1
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Xiang JS, Schafer DM, Rothamel KL, Yeo GW. Decoding protein-RNA interactions using CLIP-based methodologies. Nat Rev Genet 2024:10.1038/s41576-024-00749-3. [PMID: 38982239 DOI: 10.1038/s41576-024-00749-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 07/11/2024]
Abstract
Protein-RNA interactions are central to all RNA processing events, with pivotal roles in the regulation of gene expression and cellular functions. Dysregulation of these interactions has been increasingly linked to the pathogenesis of human diseases. High-throughput approaches to identify RNA-binding proteins and their binding sites on RNA - in particular, ultraviolet crosslinking followed by immunoprecipitation (CLIP) - have helped to map the RNA interactome, yielding transcriptome-wide protein-RNA atlases that have contributed to key mechanistic insights into gene expression and gene-regulatory networks. Here, we review these recent advances, explore the effects of cellular context on RNA binding, and discuss how these insights are shaping our understanding of cellular biology. We also review the potential therapeutic applications arising from new knowledge of protein-RNA interactions.
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Affiliation(s)
- Joy S Xiang
- Division of Biomedical Sciences, UC Riverside, Riverside, CA, USA
| | - Danielle M Schafer
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Katherine L Rothamel
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Laboratories for Innovative Medicines, La Jolla, CA, USA.
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2
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Tak H, Cha S, Hong Y, Jung M, Ryu S, Han S, Jeong SM, Kim W, Lee EK. The miR-30-5p/TIA-1 axis directs cellular senescence by regulating mitochondrial dynamics. Cell Death Dis 2024; 15:404. [PMID: 38858355 PMCID: PMC11164864 DOI: 10.1038/s41419-024-06797-1] [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: 11/12/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024]
Abstract
Senescent cells exhibit a diverse spectrum of changes in their morphology, proliferative capacity, senescence-associated secretory phenotype (SASP) production, and mitochondrial homeostasis. These cells often manifest with elongated mitochondria, a hallmark of cellular senescence. However, the precise regulatory mechanisms orchestrating this phenomenon remain predominantly unexplored. In this study, we provide compelling evidence for decreases in TIA-1, a pivotal regulator of mitochondrial dynamics, in models of both replicative senescence and ionizing radiation (IR)-induced senescence. The downregulation of TIA-1 was determined to trigger mitochondrial elongation and enhance the expression of senescence-associated β-galactosidase, a marker of cellular senescence, in human foreskin fibroblast HS27 cells and human keratinocyte HaCaT cells. Conversely, the overexpression of TIA-1 mitigated IR-induced cellular senescence. Notably, we identified the miR-30-5p family as a novel factor regulating TIA-1 expression. Augmented expression of the miR-30-5p family was responsible for driving mitochondrial elongation and promoting cellular senescence in response to IR. Taken together, our findings underscore the significance of the miR-30-5p/TIA-1 axis in governing mitochondrial dynamics and cellular senescence.
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Affiliation(s)
- Hyosun Tak
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France
| | - Seongho Cha
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Youlim Hong
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Myeongwoo Jung
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Seungyeon Ryu
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Sukyoung Han
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Seung Min Jeong
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Wook Kim
- Department of Molecular Science & Technology, Ajou University, Suwon, 16499, South Korea
| | - Eun Kyung Lee
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea.
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea.
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea.
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3
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Shen Z, Naveed M, Bao J. Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1852. [PMID: 38715192 DOI: 10.1002/wrna.1852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 06/06/2024]
Abstract
Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Zhaokang Shen
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Muhammad Naveed
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
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4
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Lewinski M, Brüggemann M, Köster T, Reichel M, Bergelt T, Meyer K, König J, Zarnack K, Staiger D. Mapping protein-RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2). Nat Protoc 2024; 19:1183-1234. [PMID: 38278964 DOI: 10.1038/s41596-023-00935-3] [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: 06/01/2023] [Accepted: 10/20/2023] [Indexed: 01/28/2024]
Abstract
Despite crucial roles of RNA-binding proteins (RBPs) in plant physiology and development, methods for determining their transcriptome-wide binding landscape are less developed than those used in other model organisms. Cross-linking and immunoprecipitation (CLIP) methods (based on UV-mediated generation of covalent bonds between RNAs and cognate RBPs in vivo, purification of the cross-linked complexes and identification of the co-purified RNAs by high-throughput sequencing) have been applied mainly in mammalian cells growing in monolayers or in translucent tissue. We have developed plant iCLIP2, an efficient protocol for performing individual-nucleotide-resolution CLIP (iCLIP) in plants, tailored to overcome the experimental hurdles posed by plant tissue. We optimized the UV dosage to efficiently cross-link RNA and proteins in plants and expressed epitope-tagged RBPs under the control of their native promoters in loss-of-function mutants. We select epitopes for which nanobodies are available, allowing stringent conditions for immunopurification of the RNA-protein complexes to be established. To overcome the inherently high RNase content of plant cells, RNase inhibitors are added and the limited RNA fragmentation step is modified. We combine the optimized isolation of RBP-bound RNAs with iCLIP2, a streamlined protocol that greatly enhances the efficiency of library preparation for high-throughput sequencing. Plant researchers with experience in molecular biology and handling of RNA can complete this iCLIP2 protocol in ~5 d. Finally, we describe a bioinformatics workflow to determine targets of Arabidopsis RBPs from iCLIP data, covering all steps from downloading sequencing reads to identifying cross-linking events ( https://github.com/malewins/Plant-iCLIPseq ), and present the R/Bioconductor package BindingSiteFinder to extract reproducible binding sites ( https://bioconductor.org/packages/release/bioc/html/BindingSiteFinder.html ).
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Affiliation(s)
- Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Thorsten Bergelt
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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5
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Ramos-Velasco B, Naranjo R, Izquierdo JM. Bibliometric Overview on T-Cell Intracellular Antigens and Their Pathological Implications. BIOLOGY 2024; 13:195. [PMID: 38534464 DOI: 10.3390/biology13030195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024]
Abstract
T-cell intracellular antigen 1 (TIA1) and TIA1-like/related protein (TIAL1/TIAR) are two members of the classical family of RNA binding proteins. Through their selective interactions with distinct RNAs and proteins, these multifunctional regulators are involved in chromatin remodeling, RNA splicing and processing and translation regulation, linking them to a wide range of diseases including neuronal disorders, cancer and other pathologies. From their discovery to the present day, many studies have focused on the behavior of these proteins in order to understand their impact on molecular and cellular processes and to understand their relationship to human pathologies. The volume of research on these proteins in various fields, including molecular biology, biochemistry, cell biology, immunology and cancer, has steadily increased, indicating a growing interest in these gene expression regulators among researchers. This information can be used to know the most productive institutions working in the field, understand the focus of research, identify key areas of involvement, delve deeper into their relationship and impact on different diseases, and to establish the level of study associated with them.
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Affiliation(s)
- Beatriz Ramos-Velasco
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Rocío Naranjo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - José M Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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6
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Podszywalow-Bartnicka P, Neugebauer KM. Multiple roles for AU-rich RNA binding proteins in the development of haematologic malignancies and their resistance to chemotherapy. RNA Biol 2024; 21:1-17. [PMID: 38798162 PMCID: PMC11135835 DOI: 10.1080/15476286.2024.2346688] [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] [Accepted: 04/08/2024] [Indexed: 05/29/2024] Open
Abstract
Post-transcriptional regulation by RNA binding proteins can determine gene expression levels and drive changes in cancer cell proteomes. Identifying mechanisms of protein-RNA binding, including preferred sequence motifs bound in vivo, provides insights into protein-RNA networks and how they impact mRNA structure, function, and stability. In this review, we will focus on proteins that bind to AU-rich elements (AREs) in nascent or mature mRNA where they play roles in response to stresses encountered by cancer cells. ARE-binding proteins (ARE-BPs) specifically impact alternative splicing, stability, decay and translation, and formation of RNA-rich biomolecular condensates like cytoplasmic stress granules (SGs). For example, recent findings highlight the role of ARE-BPs - like TIAR and HUR - in chemotherapy resistance and in translational regulation of mRNAs encoding pro-inflammatory cytokines. We will discuss emerging evidence that different modes of ARE-BP activity impact leukaemia and lymphoma development, progression, adaptation to microenvironment and chemotherapy resistance.
