells.
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Affiliation(s)
- Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Santiago Guerrero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Nadine Bley
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Ezequiel Rivero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Olga Coll
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alberto Indacochea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Carlos Casillas-Serra
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Baldomero Oliva
- Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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22
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Pérez-Ortín JE, Chávez S. Nucleo-cytoplasmic shuttling of RNA-binding factors: mRNA buffering and beyond. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194849. [PMID: 35907432 DOI: 10.1016/j.bbagrm.2022.194849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/18/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Gene expression is a highly regulated process that adapts RNAs and proteins content to the cellular context. Under steady-state conditions, mRNA homeostasis is robustly maintained by tight controls that act on both nuclear transcription and cytoplasmic mRNA stability. In recent years, it has been revealed that several RNA-binding proteins (RBPs) that perform functions in mRNA decay can move to the nucleus and regulate transcription. The RBPs involved in transcription can also travel to the cytoplasm and regulate mRNA degradation and/or translation. The multifaceted functions of these shuttling nucleo-cytoplasm RBPs have raised the possibility that they can act as mRNA metabolism coordinators. In addition, this indicates the existence of crosstalk mechanisms between the enzymatic machineries that drive the different mRNA life-cycle phases. The buffering of the mRNA concentration is the best known consequence of a transcription-degradation crosstalk counteraction, but alternative ways of RBP action can also imply enhanced gene regulation.
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Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València. C/Dr. Moliner 50, E46100 Burjassot, Spain.
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain; Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, Doña Berenguela s/n, planta 3ª C.P., 14006 Córdoba, Spain
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23
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Chu LC, Arede P, Li W, Urdaneta EC, Ivanova I, McKellar SW, Wills JC, Fröhlich T, von Kriegsheim A, Beckmann BM, Granneman S. The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins. Nat Commun 2022; 13:2883. [PMID: 35610211 PMCID: PMC9130240 DOI: 10.1038/s41467-022-30553-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/06/2022] [Indexed: 01/21/2023] Open
Abstract
RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs.
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Affiliation(s)
- Liang-Cui Chu
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Pedro Arede
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Wei Li
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Erika C Urdaneta
- IRI Life Sciences, Humboldt University Berlin, 10115, Berlin, Germany
| | - Ivayla Ivanova
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Stuart W McKellar
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Jimi C Wills
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Theresa Fröhlich
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Alexander von Kriegsheim
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | | | - Sander Granneman
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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24
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Fu Y, Sun S, Bi J, Kong C, Shi D. An RNA-binding protein-related risk signature can predict the prognosis and tumor immunity of patients with testicular germ cell tumors. Am J Transl Res 2022; 14:2825-2843. [PMID: 35702133 PMCID: PMC9185064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The functions of RNA-binding proteins (RBPs) in the occurrence and development of tumors remain largely unexplored. We established a risk signature based on RBPs to predict the prognosis, tumor-related immunity, and treatment benefits of patients with testicular germ cell tumors (TGCTs). METHODS A risk signature was built based on RBPs closely related to survival obtained from TGCT data in The Cancer Genome Atlas (TCGA) database. The ability of the signature to predict prognosis was analyzed by survival curves and Cox regression. The risk signature was validated using the Gene Expression Omnibus (GEO) database. The connection between tumor immunity and the risk score was evaluated. Risk score-related drug sensitivity and biofunctions were also explored. RESULTS A risk signature including four selected RBP genes (PARP12, USB1, POLR2E and EED) was established. The prognosis of high-risk TGCT patients was worse than that of low-risk TGCT patients. The risk score was considered a critical factor closely related to prognosis, as determined via Cox regression, and was also closely associated with multiple characteristics of tumor immunity, chemotherapy drugs and biofunctions. CONCLUSION The established risk signature including four selected RBPs in TGCTs could predict the prognosis, tumor-related immunity and treatment benefits of patients with TGCTs. Utilization of this signature could help clinicians make personalized treatment decisions.
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Affiliation(s)
- Yang Fu
- Department of Urology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Shanshan Sun
- Department of Pharmacy, People’s Hospital Affiliated of China Medical UniversityShenyang 110015, Liaoning, China
| | - Jianbin Bi
- Department of Urology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Chuize Kong
- Department of Urology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Du Shi
- Department of Urology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
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25
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Hamilton DJ, Hein AE, Holmes ZE, Wuttke DS, Batey RT. The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro. Biochemistry 2022; 61:10.1021/acs.biochem.2c00218. [PMID: 35511045 PMCID: PMC9636074 DOI: 10.1021/acs.biochem.2c00218] [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] [Indexed: 11/29/2022]
Abstract
There is a growing body of evidence that a substantial number of protein domains identified as DNA-binding also interact with RNA to regulate biological processes. Several recent studies have revealed that the Sox2 transcription factor binds RNA through its high-mobility group box (HMGB) domain in vitro and in vivo. A high degree of conservation of this domain among members of the Sox family of transcription factors suggests that RNA-binding activity may be a general feature of these proteins. To address this hypothesis, we examined a subset of HMGB domains from human Sox family of proteins for their ability to bind both DNA and RNA in vitro. We observed selective, high-affinity interactions between Sox family HMGB domains and various model RNA elements, including a four-way junction RNA, a hairpin RNA with an internal bulge, G-quadruplex RNA, and a fragment of long noncoding RNA ES2, which is known to directly interact with Sox2. Importantly, the HMGB domains bind these RNA ligands significantly tighter than nonconsensus dsDNA and in some cases with affinities rivaling those of their consensus dsDNA sequences. These data suggest that RNA binding is a conserved feature of the Sox family of transcription factors with the potential to modulate unappreciated biological functions.