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Affiliation(s)
- Paulina Podszywalow-Bartnicka
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karla M. Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
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7
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Horste EL, Fansler MM, Cai T, Chen X, Mitschka S, Zhen G, Lee FCY, Ule J, Mayr C. Subcytoplasmic location of translation controls protein output. Mol Cell 2023; 83:4509-4523.e11. [PMID: 38134885 PMCID: PMC11146010 DOI: 10.1016/j.molcel.2023.11.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/15/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
The cytoplasm is highly compartmentalized, but the extent and consequences of subcytoplasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endoplasmic reticulum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on genes that encode non-membrane proteins, we observed that 52% have transcripts enriched in specific compartments. Compartment enrichment correlates with a combinatorial code based on mRNA length, exon length, and 3' UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentalized by local translation environments.
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Affiliation(s)
- Ellen L Horste
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA; Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Mervin M Fansler
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY 10021, USA
| | - Ting Cai
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Xiuzhen Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Gang Zhen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Flora C Y Lee
- UK Dementia Research Institute, King's College London, London SE5 9NU, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jernej Ule
- UK Dementia Research Institute, King's College London, London SE5 9NU, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christine Mayr
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA; Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY 10021, USA.
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8
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Akhtar F, Ruiz JH, Liu YG, Resendez RG, Feliers D, Morales LD, Diaz-Badillo A, Lehman DM, Arya R, Lopez-Alvarenga JC, Blangero J, Duggirala R, Mummidi S. Functional characterization of the disease-associated CCL2 rs1024611G-rs13900T haplotype: The role of the RNA-binding protein HuR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564937. [PMID: 37961304 PMCID: PMC10635030 DOI: 10.1101/2023.10.31.564937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
CC-chemokine ligand 2 (CCL2) is involved in the pathogenesis of several diseases associated with monocyte/macrophage recruitment, such as HIV-associated neurocognitive disorder (HAND), tuberculosis, and atherosclerosis. The rs1024611 (alleles:A>G; G is the risk allele) polymorphism in the CCL2 cis-regulatory region is associated with increased CCL2 expression in vitro and ex vivo, leukocyte mobilization in vivo, and deleterious disease outcomes. However, the molecular basis for the rs1024611-associated differential CCL2 expression remains poorly characterized. It is conceivable that genetic variant(s) in linkage disequilibrium (LD) with rs1024611 could mediate such effects. Previously, we used rs13900 (alleles:_C>T) in the CCL2 3' untranslated region (3' UTR) that is in perfect LD with rs1024611 to demonstrate allelic expression imbalance (AEI) of CCL2 in heterozygous individuals. Here we tested the hypothesis that the rs13900 could modulate CCL2 expression by altering mRNA turnover and/or translatability. The rs13900 T allele conferred greater stability to the CCL2 transcript when compared to the rs13900 C allele. The rs13900 T allele also had increased binding to Human Antigen R (HuR), an RNA-binding protein, in vitro and ex vivo. The rs13900 alleles imparted differential activity to reporter vectors and influenced the translatability of the reporter transcript. We further demonstrated a role for HuR in mediating allele-specific effects on CCL2 expression in overexpression and silencing studies. The presence of the rs1024611G-rs13900T conferred a distinct transcriptomic signature related to inflammation and immunity. Our studies suggest that the differential interactions of HuR with rs13900 could modulate CCL2 expression and explain the interindividual differences in CCL2-mediated disease susceptibility.
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Affiliation(s)
- Feroz Akhtar
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Joselin Hernandez Ruiz
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Ya-Guang Liu
- Department of Pathology, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Roy G. Resendez
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Denis Feliers
- Department of Medicine, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Liza D. Morales
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Alvaro Diaz-Badillo
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Donna M. Lehman
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Rector Arya
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Juan Carlos Lopez-Alvarenga
- Department of Population Health and Biostatistics, School of Medicine, University of Texas Rio Grande Valley, Harlingen, Texas, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Ravindranath Duggirala
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Srinivas Mummidi
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
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9
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Vorobeva MA, Skvortsov DA, Pervouchine DD. Cooperation and Competition of RNA Secondary Structure and RNA-Protein Interactions in the Regulation of Alternative Splicing. Acta Naturae 2023; 15:23-31. [PMID: 38234601 PMCID: PMC10790352 DOI: 10.32607/actanaturae.26826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/31/2023] [Indexed: 01/19/2024] Open
Abstract
The regulation of alternative splicing in eukaryotic cells is carried out through the coordinated action of a large number of factors, including RNA-binding proteins and RNA structure. The RNA structure influences alternative splicing by blocking cis-regulatory elements, or bringing them closer or farther apart. In combination with RNA-binding proteins, it generates transcript conformations that help to achieve the necessary splicing outcome. However, the binding of regulatory proteins depends on RNA structure and, vice versa, the formation of RNA structure depends on the interaction with regulators. Therefore, RNA structure and RNA-binding proteins are inseparable components of common regulatory mechanisms. This review highlights examples of alternative splicing regulation by RNA-binding proteins, the regulation through local and long-range RNA structures, as well as how these elements work together, cooperate, and compete.
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Affiliation(s)
- M. A. Vorobeva
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. A. Skvortsov
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
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10
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Lo R, Gonçalves-Carneiro D. Sensing nucleotide composition in virus RNA. Biosci Rep 2023; 43:BSR20230372. [PMID: 37606964 PMCID: PMC10500230 DOI: 10.1042/bsr20230372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 08/23/2023] Open
Abstract
Nucleotide composition plays a crucial role in the structure, function and recognition of RNA molecules. During infection, virus RNA is exposed to multiple endogenous proteins that detect local or global compositional biases and interfere with virus replication. Recent advancements in RNA:protein mapping technologies have enabled the identification of general RNA-binding preferences in the human proteome at basal level and in the context of virus infection. In this review, we explore how cellular proteins recognise nucleotide composition in virus RNA and the impact these interactions have on virus replication. Protein-binding G-rich and C-rich sequences are common examples of how host factors detect and limit infection, and, in contrast, viruses may have evolved to purge their genomes from such motifs. We also give examples of how human RNA-binding proteins inhibit virus replication, not only by destabilising virus RNA, but also by interfering with viral protein translation and genome encapsidation. Understanding the interplay between cellular proteins and virus RNA composition can provide insights into host-virus interactions and uncover potential targets for antiviral strategies.
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Affiliation(s)
- Raymon Lo
- Imperial College London, Department of Infectious Disease, Imperial College London, London, U.K
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11
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Osma-Garcia IC, Mouysset M, Capitan-Sobrino D, Aubert Y, Turner M, Diaz-Muñoz MD. The RNA binding proteins TIA1 and TIAL1 promote Mcl1 mRNA translation to protect germinal center responses from apoptosis. Cell Mol Immunol 2023; 20:1063-1076. [PMID: 37474714 PMCID: PMC10469172 DOI: 10.1038/s41423-023-01063-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/24/2023] [Indexed: 07/22/2023] Open
Abstract
Germinal centers (GCs) are essential for the establishment of long-lasting antibody responses. GC B cells rely on post-transcriptional RNA mechanisms to translate activation-associated transcriptional programs into functional changes in the cell proteome. However, the critical proteins driving these key mechanisms are still unknown. Here, we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses. TIA1- and TIAL1-deficient GC B cells fail to undergo antigen-mediated positive selection, expansion and differentiation into B-cell clones producing high-affinity antibodies. Mechanistically, TIA1 and TIAL1 control the transcriptional identity of dark- and light-zone GC B cells and enable timely expression of the prosurvival molecule MCL1. Thus, we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.
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Affiliation(s)
- Ines C Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Mailys Mouysset
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Dunja Capitan-Sobrino
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Yann Aubert
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Martin Turner
- Immunology Program, The Babraham Institute, Cambridge, UK
| | - Manuel D Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France.