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Affiliation(s)
- Desmond J Hamilton
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Abigail E Hein
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Zachariah E Holmes
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Robert T Batey
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
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26
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Ming R, Li X, Wang E, Wei J, Liu B, Zhou P, Yu W, Zong S, Xiao H. The Prognostic Signature of Head and Neck Squamous Cell Carcinoma Constructed by Immune-Related RNA-Binding Proteins. Front Oncol 2022; 12:795781. [PMID: 35449571 PMCID: PMC9016149 DOI: 10.3389/fonc.2022.795781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/04/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose This study aimed to construct a prognostic signature consisting of immune-related RNA-binding proteins (RBPs) to predict the prognosis of patients with head and neck squamous cell carcinoma (HNSCC) effectively. Methods The transcriptome and clinical data of HNSCC were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. First, we ascertained the immunological differences in HNSCC, through single-sample gene set enrichment analysis, stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE), and cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) deconvolution algorithm. Then we used univariate proportional hazards (Cox) regression analysis and least absolute shrinkage and selection operator (LASSO) Cox regression analysis to screen immune-related RBPs and acquire the risk score of each sample. Subsequently, we further investigated the difference in prognosis, immune status, and tumor mutation burden in high- and low-risk groups. Finally, the efficacy of immunotherapy was measured by the tumor immune dysfunction and exclusion (TIDE) score. Results We derived 15 immune-related RBPs, including FRMD4A, ASNS, RAB11FIP1, FAM120C, CFLAR, CTTN, PLEKHO1, SELENBP1, CHCHD2, NPM3, ATP2A3, CFDP1, IGF2BP2, NQO1, and DENND2D. There were significant differences in the prognoses of patients in the high- and low-risk groups in the training set (p < 0.001) and the validation set (p < 0.01). Furthermore, there were statistical differences between the high-risk group and low-risk group in immune cell infiltration and pathway and tumor mutation load (p < 0.001). In the end, we found that patients in the low-risk group were more sensitive to immunotherapy (p < 0.001), and then we screened 14 small-molecule chemotherapeutics with higher sensitivity to the high-risk group (p < 0.001). Conclusion The study constructed a prognostic signature of HNSCC, which might guide clinical immunotherapy in the future.
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Affiliation(s)
- Ruijie Ming
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangrui Li
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Enhao Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Wei
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Liu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Zhou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenting Yu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shimin Zong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongjun Xiao
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Tu C, Wang L, Wei L. RNA-binding proteins in diabetic microangiopathy. J Clin Lab Anal 2022; 36:e24407. [PMID: 35385161 PMCID: PMC9102490 DOI: 10.1002/jcla.24407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/11/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND As the most common complication of diabetes, the diabetic microangiopathy characterizes diabetic retinopathy (DR) and nephropathy (DN). Diabetic microangiopathy has always been a serious clinical problem. A wide variety of nucleic acid interacting factors called the RNA binding proteins (RBPS) take part in several crucial cellular processes. METHODS Over the past decade, studies have shown that RBPs have crucial part in both malignant tumors and diabetes, especially in diabetic microangiopathy. This review examined the research history of RBPS in DR and DN. RESULTS We reviewed the literature and found that RBPS is potentially useful as therapeutic targets, diagnostic markers, or predict disease progression. CONCLUSION HuR acts as a vital therapeutic targeting protein in diabetic microangiopathy. IGF2BP2, P311, TTP, YBX1, and MBNL1 have a potential role in the treatment of DN.
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Affiliation(s)
- Chao Tu
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Liangzhi Wang
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Lan Wei
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
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28
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Abstract
RNA-binding proteins (RBPs) are of fundamental importance for post-transcriptional gene regulation and protein synthesis. They are required for pre-mRNA processing and for RNA transport, degradation and translation into protein, and can regulate every step in the life cycle of their RNA targets. In addition, RBP function can be modulated by RNA binding. RBPs also participate in the formation of ribonucleoprotein complexes that build up macromolecular machineries such as the ribosome and spliceosome. Although most research has focused on mRNA-binding proteins, non-coding RNAs are also regulated and sequestered by RBPs. Functional defects and changes in the expression levels of RBPs have been implicated in numerous diseases, including neurological disorders, muscular atrophy and cancers. RBPs also contribute to a wide spectrum of kidney disorders. For example, human antigen R has been reported to have a renoprotective function in acute kidney injury (AKI) but might also contribute to the development of glomerulosclerosis, tubulointerstitial fibrosis and diabetic kidney disease (DKD), loss of bicaudal C is associated with cystic kidney diseases and Y-box binding protein 1 has been implicated in the pathogenesis of AKI, DKD and glomerular disorders. Increasing data suggest that the modulation of RBPs and their interactions with RNA targets could be promising therapeutic strategies for kidney diseases.