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12
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Mas AM, Goñi E, Ruiz de Los Mozos I, Arcas A, Statello L, González J, Blázquez L, Lee WTC, Gupta D, Sejas Á, Hoshina S, Armaos A, Tartaglia GG, Waga S, Ule J, Rothenberg E, Gómez M, Huarte M. ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins. Nat Commun 2023; 14:4447. [PMID: 37488096 PMCID: PMC10366126 DOI: 10.1038/s41467-023-40105-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in this process remains unclear. We show that the ORC1 subunit of the human Origin Recognition Complex interacts with RNAs transcribed from genes with origins in their transcription start sites (TSSs), displaying a positive correlation between RNA binding and origin activity. RNA depletion, or the use of ORC1 RNA-binding mutant, result in inefficient activation of proximal origins, linked to impaired ORC1 chromatin release. ORC1 RNA binding activity resides in its intrinsically disordered region, involved in intra- and inter-molecular interactions, regulation by phosphorylation, and phase-separation. We show that RNA binding favors ORC1 chromatin release, by regulating its phosphorylation and subsequent degradation. Our results unveil a non-coding function of RNA as a dynamic component of the chromatin, orchestrating the activation of replication origins.
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Affiliation(s)
- Aina Maria Mas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Enrique Goñi
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Igor Ruiz de Los Mozos
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Aida Arcas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Luisa Statello
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Jovanna González
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Lorea Blázquez
- RNA Networks Lab, The Francis Crick Institute, NW11BF, London, UK
- Neurosciences Area, Biodonostia Health Research Institute, 20014, San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
| | - Wei Ting Chelsea Lee
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Álvaro Sejas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Shoko Hoshina
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, 112-8681, Japan
| | - Alexandros Armaos
- Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Biology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Shou Waga
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, 112-8681, Japan
| | - Jernej Ule
- RNA Networks Lab, The Francis Crick Institute, NW11BF, London, UK
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - María Gómez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049, Madrid, Spain
| | - Maite Huarte
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain.
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain.
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13
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West C, Capitanchik C, Cheshire C, Luscombe NM, Chakrabarti A, Ule J. nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis. Wellcome Open Res 2023; 8:286. [PMID: 37829674 PMCID: PMC10565428 DOI: 10.12688/wellcomeopenres.19453.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2023] [Indexed: 10/14/2023] Open
Abstract
Crosslinking and immunoprecipitation (CLIP) technologies have become a central component of the molecular biologists' toolkit to study protein-RNA interactions and thus to uncover core principles of RNA biology. There has been a proliferation of CLIP-based experimental protocols, as well as computational tools, especially for peak-calling. Consequently, there is an urgent need for a well-documented bioinformatic pipeline that enshrines the principles of robustness, reproducibility, scalability, portability and flexibility while embracing the diversity of experimental and computational CLIP tools. To address this, we present nf-core/clipseq - a robust Nextflow pipeline for quality control and analysis of CLIP sequencing data. It is part of the international nf-core community effort to develop and curate a best-practice, gold-standard set of pipelines for data analysis. The standards enabled by Nextflow and nf-core, including workflow management, version control, continuous integration and containerisation ensure that these key needs are met. Furthermore, multiple tools are implemented ( e.g. for peak-calling), alongside visualisation of quality control metrics to empower the user to make their own informed decisions based on their data. nf-core/clipseq remains under active development, with plans to incorporate newly released tools to ensure that pipeline remains up-to-date and relevant for the community. Engagement with users and developers is encouraged through the nf-core GitHub repository and Slack channel to promote collaboration. It is available at https://nf-co.re/clipseq.
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Affiliation(s)
| | - Charlotte Capitanchik
- The Francis Crick Institute, London, England, UK
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | | | - Nicholas M. Luscombe
- The Francis Crick Institute, London, England, UK
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | | | - Jernej Ule
- The Francis Crick Institute, London, England, UK
- UK Dementia Research Institute at King's College London, London, UK
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14
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Vatandaslar H, Garzia A, Meyer C, Godbersen S, Brandt LTL, Griesbach E, Chao JA, Tuschl T, Stoffel M. In vivo PAR-CLIP (viP-CLIP) of liver TIAL1 unveils targets regulating cholesterol synthesis and secretion. Nat Commun 2023; 14:3386. [PMID: 37296170 PMCID: PMC10256721 DOI: 10.1038/s41467-023-39135-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
System-wide cross-linking and immunoprecipitation (CLIP) approaches have unveiled regulatory mechanisms of RNA-binding proteins (RBPs) mainly in cultured cells due to limitations in the cross-linking efficiency of tissues. Here, we describe viP-CLIP (in vivo PAR-CLIP), a method capable of identifying RBP targets in mammalian tissues, thereby facilitating the functional analysis of RBP-regulatory networks in vivo. We applied viP-CLIP to mouse livers and identified Insig2 and ApoB as prominent TIAL1 target transcripts, indicating an important role of TIAL1 in cholesterol synthesis and secretion. The functional relevance of these targets was confirmed by showing that TIAL1 influences their translation in hepatocytes. Mutant Tial1 mice exhibit altered cholesterol synthesis, APOB secretion and plasma cholesterol levels. Our results demonstrate that viP-CLIP can identify physiologically relevant RBP targets by finding a factor implicated in the negative feedback regulation of cholesterol biosynthesis.
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Affiliation(s)
- Hasan Vatandaslar
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10021, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10021, USA
| | - Svenja Godbersen
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland
| | - Laura T L Brandt
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland
| | - Esther Griesbach
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10021, USA
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland.
- Medical Faculty, University of Zürich, 8091, Zürich, Switzerland.
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15
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Ye R, Hu N, Cao C, Su R, Xu S, Yang C, Zhou X, Xue Y. Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation. Mol Cell 2023; 83:1311-1327.e7. [PMID: 36958328 DOI: 10.1016/j.molcel.2023.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/10/2023] [Accepted: 02/27/2023] [Indexed: 03/25/2023]
Abstract
RNA-binding proteins (RBPs) bind at different positions of the pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a capture RIC-seq (CRIC-seq) method to enrich specific RBP-associated in situ proximal RNA-RNA fragments for deep sequencing. We determine hnRNPA1-, SRSF1-, and PTBP1-associated proximal RNA-RNA contacts and regulatory mechanisms in HeLa cells. Unexpectedly, the 3D RNA map analysis shows that PTBP1-associated loops in individual introns preferentially promote cassette exon splicing by accelerating asymmetric intron removal, whereas the loops spanning across cassette exon primarily repress splicing. These "positional rules" can faithfully predict PTBP1-regulated splicing outcomes. We further demonstrate that cancer-related splicing quantitative trait loci can disrupt RNA loops by reducing PTBP1 binding on pre-mRNAs to cause aberrant splicing in tumors. Our study presents a powerful method for exploring the functions of RBP-associated RNA-RNA proximal contacts in gene regulation and disease.
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Affiliation(s)
- Rong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruibao Su
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihan Xu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, Zhejiang 325003, China
| | - Chen Yang
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, Zhejiang 325003, China
| | - Xiangtian Zhou
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, Zhejiang 325003, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Horn T, Gosliga A, Li C, Enculescu M, Legewie S. Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing. NPJ Syst Biol Appl 2023; 9:1. [PMID: 36653378 PMCID: PMC9849329 DOI: 10.1038/s41540-022-00264-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/08/2022] [Indexed: 01/19/2023] Open
Abstract
Alternative splicing is an important step in eukaryotic mRNA pre-processing which increases the complexity of gene expression programs, but is frequently altered in disease. Previous work on the regulation of alternative splicing has demonstrated that splicing is controlled by RNA-binding proteins (RBPs) and by epigenetic DNA/histone modifications which affect splicing by changing the speed of polymerase-mediated pre-mRNA transcription. The interplay of these different layers of splicing regulation is poorly understood. In this paper, we derived mathematical models describing how splicing decisions in a three-exon gene are made by combinatorial spliceosome binding to splice sites during ongoing transcription. We additionally take into account the effect of a regulatory RBP and find that the RBP binding position within the sequence is a key determinant of how RNA polymerase velocity affects splicing. Based on these results, we explain paradoxical observations in the experimental literature and further derive rules explaining why the same RBP can act as inhibitor or activator of cassette exon inclusion depending on its binding position. Finally, we derive a stochastic description of co-transcriptional splicing regulation at the single-cell level and show that splicing outcomes show little noise and follow a binomial distribution despite complex regulation by a multitude of factors. Taken together, our simulations demonstrate the robustness of splicing outcomes and reveal that quantitative insights into kinetic competition of co-transcriptional events are required to fully understand this important mechanism of gene expression diversity.