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Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
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Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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30
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Rafiee MR, Zagalak JA, Sidorov S, Steinhauser S, Davey K, Ule J, Luscombe NM. Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs. Nucleic Acids Res 2021; 49:13092-13107. [PMID: 34871434 PMCID: PMC8682780 DOI: 10.1093/nar/gkab1180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play diverse roles in regulating co-transcriptional RNA-processing and chromatin functions, but our knowledge of the repertoire of chromatin-associated RBPs (caRBPs) and their interactions with chromatin remains limited. Here, we developed SPACE (Silica Particle Assisted Chromatin Enrichment) to isolate global and regional chromatin components with high specificity and sensitivity, and SPACEmap to identify the chromatin-contact regions in proteins. Applied to mouse embryonic stem cells, SPACE identified 1459 chromatin-associated proteins, ∼48% of which are annotated as RBPs, indicating their dual roles in chromatin and RNA-binding. Additionally, SPACEmap stringently verified chromatin-binding of 403 RBPs and identified their chromatin-contact regions. Notably, SPACEmap showed that about 40% of the caRBPs bind chromatin by intrinsically disordered regions (IDRs). Studying SPACE and total proteome dynamics from mES cells grown in 2iL and serum medium indicates significant correlation (R = 0.62). One of the most dynamic caRBPs is Dazl, which we find co-localized with PRC2 at transcription start sites of genes that are distinct from Dazl mRNA binding. Dazl and other PRC2-colocalised caRBPs are rich in intrinsically disordered regions (IDRs), which could contribute to the formation and regulation of phase-separated PRC condensates. Together, our approach provides an unprecedented insight into IDR-mediated interactions and caRBPs with moonlighting functions in native chromatin.
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Affiliation(s)
| | - Julian A Zagalak
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | | | | | - Karen Davey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.,Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
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31
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Zhao D, Wang C, Yan S, Chen R. Advances in the identification of long non-coding RNA binding proteins. Anal Biochem 2021; 639:114520. [PMID: 34896376 DOI: 10.1016/j.ab.2021.114520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/04/2021] [Accepted: 12/04/2021] [Indexed: 02/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nt without evident protein coding function. They play important regulatory roles in many biological processes, e.g., gene regulation, chromatin remodeling, and cell fate determination during development. Dysregulation of lncRNAs has been observed in various diseases including cancer. Interacting with proteins is a crucial way for lncRNAs to play their biological roles. Therefore, the characterization of lncRNA binding proteins is important to understand their functions and to delineate the underlying molecular mechanism. Large-scale studies based on mass spectrometry have characterized over a thousand new RNA binding proteins without known RNA-binding domains, thus revealing the complexity and diversity of RNA-protein interactions. In addition, several methods have been developed to identify the binding proteins for particular RNAs of interest. Here we review the progress of the RNA-centric methods for the identification of RNA-protein interactions, focusing on the studies involving lncRNAs, and discuss their strengths and limitations.
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Affiliation(s)
- Dongqing Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Chunqing Wang
- The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
| | - Shuai Yan
- Peking University First Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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32
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Guo X, Tariq M, Lai Y, Kanwal S, Lv Y, Wang X, Li N, Jiang M, Meng J, Hu J, Yuan J, Luo Z, Ward C, Volpe G, Wang D, Yin M, Qin B, Zhang B, Bao X, Esteban MA. Capture of the newly transcribed RNA interactome using click chemistry. Nat Protoc 2021; 16:5193-5219. [PMID: 34697467 DOI: 10.1038/s41596-021-00609-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
Application of synthetic nucleoside analogues to capture newly transcribed RNAs has unveiled key features of RNA metabolism. Whether this approach could be adapted to isolate the RNA-bound proteome (RNA interactome) was, however, unexplored. We have developed a new method (capture of the newly transcribed RNA interactome using click chemistry, or RICK) for the systematic identification of RNA-binding proteins based on the incorporation of 5-ethynyluridine into newly transcribed RNAs followed by UV cross-linking and click chemistry-mediated biotinylation. The RNA-protein adducts are then isolated by affinity capture using streptavidin-coated beads. Through high-throughput RNA sequencing and mass spectrometry, the RNAs and proteins can be elucidated globally. A typical RICK experimental procedure takes only 1 d, excluding the steps of cell preparation, 5-ethynyluridine labeling, validation (silver staining, western blotting, quantitative reverse-transcription PCR (qRT-PCR) or RNA sequencing (RNA-seq)) and proteomics. Major advantages of RICK are the capture of RNA-binding proteins interacting with any type of RNA and, particularly, the ability to discern between newly transcribed and steady-state RNAs through controlled labeling. Thanks to its versatility, RICK will facilitate the characterization of the total and newly transcribed RNA interactome in different cell types and conditions.
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Affiliation(s)
- Xiangpeng Guo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Muqddas Tariq
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shahzina Kanwal
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiwei Wang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Na Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mengling Jiang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jin Meng
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Jieyi Hu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianwen Yuan
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Giacomo Volpe
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Dongye Wang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Menghui Yin
- Laboratory of RNA Chemical Biology, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Baoming Qin
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Biliang Zhang
- Laboratory of RNA Chemical Biology, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Xichen Bao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
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33
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Hojka-Osinska A, Chlebowski A, Grochowska J, Owczarek EP, Affek K, Kłosowska-Kosicka K, Szczesny RJ, Dziembowski A. Landscape of functional interactions of human processive ribonucleases revealed by high-throughput siRNA screenings. iScience 2021; 24:103036. [PMID: 34541468 PMCID: PMC8437785 DOI: 10.1016/j.isci.2021.103036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/09/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Processive exoribonucleases are executors of RNA decay. In humans, their physical but not functional interactions were thoughtfully investigated. Here we have screened cells deficient in DIS3, XRN2, EXOSC10, DIS3L, and DIS3L2 with a custom siRNA library and determined their genetic interactions (GIs) with diverse pathways of RNA metabolism. We uncovered a complex network of positive interactions that buffer alterations in RNA degradation and reveal reciprocal cooperation with genes involved in transcription, RNA export, and splicing. Further, we evaluated the functional distinctness of nuclear DIS3 and cytoplasmic DIS3L using a library of all known genes associated with RNA metabolism. Our analysis revealed that DIS3 mutation suppresses RNA splicing deficiency, while DIS3L GIs disclose the interplay of cytoplasmic RNA degradation with nuclear RNA processing. Finally, genome-wide DIS3 GI map uncovered relations with genes not directly involved in RNA metabolism, like microtubule organization or regulation of telomerase activity.