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Affiliation(s)
- Timur Horn
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Alison Gosliga
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- University of Stuttgart, Department of Systems Biology and Stuttgart Research Center Systems Biology (SRCSB), Allmandring 31, 70569, Stuttgart, Germany
| | - Congxin Li
- University of Stuttgart, Department of Systems Biology and Stuttgart Research Center Systems Biology (SRCSB), Allmandring 31, 70569, Stuttgart, Germany
| | - Mihaela Enculescu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
- University of Stuttgart, Department of Systems Biology and Stuttgart Research Center Systems Biology (SRCSB), Allmandring 31, 70569, Stuttgart, Germany.
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17
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Xue X, Wang M, Zhang X, Ma L, Wang J. PAR-CLIP Assay in Ferroptosis. Methods Mol Biol 2023; 2712:29-43. [PMID: 37578694 DOI: 10.1007/978-1-0716-3433-2_4] [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: 08/15/2023]
Abstract
Ferroptosis is a regulatory cell death process that is accompanied by large amounts of iron ion accumulation and lipid peroxidation. Photoactivated ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) is a method used to identify the binding sites of RNA-binding proteins (RBPs) on target RNAs with high resolution at the nucleotide level. By inserting photosensitive ribonucleoside analogs into new RNA transcripts of living cells, characteristic mutations can be generated during reverse transcription and be used to accurately locate the crosslinking position of RNAs and RBPs. The use of PAR-CLIP to detect interactions and determine precise crosslinking sites between RNAs and RBPs, or to search for RNAs upstream or downstream of ferroptosis pathways genes through known proteins, can help to clarify and verify the occurrence and regulation mechanisms of the various signaling pathways of ferroptosis. Furthermore, it may reveal new targets for ferroptosis detection and improve the treatment efficiency of ferroptosis-related diseases such as cancer and neurodegenerative diseases. Here, we introduce a specific PAR-CLIP protocol for monitoring the ferroptosis process.
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Affiliation(s)
- Xiangfei Xue
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Manyuan Wang
- College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lifang Ma
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiayi Wang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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18
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Osma-Garcia IC, Capitan-Sobrino D, Mouysset M, Aubert Y, Maloudi O, Turner M, Diaz-Muñoz MD. The splicing regulators TIA1 and TIAL1 are required for the expression of the DNA damage repair machinery during B cell lymphopoiesis. Cell Rep 2022; 41:111869. [PMID: 36543128 PMCID: PMC9794549 DOI: 10.1016/j.celrep.2022.111869] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/01/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
B cell lymphopoiesis requires dynamic modulation of the B cell transcriptome for timely coordination of somatic mutagenesis and DNA repair in progenitor B (pro-B) cells. Here, we show that, in pro-B cells, the RNA-binding proteins T cell intracellular antigen 1 (TIA1) and TIA1-like protein (TIAL1) act redundantly to enable developmental progression. They are global splicing regulators that control the expression of hundreds of mRNAs, including those involved in DNA damage repair. Mechanistically, TIA1 and TIAL1 bind to 5' splice sites for exon definition, splicing, and expression of DNA damage sensors, such as Chek2 and Rif1. In their absence, pro-B cells show exacerbated DNA damage, altered P53 expression, and increased cell death. Our study uncovers the importance of tight regulation of RNA splicing by TIA1 and TIAL1 for the expression of integrative transcriptional programs that control DNA damage sensing and repair during B cell development.
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Affiliation(s)
- Ines C. Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Dunja Capitan-Sobrino
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Mailys Mouysset
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Yann Aubert
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Orlane Maloudi
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Martin Turner
- Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Manuel D. Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France,Corresponding author
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19
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Kuret K, Amalietti AG, Jones DM, Capitanchik C, Ule J. Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP. Genome Biol 2022; 23:191. [PMID: 36085079 PMCID: PMC9461102 DOI: 10.1186/s13059-022-02755-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/22/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Crosslinking and immunoprecipitation (CLIP) is a method used to identify in vivo RNA-protein binding sites on a transcriptome-wide scale. With the increasing amounts of available data for RNA-binding proteins (RBPs), it is important to understand to what degree the enriched motifs specify the RNA-binding profiles of RBPs in cells. RESULTS We develop positionally enriched k-mer analysis (PEKA), a computational tool for efficient analysis of enriched motifs from individual CLIP datasets, which minimizes the impact of technical and regional genomic biases by internal data normalization. We cross-validate PEKA with mCross and show that the use of input control for background correction is not required to yield high specificity of enriched motifs. We identify motif classes with common enrichment patterns across eCLIP datasets and across RNA regions, while also observing variations in the specificity and the extent of motif enrichment across eCLIP datasets, between variant CLIP protocols, and between CLIP and in vitro binding data. Thereby, we gain insights into the contributions of technical and regional genomic biases to the enriched motifs, and find how motif enrichment features relate to the domain composition and low-complexity regions of the studied proteins. CONCLUSIONS Our study provides insights into the overall contributions of regional binding preferences, protein domains, and low-complexity regions to the specificity of protein-RNA interactions, and shows the value of cross-motif and cross-RBP comparison for data interpretation. Our results are presented for exploratory analysis via an online platform in an RBP-centric and motif-centric manner ( https://imaps.goodwright.com/apps/peka/ ).
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Affiliation(s)
- Klara Kuret
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- Jozef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT UK
| | - Aram Gustav Amalietti
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT UK
| | - D. Marc Jones
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT UK
- UK Dementia Research Institute, King’s College London, London, UK
| | - Charlotte Capitanchik
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT UK
- UK Dementia Research Institute, King’s College London, London, UK
| | - Jernej Ule
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT UK
- UK Dementia Research Institute, King’s College London, London, UK
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20
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Velasco BR, Izquierdo JM. T-Cell Intracellular Antigen 1-Like Protein in Physiology and Pathology. Int J Mol Sci 2022; 23:ijms23147836. [PMID: 35887183 PMCID: PMC9318959 DOI: 10.3390/ijms23147836] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
T-cell intracellular antigen 1 (TIA1)-related/like (TIAR/TIAL1) protein is a multifunctional RNA-binding protein (RBP) involved in regulating many aspects of gene expression, independently or in combination with its paralog TIA1. TIAR was first described in 1992 by Paul Anderson’s lab in relation to the development of a cell death phenotype in immune system cells, as it possesses nucleolytic activity against cytotoxic lymphocyte target cells. Similar to TIA1, it is characterized by a subcellular nucleo-cytoplasmic localization and ubiquitous expression in the cells of different tissues of higher organisms. In this paper, we review the relevant structural and functional information available about TIAR from a triple perspective (molecular, cellular and pathophysiological), paying special attention to its expression and regulation in cellular events and processes linked to human pathophysiology.
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21
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Karmakar S, Ramirez O, Paul KV, Gupta AK, Kumari V, Botti V, de Los Mozos IR, Neuenkirchen N, Ross RJ, Karanicolas J, Neugebauer KM, Pillai MM. Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2). NAR Cancer 2022; 4:zcac015. [PMID: 35528200 PMCID: PMC9070473 DOI: 10.1093/narcan/zcac015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 01/29/2023] Open
Abstract
Musashi 2 (MSI2) is an RNA binding protein (RBP) that regulates asymmetric cell division and cell fate decisions in normal and cancer stem cells. MSI2 appears to repress translation by binding to 3′ untranslated regions (3′UTRs) of mRNA, but the identity of functional targets remains unknown. Here, we used individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP) to identify direct RNA binding partners of MSI2 and integrated these data with polysome profiling to obtain insights into MSI2 function. iCLIP revealed specific MSI2 binding to thousands of mRNAs largely in 3′UTRs, but translational differences were restricted to a small fraction of these transcripts, indicating that MSI2 regulation is not triggered by simple binding. Instead, the functional targets identified here were bound at higher density and contain more ‘UAG’ motifs compared to targets bound nonproductively. To further distinguish direct and indirect targets, MSI2 was acutely depleted. Surprisingly, only 50 transcripts were found to undergo translational induction on acute loss. Using complementary approaches, we determined eukaryotic translation initiation factor 3A (EIF3A) to be an immediate, direct target. We propose that MSI2 downregulation of EIF3A amplifies these effects on translation. Our results also underscore the challenges in defining functional targets of RBPs since mere binding does not imply a discernible functional interaction.
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Affiliation(s)
| | - Oscar Ramirez
- Section of Hematology, Yale Cancer Center, New Haven, CT 06511, USA
| | - Kiran V Paul
- Section of Hematology, Yale Cancer Center, New Haven, CT 06511, USA
| | - Abhishek K Gupta
- Section of Hematology, Yale Cancer Center, New Haven, CT 06511, USA
| | - Vandana Kumari
- Section of Hematology, Yale Cancer Center, New Haven, CT 06511, USA
| | - Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Igor Ruiz de Los Mozos
- Institute of Neurology, University College London and The Francis Crick Institute, London NW1 1AT, UK
| | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Robert J Ross
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Manoj M Pillai
- Section of Hematology, Yale Cancer Center, New Haven, CT 06511, USA
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22
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Zhou Y, Sotcheff SL, Routh AL. Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. J Biol Chem 2022; 298:101924. [PMID: 35413291 PMCID: PMC8994257 DOI: 10.1016/j.jbc.2022.101924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 10/25/2022] Open
Abstract
The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral lifecycle is accompanied by a myriad of RNA-protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA-protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA-protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA-protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.
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Affiliation(s)
- Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA.
| | - Stephanea L Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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23
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Yamada K, Hamada M. Prediction of RNA-protein interactions using a nucleotide language model. BIOINFORMATICS ADVANCES 2022; 2:vbac023. [PMID: 36699410 PMCID: PMC9710633 DOI: 10.1093/bioadv/vbac023] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/28/2022] [Accepted: 04/05/2022] [Indexed: 01/28/2023]
Abstract
Motivation The accumulation of sequencing data has enabled researchers to predict the interactions between RNA sequences and RNA-binding proteins (RBPs) using novel machine learning techniques. However, existing models are often difficult to interpret and require additional information to sequences. Bidirectional encoder representations from transformer (BERT) is a language-based deep learning model that is highly interpretable. Therefore, a model based on BERT architecture can potentially overcome such limitations. Results Here, we propose BERT-RBP as a model to predict RNA-RBP interactions by adapting the BERT architecture pretrained on a human reference genome. Our model outperformed state-of-the-art prediction models using the eCLIP-seq data of 154 RBPs. The detailed analysis further revealed that BERT-RBP could recognize both the transcript region type and RNA secondary structure only based on sequence information. Overall, the results provide insights into the fine-tuning mechanism of BERT in biological contexts and provide evidence of the applicability of the model to other RNA-related problems. Availability and implementation Python source codes are freely available at https://github.com/kkyamada/bert-rbp. The datasets underlying this article were derived from sources in the public domain: [RBPsuite (http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/), Ensembl Biomart (http://asia.ensembl.org/biomart/martview/)]. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Keisuke Yamada
- Department of Electrical Engineering and Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Okubo, Shinjuku, Tokyo 169-8555, Japan
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24
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Fernández-Gómez A, Velasco BR, Izquierdo JM. Dynamics of T-Cell Intracellular Antigen 1-Dependent Stress Granules in Proteostasis and Welander Distal Myopathy under Oxidative Stress. Cells 2022; 11:cells11050884. [PMID: 35269506 PMCID: PMC8909843 DOI: 10.3390/cells11050884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is primarily involved in the post-transcriptional regulation of cellular RNAs. Furthermore, it is a key component of stress granules (SGs), RNA, and protein aggregates that are formed in response to stressful stimuli to reduce cellular activity as a survival mechanism. TIA1 p.E384K mutation is the genetic cause of Welander distal myopathy (WDM), a late-onset muscular dystrophy whose pathogenesis has been related to modifying SG dynamics. In this study, we present the results obtained by analyzing two specific aspects: (i) SGs properties and dynamics depending on the amino acid at position 384 of TIA1; and (ii) the formation/disassembly time-course of TIA1WT/WDM-dependent SGs under oxidative stress. The generation of TIA1 variants—in which the amino acid mutated in WDM and the adjacent ones were replaced by lysines, glutamic acids, or alanines—allowed us to verify that the inclusion of a single lysine is necessary and sufficient to alter SGs dynamics. Moreover, time-lapse microscopy analysis allowed us to establish in vivo the dynamics of TIA1WT/WDM-dependent SG formation and disassembly, after the elimination of the oxidizing agent, for 1 and 3 h, respectively. Our observations show distinct dynamics between the formation and disassembly of TIA1WT/WDM-dependent SGs. Taken together, this study has allowed us to expand the existing knowledge on the role of TIA1 and the WDM mutation in SG formation.
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25
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Gourdomichali O, Zonke K, Kattan FG, Makridakis M, Kontostathi G, Vlahou A, Doxakis E. In Situ Peroxidase Labeling Followed by Mass-Spectrometry Reveals TIA1 Interactome. BIOLOGY 2022; 11:biology11020287. [PMID: 35205152 PMCID: PMC8869308 DOI: 10.3390/biology11020287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 01/15/2023]
Abstract
TIA1 is a broadly expressed DNA/RNA binding protein that regulates multiple aspects of RNA metabolism. It is best known for its role in stress granule assembly during the cellular stress response. Three RNA recognition motifs mediate TIA1 functions along with a prion-like domain that supports multivalent protein-protein interactions that are yet poorly characterized. Here, by fusing the enhanced ascorbate peroxidase 2 (APEX2) biotin-labeling enzyme to TIA1 combined with mass spectrometry, the proteins in the immediate vicinity of TIA1 were defined in situ. Eighty-six and 203 protein partners, mostly associated with ribonucleoprotein complexes, were identified in unstressed control and acute stress conditions, respectively. Remarkably, the repertoire of TIA1 protein partners was highly dissimilar between the two cellular states. Under unstressed control conditions, the biological processes associated with the TIA1 interactome were enriched for cytosolic ontologies related to mRNA metabolism, such as translation initiation, nucleocytoplasmic transport, and RNA catabolism, while the protein identities were primarily represented by RNA binding proteins, ribosomal subunits, and eicosanoid regulators. Under acute stress, TIA1-labeled partners displayed a broader subcellular distribution that included the chromosomes and mitochondria. The enriched biological processes included splicing, translation, and protein synthesis regulation, while the molecular function of the proteins was enriched for RNA binding activity, ribosomal subunits, DNA double-strand break repair, and amide metabolism. Altogether, these data highlight the TIA1 spatial environment with its different partners in diverse cellular states and pave the way to dissect TIA1 role in these processes.
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Affiliation(s)
- Olga Gourdomichali
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Katerina Zonke
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Fedon-Giasin Kattan
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
- Department of Biological Applications and Technology, Faculty of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Manousos Makridakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Georgia Kontostathi
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Antonia Vlahou
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
- Correspondence:
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26
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The Multifunctional Faces of T-Cell Intracellular Antigen 1 in Health and Disease. Int J Mol Sci 2022; 23:ijms23031400. [PMID: 35163320 PMCID: PMC8836218 DOI: 10.3390/ijms23031400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 02/06/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is expressed in many tissues and in the vast majority of species, although it was first discovered as a component of human cytotoxic T lymphocytes. TIA1 has a dual localization in the nucleus and cytoplasm, where it plays an important role as a regulator of gene-expression flux. As a multifunctional master modulator, TIA1 controls biological processes relevant to the physiological functioning of the organism and the development and/or progression of several human pathologies. This review summarizes our current knowledge of the molecular aspects and cellular processes involving TIA1, with relevance for human pathophysiology.
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27
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Carrascoso I, Velasco BR, Izquierdo JM. Deficiency of T-Cell Intracellular Antigen 1 in Murine Embryonic Fibroblasts Is Associated with Changes in Mitochondrial Morphology and Respiration. Int J Mol Sci 2021; 22:ijms222312775. [PMID: 34884582 PMCID: PMC8657690 DOI: 10.3390/ijms222312775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 01/14/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is a multifunctional RNA-binding protein involved in regulating gene expression and splicing during development and in response to environmental stress, to maintain cell homeostasis and promote survival. Herein, we used TIA1-deficient murine embryonic fibroblasts (MEFs) to study their role in mitochondria homeostasis. We found that the loss of TIA1 was associated with changes in mitochondrial morphology, promoting the appearance of elongated mitochondria with heterogeneous cristae density and size. The proteomic patterns of TIA1-deficient MEFs were consistent with expression changes in molecular components related to mitochondrial dynamics/organization and respiration. Bioenergetics analysis illustrated that TIA1 deficiency enhances mitochondrial respiration. Overall, our findings shed light on the role of TIA1 in mitochondrial dynamics and highlight a point of crosstalk between potential pro-survival and pro-senescence pathways.