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Affiliation(s)
- Anna Hojka-Osinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Joanna Grochowska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Ewelina P. Owczarek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Kamila Affek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Roman J. Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
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34
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Qin W, Myers SA, Carey DK, Carr SA, Ting AY. Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery. Nat Commun 2021; 12:4980. [PMID: 34404792 PMCID: PMC8370977 DOI: 10.1038/s41467-021-25259-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Proximity labeling (PL) with genetically-targeted promiscuous enzymes has emerged as a powerful tool for unbiased proteome discovery. By combining the spatiotemporal specificity of PL with methods for functional protein enrichment, we show that it is possible to map specific protein subclasses within distinct compartments of living cells. In particular, we develop a method to enrich subcompartment-specific RNA binding proteins (RBPs) by combining peroxidase-catalyzed PL with organic-aqueous phase separation of crosslinked protein-RNA complexes (“APEX-PS”). We use APEX-PS to generate datasets of nuclear, nucleolar, and outer mitochondrial membrane (OMM) RBPs, which can be mined for novel functions. For example, we find that the OMM RBP SYNJ2BP retains specific nuclear-encoded mitochondrial mRNAs at the OMM during translation stress, facilitating their local translation and import of protein products into the mitochondrion during stress recovery. Functional PL in general, and APEX-PS in particular, represent versatile approaches for the discovery of proteins with novel function in specific subcellular compartments. Proximity labeling is used to map and discover proteins in specific subcellular compartments. Here the authors combine APEX-mediated proximity labeling with organic-aqueous phase separation to identify nuclear, nucleolar, and outer mitochondrial membrane RNA binding proteins.
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Affiliation(s)
- Wei Qin
- Departments of Biology, Genetics, and Chemistry, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Samuel A Myers
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Y Ting
- Departments of Biology, Genetics, and Chemistry, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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35
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Skalska L, Begley V, Beltran M, Lukauskas S, Khandelwal G, Faull P, Bhamra A, Tavares M, Wellman R, Tvardovskiy A, Foster BM, Ruiz de Los Mozos I, Herrero J, Surinova S, Snijders AP, Bartke T, Jenner RG. Nascent RNA antagonizes the interaction of a set of regulatory proteins with chromatin. Mol Cell 2021; 81:2944-2959.e10. [PMID: 34166609 DOI: 10.1016/j.molcel.2021.05.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 12/30/2022]
Abstract
A number of regulatory factors are recruited to chromatin by specialized RNAs. Whether RNA has a more general role in regulating the interaction of proteins with chromatin has not been determined. We used proteomics methods to measure the global impact of nascent RNA on chromatin in embryonic stem cells. Surprisingly, we found that nascent RNA primarily antagonized the interaction of chromatin modifiers and transcriptional regulators with chromatin. Transcriptional inhibition and RNA degradation induced recruitment of a set of transcriptional regulators, chromatin modifiers, nucleosome remodelers, and regulators of higher-order structure. RNA directly bound to factors, including BAF, NuRD, EHMT1, and INO80 and inhibited their interaction with nucleosomes. The transcriptional elongation factor P-TEFb directly bound pre-mRNA, and its recruitment to chromatin upon Pol II inhibition was regulated by the 7SK ribonucleoprotein complex. We postulate that by antagonizing the interaction of regulatory proteins with chromatin, nascent RNA links transcriptional output with chromatin composition.
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Affiliation(s)
- Lenka Skalska
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Victoria Begley
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Manuel Beltran
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Garima Khandelwal
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Peter Faull
- The Francis Crick Institute, London NW1 1AT, UK
| | - Amandeep Bhamra
- Proteomics Research Translational Technology Platform, UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Manuel Tavares
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Rachel Wellman
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Benjamin M Foster
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Igor Ruiz de Los Mozos
- The Francis Crick Institute, London NW1 1AT, UK; Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Javier Herrero
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | - Silvia Surinova
- Proteomics Research Translational Technology Platform, UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK
| | | | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Richard G Jenner
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London WC1E 6BT, UK.
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36
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Zhang Z, Liu T, Dong H, Li J, Sun H, Qian X, Qin W. An RNA tagging approach for system-wide RNA-binding proteome profiling and dynamics investigation upon transcription inhibition. Nucleic Acids Res 2021; 49:e65. [PMID: 33693821 PMCID: PMC8216453 DOI: 10.1093/nar/gkab156] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 02/17/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
RNA-protein interactions play key roles in epigenetic, transcriptional and posttranscriptional regulation. To reveal the regulatory mechanisms of these interactions, global investigation of RNA-binding proteins (RBPs) and monitor their changes under various physiological conditions are needed. Herein, we developed a psoralen probe (PP)-based method for RNA tagging and ribonucleic-protein complex (RNP) enrichment. Isolation of both coding and noncoding RNAs and mapping of 2986 RBPs including 782 unknown candidate RBPs from HeLa cells was achieved by PP enrichment, RNA-sequencing and mass spectrometry analysis. The dynamics study of RNPs by PP enrichment after the inhibition of RNA synthesis provides the first large-scale distribution profile of RBPs bound to RNAs with different decay rates. Furthermore, the remarkably greater decreases in the abundance of the RBPs obtained by PP-enrichment than by global proteome profiling suggest that PP enrichment after transcription inhibition offers a valuable way for large-scale evaluation of the candidate RBPs.
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Affiliation(s)
- Zheng Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Tong Liu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hangyan Dong
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jian Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Haofan Sun
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China.,College of Basic Medicine, Anhui Medical University, Hefei 230032, China
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Audoynaud C, Vagner S, Lambert S. Non-homologous end-joining at challenged replication forks: an RNA connection? Trends Genet 2021; 37:973-985. [PMID: 34238592 DOI: 10.1016/j.tig.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022]
Abstract
Defective DNA replication, known as 'replication stress', is a source of DNA damage, a hallmark of numerous human diseases, including cancer, developmental defect, neurological disorders, and premature aging. Recent work indicates that non-homologous end-joining (NHEJ) is unexpectedly active during DNA replication to repair replication-born DNA lesions and to safeguard replication fork integrity. However, erroneous NHEJ events are deleterious to genome stability. RNAs are novel regulators of NHEJ activity through their ability to modulate the assembly of repair complexes in trans. At DNA damage sites, RNAs and DNA-embedded ribonucleotides modulate repair efficiency and fidelity. We discuss here how RNAs and associated proteins, including RNA binding proteins, may regulate NHEJ to sustain genome stability during DNA replication.
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Affiliation(s)
- Charlotte Audoynaud
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Stéphan Vagner
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France.
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38
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Satterwhite ER, Mansfield KD. RNA methyltransferase METTL16: Targets and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1681. [PMID: 34227247 PMCID: PMC9286414 DOI: 10.1002/wrna.1681] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022]
Abstract
The N6-methyladenosine (m6A) RNA methyltransferase METTL16 is an emerging player in the RNA modification landscape of the human cell. Originally thought to be a ribosomal RNA methyltransferase, it has now been shown to bind and methylate the MAT2A messenger RNA (mRNA) and U6 small nuclear RNA (snRNA). It has also been shown to bind the MALAT1 long noncoding RNA and several other RNAs. METTL16's methyltransferase domain contains the Rossmann-like fold of class I methyltransferases and uses S-adenosylmethionine (SAM) as the methyl donor. It has an RNA methylation consensus sequence of UACAGARAA (modified A underlined), and structural requirements for its known RNA interactors. In addition to the methyltransferase domain, METTL16 protein has two other RNA binding domains, one of which resides in a vertebrate conserved region, and a putative nuclear localization signal. The role of METTL16 in the cell is still being explored, however evidence suggests it is essential for most cells. This is currently hypothesized to be due to its role in regulating the splicing of MAT2A mRNA in response to cellular SAM levels. However, one of the more pressing questions remaining is what role METTL16's methylation of U6 snRNA plays in splicing and potentially cellular survival. METTL16 also has several other putative coding and noncoding RNA interactors but the definitive methylation status of those RNAs and the role METTL16 plays in their life cycle is yet to be determined. Overall, METTL16 is an intriguing RNA binding protein and methyltransferase whose important functions in the cell are just beginning to be understood. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Emily R Satterwhite
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Kyle D Mansfield
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
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39
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The expanding world of metabolic enzymes moonlighting as RNA binding proteins. Biochem Soc Trans 2021; 49:1099-1108. [PMID: 34110361 DOI: 10.1042/bst20200664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022]
Abstract
RNA binding proteins play key roles in many aspects of RNA metabolism and function, including splicing, transport, translation, localization, stability and degradation. Within the past few years, proteomics studies have identified dozens of enzymes in intermediary metabolism that bind to RNA. The wide occurrence and conservation of RNA binding ability across distant branches of the evolutionary tree suggest that these moonlighting enzymes are involved in connections between intermediary metabolism and gene expression that comprise far more extensive regulatory networks than previously thought. There are many outstanding questions about the molecular structures and mechanisms involved, the effects of these interactions on enzyme and RNA functions, and the factors that regulate the interactions. The effects on RNA function are likely to be wider than regulation of translation, and some enzyme-RNA interactions have been found to regulate the enzyme's catalytic activity. Several enzyme-RNA interactions have been shown to be affected by cellular factors that change under different intracellular and environmental conditions, including concentrations of substrates and cofactors. Understanding the molecular mechanisms involved in the interactions between the enzymes and RNA, the factors involved in regulation, and the effects of the enzyme-RNA interactions on both the enzyme and RNA functions will lead to a better understanding of the role of the many newly identified enzyme-RNA interactions in connecting intermediary metabolism and gene expression.