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28
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DHX15-independent roles for TFIP11 in U6 snRNA modification, U4/U6.U5 tri-snRNP assembly and pre-mRNA splicing fidelity. Nat Commun 2021; 12:6648. [PMID: 34789764 PMCID: PMC8599867 DOI: 10.1038/s41467-021-26932-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 10/22/2021] [Indexed: 11/29/2022] Open
Abstract
The U6 snRNA, the core catalytic component of the spliceosome, is extensively modified post-transcriptionally, with 2'-O-methylation being most common. However, how U6 2'-O-methylation is regulated remains largely unknown. Here we report that TFIP11, the human homolog of the yeast spliceosome disassembly factor Ntr1, localizes to nucleoli and Cajal Bodies and is essential for the 2'-O-methylation of U6. Mechanistically, we demonstrate that TFIP11 knockdown reduces the association of U6 snRNA with fibrillarin and associated snoRNAs, therefore altering U6 2'-O-methylation. We show U6 snRNA hypomethylation is associated with changes in assembly of the U4/U6.U5 tri-snRNP leading to defects in spliceosome assembly and alterations in splicing fidelity. Strikingly, this function of TFIP11 is independent of the RNA helicase DHX15, its known partner in yeast. In sum, our study demonstrates an unrecognized function for TFIP11 in U6 snRNP modification and U4/U6.U5 tri-snRNP assembly, identifying TFIP11 as a critical spliceosome assembly regulator.
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29
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Tayara H, Chong KT. Improved Predicting of The Sequence Specificities of RNA Binding Proteins by Deep Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2526-2534. [PMID: 32191896 DOI: 10.1109/tcbb.2020.2981335] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA-binding proteins (RBPs) have a significant role in various regulatory tasks. However, the mechanism by which RBPs identify the subsequence target RNAs is still not clear. In recent years, several machine and deep learning-based computational models have been proposed for understanding the binding preferences of RBPs. These methods required integrating multiple features with raw RNA sequences such as secondary structure and their performances can be further improved. In this paper, we propose an efficient and simple convolution neural network, RBPCNN, that relies on the combination of the raw RNA sequence and evolutionary information. We show that conservation scores (evolutionary information) for the RNA sequences can significantly improve the overall performance of the proposed predictor. In addition, the automatic extraction of the binding sequence motifs can enhance our understanding of the binding specificities of RBPs. The experimental results show that RBPCNN outperforms significantly the current state-of-the-art methods. More specifically, the average area under the receiver operator curve was improved by 2.67 percent and the mean average precision was improved by 8.03 percent. The datasets and results can be downloaded from https://home.jbnu.ac.kr/NSCL/RBPCNN.htm.
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30
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Byres LP, Mufteev M, Yuki KE, Wei W, Piekna A, Wilson MD, Rodrigues DC, Ellis J. Identification of TIA1 mRNA targets during human neuronal development. Mol Biol Rep 2021; 48:6349-6361. [PMID: 34410578 PMCID: PMC8437838 DOI: 10.1007/s11033-021-06634-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022]
Abstract
Background Neuronal development is a tightly controlled process involving multi-layered regulatory mechanisms. While transcriptional pathways regulating neurodevelopment are well characterized, post-transcriptional programs are still poorly understood. TIA1 is an RNA-binding protein that can regulate splicing, stability, or translation of target mRNAs, and has been shown to play critical roles in stress response and neurodevelopment. However, the identity of mRNAs regulated by TIA1 during neurodevelopment under unstressed conditions is still unknown. Methods and Results To identify the mRNAs targeted by TIA1 during the first stages of human neurodevelopment, we performed RNA immunoprecipitation-sequencing (RIP-seq) on human embryonic stem cells (hESCs) and derived neural progenitor cells (NPCs), and cortical neurons under unstressed conditions. While there was no change in TIA1 protein levels, the number of TIA1 targeted mRNAs decreased from pluripotent cells to neurons. We identified 2400, 845, and 330 TIA1 mRNA targets in hESCs, NPC, and neurons, respectively. The vast majority of mRNA targets in hESC were genes associated with neurodevelopment and included autism spectrum disorder-risk genes that were not bound in neurons. Additionally, we found that most TIA1 mRNA targets have reduced ribosomal engagement levels. Conclusion Our results reveal TIA1 mRNA targets in hESCs and during human neurodevelopment, indicate that translation repression is a key process targeted by TIA1 binding and implicate TIA1 function in neuronal differentiation. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-021-06634-0.
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Affiliation(s)
- Loryn P Byres
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Marat Mufteev
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kyoko E Yuki
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wei Wei
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alina Piekna
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Deivid C Rodrigues
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
| | - James Ellis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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31
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Larrasa-Alonso J, Villalba-Orero M, Martí-Gómez C, Ortiz-Sánchez P, López-Olañeta MM, Rey-Martín MA, Sánchez-Cabo F, McNicoll F, Müller-McNicoll M, García-Pavía P, Lara-Pezzi E. The SRSF4-GAS5-Glucocorticoid Receptor Axis Regulates Ventricular Hypertrophy. Circ Res 2021; 129:669-683. [PMID: 34333993 PMCID: PMC8409900 DOI: 10.1161/circresaha.120.318577] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Supplemental Digital Content is available in the text. RBPs (RNA-binding proteins) play critical roles in human biology and disease. Aberrant RBP expression affects various steps in RNA processing, altering the function of the target RNAs. The RBP SRSF4 (serine/arginine-rich splicing factor 4) has been linked to neuropathies and cancer. However, its role in the heart is completely unknown.
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Affiliation(s)
- Javier Larrasa-Alonso
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - María Villalba-Orero
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.).,Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV), Madrid, Spain (M.V.-O., P.G.-P., E.L.-P.)
| | - Carlos Martí-Gómez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - Paula Ortiz-Sánchez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - Marina M López-Olañeta
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - M Ascensión Rey-Martín
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - Fátima Sánchez-Cabo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.)
| | - François McNicoll
- Goethe University Frankfurt, Institute of Molecular Biosciences, Frankfurt/Main, Germany (F.M., M.M.-M.)
| | - Michaela Müller-McNicoll
- Goethe University Frankfurt, Institute of Molecular Biosciences, Frankfurt/Main, Germany (F.M., M.M.-M.)
| | - Pablo García-Pavía
- Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV), Madrid, Spain (M.V.-O., P.G.-P., E.L.-P.).,Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, Madrid, Spain (P.G.-P.).,Facultad de Ciencias de la Salud, Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, Madrid, Spain (P.G.-P.)
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.-A., M.V.-O., C.M.-G., P.O.S., M.M.L.-O., M.A.R.-M., F.S.C., E.L.-P.).,Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV), Madrid, Spain (M.V.-O., P.G.-P., E.L.-P.)
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32
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Vivori C, Papasaikas P, Stadhouders R, Di Stefano B, Rubio AR, Balaguer CB, Generoso S, Mallol A, Sardina JL, Payer B, Graf T, Valcárcel J. Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1. Genome Biol 2021; 22:171. [PMID: 34082786 PMCID: PMC8173870 DOI: 10.1186/s13059-021-02372-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/05/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we study the dynamics of alternative splicing changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells and compare them to those occurring during reprogramming of mouse embryonic fibroblasts. RESULTS We observe a significant overlap between alternative splicing changes detected in the two reprogramming systems, which are generally uncoupled from changes in transcriptional levels. Correlation between gene expression of potential regulators and specific clusters of alternative splicing changes enables the identification and subsequent validation of CPSF3 and hnRNP UL1 as facilitators, and TIA1 as repressor of mouse embryonic fibroblasts reprogramming. We further find that these RNA-binding proteins control partially overlapping programs of splicing regulation, involving genes relevant for developmental and morphogenetic processes. CONCLUSIONS Our results reveal common programs of splicing regulation during reprogramming of different cell types and identify three novel regulators of this process and their targets.