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40
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Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep 2021; 35:109198. [PMID: 34077720 DOI: 10.1016/j.celrep.2021.109198] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
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Affiliation(s)
- Shlomi Dvir
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Chen Lesnik
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | | | | | - Michal Amit
- Accellta LTD, Haifa 320003, Israel; Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College, Karmiel 2161002, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel; Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel.
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Yan S, Zhao D, Wang C, Wang H, Guan X, Gao Y, Zhang X, Zhang N, Chen R. Characterization of RNA-binding proteins in the cell nucleus and cytoplasm. Anal Chim Acta 2021; 1168:338609. [PMID: 34051998 DOI: 10.1016/j.aca.2021.338609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/14/2021] [Accepted: 05/02/2021] [Indexed: 02/08/2023]
Abstract
As critical players in the regulation of gene expression, RNA-binding proteins (RBPs) play fundamental roles in cellular functions and diseases. In this study, we established an analytical strategy to characterize RBPs from different subcellular regions by combining subcellular fractionation, acidic guanidinium-thiocyanate-phenol-chloroform biphasic extraction, and quantitative mass spectrometry. Using this method, we identified 1775 and 2245 RBPs from the cell nucleus and cytoplasm. The data confirmed a large spectrum of known RBPs, revealed 614 novel ones that have never been reported before, and cataloged their subcellular localizations. Intriguingly, 200 metabolic enzymes from diverse metabolic pathways were observed as RBPs, some of which were further validated through western blotting following UV-mediated crosslinking and biphasic extraction. Furthermore, we characterized 2157 RNA-binding interfaces, providing structural information regarding the complex nature of RNA-protein interactions. Taken together, our data greatly expand the current reservoir of known RBPs and highlight the potential role of RNA-binding in the regulation of cellular metabolism.
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Affiliation(s)
- Shuai Yan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Peking University First Hospital, Peking University Health Science Center, Beijing, 100034, China
| | - Dongqing Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Chunqing Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Hao Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xinyu Guan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ning Zhang
- Peking University First Hospital, Peking University Health Science Center, Beijing, 100034, China; Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University, Tianjin, 300070, China.
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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Wang M, Jiang F, Wei K, Wang J, Zhou G, Wu C, Yin G. Development and Validation of a RNA Binding Protein-Associated Prognostic Model for Hepatocellular Carcinoma. Technol Cancer Res Treat 2021; 20:15330338211004936. [PMID: 33910445 PMCID: PMC8111555 DOI: 10.1177/15330338211004936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Dysregulation of RNA binding proteins (RBPs) has been identified in multiple malignant tumors correlated with tumor progression and occurrence. However, the function of RBPs is not well understood in hepatocellular carcinoma (HCC). METHODS The RNA sequence data of HCC was extracted out of the Cancer Genome Atlas (TCGA) database and different RBPs were calculated between regular and cancerous tissue. The study explored the expression and predictive value of the RBPs systemically with a series of bioinformatic analyzes. RESULTS A total of 330 RBPs, including 208 up-regulated and 122 down-regulated RBPs, were classified differently. Four RBPs (MRPL54, EZH2, PPARGC1A, EIF2AK4) were defined as the forecast related hub gene and used to construct a model for prediction. Further study showed that the high-risk subgroup is poor survived (OS) compared to the model-based low-risk subgroup. The area of the prognostic model under the time-dependent receiver operator characteristic (ROC) curve is 0.814 in TCGA training group and 0.729 in validation group, indicating a strong prognostic model. We also created a predictive nomogram and a web-based calculator (https://dxyjiang.shinyapps.io/RBPpredict/) based on the 4 RBPs and internal validation in the TCGA cohort, which displayed a beneficial predictive ability for HCC. CONCLUSIONS Our results provide new insights into HCC pathogenesis. The 4-RBP gene signature showed a reliable HCC prediction ability with possible applications in therapeutic decision making and personalized therapy.
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Affiliation(s)
- Ming Wang
- Department of Plastic and Burn Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Jiang
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Neonatology, 92276Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ke Wei
- Medical Service Section, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jimei Wang
- Department of Neonatology, 92276Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Guoping Zhou
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chuyan Wu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guoyong Yin
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Weissinger R, Heinold L, Akram S, Jansen RP, Hermesh O. RNA Proximity Labeling: A New Detection Tool for RNA-Protein Interactions. Molecules 2021; 26:2270. [PMID: 33919831 PMCID: PMC8070807 DOI: 10.3390/molecules26082270] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/26/2022] Open
Abstract
Multiple cellular functions are controlled by the interaction of RNAs and proteins. Together with the RNAs they control, RNA interacting proteins form RNA protein complexes, which are considered to serve as the true regulatory units for post-transcriptional gene expression. To understand how RNAs are modified, transported, and regulated therefore requires specific knowledge of their interaction partners. To this end, multiple techniques have been developed to characterize the interaction between RNAs and proteins. In this review, we briefly summarize the common methods to study RNA-protein interaction including crosslinking and immunoprecipitation (CLIP), and aptamer- or antisense oligonucleotide-based RNA affinity purification. Following this, we focus on in vivo proximity labeling to study RNA-protein interactions. In proximity labeling, a labeling enzyme like ascorbate peroxidase or biotin ligase is targeted to specific RNAs, RNA-binding proteins, or even cellular compartments and uses biotin to label the proteins and RNAs in its vicinity. The tagged molecules are then enriched and analyzed by mass spectrometry or RNA-Seq. We highlight the latest studies that exemplify the strength of this approach for the characterization of RNA protein complexes and distribution of RNAs in vivo.
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Affiliation(s)
| | | | | | | | - Orit Hermesh
- Interfaculty Institute for Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany; (R.W.); (L.H.); (S.A.); (R.-P.J.)
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44
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Caudron-Herger M, Jansen RE, Wassmer E, Diederichs S. RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. Nucleic Acids Res 2021; 49:D425-D436. [PMID: 33196814 PMCID: PMC7778890 DOI: 10.1093/nar/gkaa1040] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/01/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
RNA-protein complexes have emerged as central players in numerous key cellular processes with significant relevance in health and disease. To further deepen our knowledge of RNA-binding proteins (RBPs), multiple proteome-wide strategies have been developed to identify RBPs in different species leading to a large number of studies contributing experimentally identified as well as predicted RBP candidate catalogs. However, the rapid evolution of the field led to an accumulation of isolated datasets, hampering the access and comparison of their valuable content. Moreover, tools to link RBPs to cellular pathways and functions were lacking. Here, to facilitate the efficient screening of the RBP resources, we provide RBP2GO (https://RBP2GO.DKFZ.de), a comprehensive database of all currently available proteome-wide datasets for RBPs across 13 species from 53 studies including 105 datasets identifying altogether 22 552 RBP candidates. These are combined with the information on RBP interaction partners and on the related biological processes, molecular functions and cellular compartments. RBP2GO offers a user-friendly web interface with an RBP scoring system and powerful advanced search tools allowing forward and reverse searches connecting functions and RBPs to stimulate new research directions.
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Affiliation(s)
- Maiwen Caudron-Herger
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ralf E Jansen
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Elsa Wassmer
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, 79106 Freiburg, Germany
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45
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The search for RNA-binding proteins: a technical and interdisciplinary challenge. Biochem Soc Trans 2021; 49:393-403. [PMID: 33492363 PMCID: PMC7925008 DOI: 10.1042/bst20200688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins are customarily regarded as important facilitators of gene expression. In recent years, RNA–protein interactions have also emerged as a pervasive force in the regulation of homeostasis. The compendium of proteins with provable RNA-binding function has swelled from the hundreds to the thousands astride the partnership of mass spectrometry-based proteomics and RNA sequencing. At the foundation of these advances is the adaptation of RNA-centric capture methods that can extract bound protein that has been cross-linked in its native environment. These methods reveal snapshots in time displaying an extensive network of regulation and a wealth of data that can be used for both the discovery of RNA-binding function and the molecular interfaces at which these interactions occur. This review will focus on the impact of these developments on our broader perception of post-transcriptional regulation, and how the technical features of current capture methods, as applied in mammalian systems, create a challenging medium for interpretation by systems biologists and target validation by experimental researchers.
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46
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Gebauer F, Schwarzl T, Valcárcel J, Hentze MW. RNA-binding proteins in human genetic disease. Nat Rev Genet 2020; 22:185-198. [PMID: 33235359 DOI: 10.1038/s41576-020-00302-y] [Citation(s) in RCA: 324] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2020] [Indexed: 12/27/2022]
Abstract
RNA-binding proteins (RBPs) are critical effectors of gene expression, and as such their malfunction underlies the origin of many diseases. RBPs can recognize hundreds of transcripts and form extensive regulatory networks that help to maintain cell homeostasis. System-wide unbiased identification of RBPs has increased the number of recognized RBPs into the four-digit range and revealed new paradigms: from the prevalence of structurally disordered RNA-binding regions with roles in the formation of membraneless organelles to unsuspected and potentially pervasive connections between intermediary metabolism and RNA regulation. Together with an increasingly detailed understanding of molecular mechanisms of RBP function, these insights are facilitating the development of new therapies to treat malignancies. Here, we provide an overview of RBPs involved in human genetic disorders, both Mendelian and somatic, and discuss emerging aspects in the field with emphasis on molecular mechanisms of disease and therapeutic interventions.
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Affiliation(s)
- Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain. .,University Pompeu Fabra (UPF), Barcelona, Spain.
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Muleya V, Marondedze C. Functional Roles of RNA-Binding Proteins in Plant Signaling. Life (Basel) 2020; 10:life10110288. [PMID: 33217949 PMCID: PMC7698727 DOI: 10.3390/life10110288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
RNA-binding proteins (RBPs) are typical proteins that bind RNA through single or multiple RNA-binding domains (RBDs). These proteins have a functional role in determining the fate or function of the bound RNAs. A few hundred RBPs were known through in silico prediction based on computational assignment informed by structural similarity and the presence of classical RBDs. However, RBPs lacking such conventional RBDs were omitted. Owing to the recent mRNA interactome capture technology based on UV-crosslinking and fixing proteins to their mRNA targets followed by affinity capture purification and identification of RBPs by tandem mass spectrometry, several hundreds of RBPs have recently been discovered. These proteome-wide studies have colossally increased the number of proteins implicated in RNA binding and unearthed hundreds of novel RBPs lacking classical RBDs, such as proteins involved in intermediary metabolism. These discoveries provide wide insights into the post-transcriptional gene regulation players and their role in plant signaling, such as environmental stress conditions. In this review, novel discoveries of RBPs are explored, particularly on the evolving knowledge of their role in stress responses. The molecular functions of these RBPs, particularly focusing on those that do not have classical RBDs, are also elucidated at the systems level.