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Affiliation(s)
- Claudia Vivori
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: The Francis Crick Institute, 1 Midland Road, London, NW1 1AT UK
| | - Panagiotis Papasaikas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66/Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Ralph Stadhouders
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Departments of Pulmonary Medicine and Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Bruno Di Stefano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Alkek Bldg Room N1020, Houston, TX 77030 USA
| | - Anna Ribó Rubio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Clara Berenguer Balaguer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Josep Carreras Leukaemia Research Institute, Carretera de Can Ruti, Camí de les Escoles, s/n, 08916 Badalona, Spain
| | - Serena Generoso
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anna Mallol
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - José Luis Sardina
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Josep Carreras Leukaemia Research Institute, Carretera de Can Ruti, Camí de les Escoles, s/n, 08916 Badalona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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Krismer K, Bird MA, Varmeh S, Handly ED, Gattinger A, Bernwinkler T, Anderson DA, Heinzel A, Joughin BA, Kong YW, Cannell IG, Yaffe MB. Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression. Cell Rep 2021; 32:108064. [PMID: 32846122 PMCID: PMC8204639 DOI: 10.1016/j.celrep.2020.108064] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/28/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play critical roles in regulating gene expression by modulating splicing, RNA stability, and protein translation. Stimulus-induced alterations in RBP function contribute to global changes in gene expression, but identifying which RBPs are responsible for the observed changes remains an unmet need. Here, we present Transite, a computational approach that systematically infers RBPs influencing gene expression through changes in RNA stability and degradation. As a proof of principle, we apply Transite to RNA expression data from human patients with non-small-cell lung cancer whose tumors were sampled at diagnosis or after recurrence following treatment with platinum-based chemotherapy. Transite implicates known RBP regulators of the DNA damage response and identifies hnRNPC as a new modulator of chemotherapeutic resistance, which we subsequently validated experimentally. Transite serves as a framework for the identification of RBPs that drive cell-state transitions and adds additional value to the vast collection of publicly available gene expression datasets. Krismer et al. present a computational approach to identify RNA-binding proteins (RBPs) that modulate post-transcriptional control of gene expression using RNA expression data as inputs. By applying this approach to publicly available patient datasets, they identify and experimentally confirm that the RBP hnRNPC contributes to chemotherapy resistance in lung cancer.
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Affiliation(s)
- Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Molly A Bird
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Shohreh Varmeh
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA
| | - Erika D Handly
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Anna Gattinger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Thomas Bernwinkler
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Daniel A Anderson
- Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Andreas Heinzel
- Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Brian A Joughin
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yi Wen Kong
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA.
| | - Ian G Cannell
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
| | - Michael B Yaffe
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Divisions of Acute Care Surgery, Trauma and Surgical Critical Care, and Surgical Oncology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.
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34
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Schwich OD, Blümel N, Keller M, Wegener M, Setty ST, Brunstein ME, Poser I, Mozos IRDL, Suess B, Münch C, McNicoll F, Zarnack K, Müller-McNicoll M. SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biol 2021; 22:82. [PMID: 33706811 PMCID: PMC7948361 DOI: 10.1186/s13059-021-02298-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/11/2021] [Indexed: 12/23/2022] Open
Abstract
Background Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3′ untranslated regions (3′UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown. Results Here we combine iCLIP and 3′-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3′UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3′UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3′UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3′UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3′UTRs. Conclusions We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02298-y.
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Affiliation(s)
- Oliver Daniel Schwich
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Nicole Blümel
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Mario Keller
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Marius Wegener
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Samarth Thonta Setty
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Melinda Elaine Brunstein
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | | | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - François McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. .,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Michaela Müller-McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.
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35
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Hafner M, Katsantoni M, Köster T, Marks J, Mukherjee J, Staiger D, Ule J, Zavolan M. CLIP and complementary methods. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00018-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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36
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Grønning AGB, Doktor TK, Larsen SJ, Petersen USS, Holm LL, Bruun GH, Hansen MB, Hartung AM, Baumbach J, Andresen BS. DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning. Nucleic Acids Res 2020; 48:7099-7118. [PMID: 32558887 PMCID: PMC7367176 DOI: 10.1093/nar/gkaa530] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 05/11/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling of protein-RNA binding is critical when predicting the effects of sequence variations. Many RNA-binding proteins recognize a diverse set of motifs and binding is typically also dependent on the genomic context, making this task particularly challenging. Here, we present DeepCLIP, the first method for context-aware modeling and predicting protein binding to RNA nucleic acids using exclusively sequence data as input. We show that DeepCLIP outperforms existing methods for modeling RNA-protein binding. Importantly, we demonstrate that DeepCLIP predictions correlate with the functional outcomes of nucleotide variants in independent wet lab experiments. Furthermore, we show how DeepCLIP binding profiles can be used in the design of therapeutically relevant antisense oligonucleotides, and to uncover possible position-dependent regulation in a tissue-specific manner. DeepCLIP is freely available as a stand-alone application and as a webtool at http://deepclip.compbio.sdu.dk.
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Affiliation(s)
- Alexander Gulliver Bjørnholt Grønning
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark.,Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Simon Jonas Larsen
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ulrika Simone Spangsberg Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Gitte Hoffmann Bruun
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Michael Birkerod Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Anne-Mette Hartung
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark.,Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
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37
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Shen Z, Deng SP, Huang DS. RNA-Protein Binding Sites Prediction via Multi Scale Convolutional Gated Recurrent Unit Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1741-1750. [PMID: 30990191 DOI: 10.1109/tcbb.2019.2910513] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
RNA-Protein binding plays important roles in the field of gene expression. With the development of high throughput sequencing, several conventional methods and deep learning-based methods have been proposed to predict the binding preference of RNA-protein binding. These methods can hardly meet the need of consideration of the dependencies between subsequence and the various motif lengths of different translation factors (TFs). To overcome such limitations, we propose a predictive model that utilizes a combination of multi-scale convolutional layers and bidirectional gated recurrent unit (GRU) layer. Multi-scale convolution layer has the ability to capture the motif features of different lengths, and bidirectional GRU layer is able to capture the dependencies among subsequence. Experimental results show that the proposed method performs better than four state-of-the-art methods in this field. In addition, we investigate the effect of model structure on model performance by performing our proposed method with a different convolution layer and a different number of kernel size. We also demonstrate the effectiveness of bidirectional GRU in improving model performance through comparative experiments.
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38
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Obrdlik A, Lin G, Haberman N, Ule J, Ephrussi A. The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila. Cell Rep 2020; 28:1219-1236.e11. [PMID: 31365866 DOI: 10.1016/j.celrep.2019.06.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/30/2019] [Accepted: 06/24/2019] [Indexed: 12/27/2022] Open
Abstract
Exon junction complex (EJC) assembles after splicing at specific positions upstream of exon-exon junctions in mRNAs of all higher eukaryotes, affecting major regulatory events. In mammalian cell cytoplasm, EJC is essential for efficient RNA surveillance, while in Drosophila, EJC is essential for localization of oskar mRNA. Here we developed a method for isolation of protein complexes and associated RNA targets (ipaRt) to explore the EJC RNA-binding landscape in a transcriptome-wide manner in adult Drosophila. We find the EJC at canonical positions, preferably on mRNAs from genes comprising multiple splice sites and long introns. Moreover, EJC occupancy is highest at junctions adjacent to strong splice sites, CG-rich hexamers, and RNA structures. Highly occupied mRNAs tend to be maternally localized and derive from genes involved in differentiation or development. These modalities, which have not been reported in mammals, specify EJC assembly on a biologically coherent set of transcripts in Drosophila.
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Affiliation(s)
- Ales Obrdlik
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Gen Lin
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nejc Haberman
- Department for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Jernej Ule
- Department for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK; The Francis Crick Institute, London NW1 1AT, UK
| | - Anne Ephrussi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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39
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Plant Individual Nucleotide Resolution Cross-Linking and Immunoprecipitation to Characterize RNA-Protein Complexes. Methods Mol Biol 2020. [PMID: 32710414 DOI: 10.1007/978-1-0716-0712-1_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
In recent years, it has become increasingly recognized that regulation at the RNA level pervasively shapes the transcriptome in eukaryotic cells. This has fostered an interest in the mode of action of RNA-binding proteins that, via interaction with specific RNA sequence motifs, modulate gene expression. Understanding such posttranscriptional networks controlled by an RNA-binding protein requires a comprehensive identification of its in vivo targets. In metazoans and yeast, methods have been devised to stabilize RNA-protein interactions by UV cross-linking before isolating RNA-protein complexes using antibodies, followed by identification of associated RNAs by next-generation sequencing. These methods are collectively referred to as CLIP-Seq (cross-linking immunoprecipitation-high-throughput sequencing). Here, we present a version of the individual nucleotide resolution cross-linking and immunoprecipitation procedure that is suitable for use in the model plant Arabidopsis thaliana.