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Affiliation(s)
- Victor Muleya
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Main Campus, Senga Road, Gweru P Bag 9055, Zimbabwe;
| | - Claudius Marondedze
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Main Campus, Senga Road, Gweru P Bag 9055, Zimbabwe;
- Rijk Zwaan, 2678 ZG De Lier, The Netherlands
- Correspondence: or or
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Hepatitis B virus Core protein nuclear interactome identifies SRSF10 as a host RNA-binding protein restricting HBV RNA production. PLoS Pathog 2020; 16:e1008593. [PMID: 33180834 PMCID: PMC7707522 DOI: 10.1371/journal.ppat.1008593] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/01/2020] [Accepted: 10/04/2020] [Indexed: 12/11/2022] Open
Abstract
Despite the existence of a preventive vaccine, chronic infection with Hepatitis B virus (HBV) affects more than 250 million people and represents a major global cause of hepatocellular carcinoma (HCC) worldwide. Current clinical treatments, in most of cases, do not eliminate viral genome that persists as a DNA episome in the nucleus of hepatocytes and constitutes a stable template for the continuous expression of viral genes. Several studies suggest that, among viral factors, the HBV core protein (HBc), well-known for its structural role in the cytoplasm, could have critical regulatory functions in the nucleus of infected hepatocytes. To elucidate these functions, we performed a proteomic analysis of HBc-interacting host-factors in the nucleus of differentiated HepaRG, a surrogate model of human hepatocytes. The HBc interactome was found to consist primarily of RNA-binding proteins (RBPs), which are involved in various aspects of mRNA metabolism. Among them, we focused our studies on SRSF10, a RBP that was previously shown to regulate alternative splicing (AS) in a phosphorylation-dependent manner and to control stress and DNA damage responses, as well as viral replication. Functional studies combining SRSF10 knockdown and a pharmacological inhibitor of SRSF10 phosphorylation (1C8) showed that SRSF10 behaves as a restriction factor that regulates HBV RNAs levels and that its dephosphorylated form is likely responsible for the anti-viral effect. Surprisingly, neither SRSF10 knock-down nor 1C8 treatment modified the splicing of HBV RNAs but rather modulated the level of nascent HBV RNA. Altogether, our work suggests that in the nucleus of infected cells HBc interacts with multiple RBPs that regulate viral RNA metabolism. Our identification of SRSF10 as a new anti-HBV restriction factor offers new perspectives for the development of new host-targeted antiviral strategies. Chronic infection with Hepatitis B virus (HBV) affects more than 250 million of people world-wide and is a major global cause of liver cancer. Current treatments lead to a significant reduction of viremia in patients. However, viral clearance is rarely obtained and the persistence of the HBV genome in the hepatocyte’s nucleus generates a stable source of viral RNAs and subsequently proteins which play important roles in immune escape mechanisms and liver disease progression. Therapies aiming at efficiently and durably eliminating viral gene expression are still required. In this study, we identified the nuclear partners of the HBV Core protein (HBc) to understand how this structural protein, responsible for capsid assembly in the cytoplasm, could also regulate viral gene expression. The HBc interactome was found to consist primarily of RNA-binding proteins (RBPs). One of these RBPs, SRSF10, was demonstrated to restrict HBV RNA levels and a drug, able to alter its phosphorylation, behaved as an antiviral compound capable of reducing viral gene expression. Altogether, this study sheds new light on novel regulatory functions of HBc and provides information relevant for the development of antiviral strategies aiming at preventing viral gene expression.
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Backlund M, Stein F, Rettel M, Schwarzl T, Perez-Perri JI, Brosig A, Zhou Y, Neu-Yilik G, Hentze MW, Kulozik AE. Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins. Nucleic Acids Res 2020; 48:4725-4740. [PMID: 32313943 PMCID: PMC7229827 DOI: 10.1093/nar/gkaa256] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular stress causes multifaceted reactions to trigger adaptive responses to environmental cues at all levels of the gene expression pathway. RNA-binding proteins (RBP) are key contributors to stress-induced regulation of RNA fate and function. Here, we uncover the plasticity of the RNA interactome in stressed cells, differentiating between responses in the nucleus and in the cytoplasm. We applied enhanced RNA interactome capture (eRIC) analysis preceded by nucleo-cytoplasmic fractionation following arsenite-induced oxidative stress. The data reveal unexpectedly compartmentalized RNA interactomes and their responses to stress, including differential responses of RBPs in the nucleus versus the cytoplasm, which would have been missed by whole cell analyses.
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Affiliation(s)
- Michael Backlund
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- To whom correspondence should be addressed. Tel: +49 6221 564555;
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Joel I Perez-Perri
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Annika Brosig
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Yang Zhou
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence may also be addressed to Matthias W. Hentze.
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Correspondence may also be addressed to Andreas E. Kulozik.
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Proteomics-Based Systematic Identification of Nuclear Proteins Anchored to Chromatin via RNA. Methods Mol Biol 2020. [PMID: 32681508 DOI: 10.1007/978-1-0716-0680-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Chromatin serves as a platform for a multitude of biological processes, including transcription and co-transcriptional RNA processing. Consequently, chromatin is likely to be covered with many RNA molecules.Here we describe a simple, reliable, and cross-link-free method for the systematic identification of chromatin-associated RBPs that exhibit RNA-dependent chromatin association.
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