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40
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Taylor K, Sobczak K. Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control. Int J Mol Sci 2020; 21:ijms21145161. [PMID: 32708277 PMCID: PMC7404189 DOI: 10.3390/ijms21145161] [Citation(s) in RCA: 13] [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: 07/01/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is a highly sophisticated process, playing a significant role in posttranscriptional gene expression and underlying the diversity and complexity of organisms. Its regulation is multilayered, including an intrinsic role of RNA structural arrangement which undergoes time- and tissue-specific alterations. In this review, we describe the principles of RNA structural arrangement and briefly decipher its cis- and trans-acting cellular modulators which serve as crucial determinants of biological functionality of the RNA structure. Subsequently, we engage in a discussion about the RNA structure-mediated mechanisms of alternative splicing regulation. On one hand, the impairment of formation of optimal RNA structures may have critical consequences for the splicing outcome and further contribute to understanding the pathomechanism of severe disorders. On the other hand, the structural aspects of RNA became significant features taken into consideration in the endeavor of finding potential therapeutic treatments. Both aspects have been addressed by us emphasizing the importance of ongoing studies in both fields.
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41
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Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, McGurk MP, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu XD, Lécuyer E, Burge CB, Graveley BR, Yeo GW. A large-scale binding and functional map of human RNA-binding proteins. Nature 2020; 583:711-719. [PMID: 32728246 PMCID: PMC7410833 DOI: 10.1038/s41586-020-2077-3] [Citation(s) in RCA: 577] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 07/10/2019] [Indexed: 11/09/2022]
Abstract
Many proteins regulate the expression of genes by binding to specific regions encoded in the genome1. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part of the Encyclopedia of DNA Elements (ENCODE) project phase III. This class of regulatory elements functions only when transcribed into RNA, as they serve as the binding sites for RBPs that control post-transcriptional processes such as splicing, cleavage and polyadenylation, and the editing, localization, stability and translation of mRNAs. We describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. Integrative analyses using five assays identify RBP binding sites on RNA and chromatin in vivo, the in vitro binding preferences of RBPs, the function of RBP binding sites and the subcellular localization of RBPs, producing 1,223 replicated data sets for 356 RBPs. We describe the spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization. These data expand the catalogue of functional elements encoded in the human genome by the addition of a large set of elements that function at the RNA level by interacting with RBPs.
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Affiliation(s)
- Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Peter Freese
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Xiaofeng Wang
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Rui Xiao
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Neal A L Cody
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Daniel Dominguez
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Balaji Sundararaman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Cassandra Bazile
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Louis Philip Benoit Bouvrette
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Julie Bergalet
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Michael O Duff
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Keri E Garcia
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chelsea Gelboin-Burkhart
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Myles Hochman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole J Lambert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael P McGurk
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thai B Nguyen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tsultrim Palden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ines Rabano
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rebecca Stanton
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Amanda Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ruth Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ashley L Louie
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada.
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada.
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
| | - Christopher B Burge
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
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42
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SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly. Nat Struct Mol Biol 2020; 27:260-273. [PMID: 32123389 PMCID: PMC7096898 DOI: 10.1038/s41594-020-0385-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/23/2020] [Indexed: 02/08/2023]
Abstract
SRSF7 is an essential RNA-binding protein whose misexpression promotes cancer. Here, we describe how SRSF7 maintains its protein homeostasis in murine P19 cells using an intricate negative feedback mechanism. SRSF7 binding to its premessenger RNA promotes inclusion of a poison cassette exon and transcript degradation via nonsense-mediated decay (NMD). However, elevated SRSF7 levels inhibit NMD and promote translation of two protein halves, termed Split-ORFs, from the bicistronic SRSF7-PCE transcript. The first half acts as dominant-negative isoform suppressing poison cassette exon inclusion and instead promoting the retention of flanking introns containing repeated SRSF7 binding sites. Massive SRSF7 binding to these sites and its oligomerization promote the assembly of large nuclear bodies, which sequester SRSF7 transcripts at their transcription site, preventing their export and restoring normal SRSF7 protein levels. We further show that hundreds of human and mouse NMD targets, especially RNA-binding proteins, encode potential Split-ORFs, some of which are expressed under specific cellular conditions.
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43
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Abstract
High-throughput sequencing-based methods and their applications in the study of transcriptomes have revolutionized our understanding of alternative splicing. Networks of functionally coordinated and biologically important alternative splicing events continue to be discovered in an ever-increasing diversity of cell types in the context of physiologically normal and disease states. These studies have been complemented by efforts directed at defining sequence codes governing splicing and their cognate trans-acting factors, which have illuminated important combinatorial principles of regulation. Additional studies have revealed critical roles of position-dependent, multivalent protein-RNA interactions that direct splicing outcomes. Investigations of evolutionary changes in RNA binding proteins, splice variants, and associated cis elements have further shed light on the emergence, mechanisms, and functions of splicing networks. Progress in these areas has emphasized the need for a coordinated, community-based effort to systematically address the functions of individual splice variants associated with normal and disease biology.
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44
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Apicco DJ, Zhang C, Maziuk B, Jiang L, Ballance HI, Boudeau S, Ung C, Li H, Wolozin B. Dysregulation of RNA Splicing in Tauopathies. Cell Rep 2019; 29:4377-4388.e4. [PMID: 31875547 PMCID: PMC6941411 DOI: 10.1016/j.celrep.2019.11.093] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/28/2019] [Accepted: 11/22/2019] [Indexed: 12/13/2022] Open
Abstract
Pathological aggregation of RNA binding proteins (RBPs) is associated with dysregulation of RNA splicing in PS19 P301S tau transgenic mice and in Alzheimer's disease brain tissues. The dysregulated splicing particularly affects genes involved in synaptic transmission. The effects of neuroprotective TIA1 reduction on PS19 mice are also examined. TIA1 reduction reduces disease-linked alternative splicing events for the major synaptic mRNA transcripts examined, suggesting that normalization of RBP functions is associated with the neuroprotection. Use of the NetDecoder informatics algorithm identifies key upstream biological targets, including MYC and EGFR, underlying the transcriptional and splicing changes in the protected compared to tauopathy mice. Pharmacological inhibition of MYC and EGFR activity in neuronal cultures tau recapitulates the neuroprotective effects of TIA1 reduction. These results demonstrate that dysfunction of RBPs and RNA splicing processes are major elements of the pathophysiology of tauopathies, as well as potential therapeutic targets for tauopathies.
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Affiliation(s)
- Daniel J Apicco
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | | | - Brandon Maziuk
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | - Lulu Jiang
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | - Heather I Ballance
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | - Samantha Boudeau
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA
| | | | - Hu Li
- Mayo Clinic, Rochester, MN, USA.
| | - Benjamin Wolozin
- Boston University School of Medicine, Department of Pharmacology and Experimental Therapeutics, Boston, MA, USA; Boston University School of Medicine, Department of Neurology, Boston, MA, USA.
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45
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Carter JM, Emmett W, Mozos IR, Kotter A, Helm M, Ule J, Hussain S. FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA. Nucleic Acids Res 2019; 47:e113. [PMID: 31361898 PMCID: PMC6821191 DOI: 10.1093/nar/gkz658] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/03/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
Methyl-5-uridine (m5U) is one the most abundant non-canonical bases present in cellular RNA, and in yeast is found at position U54 of tRNAs where modification is catalysed by the methyltransferase Trm2. Although the mammalian enzymes that catalyse m5U formation are yet to be identified via experimental evidence, based on sequence homology to Trm2, two candidates currently exist, TRMT2A and TRMT2B. Here we developed a genome-wide single-nucleotide resolution mapping method, Fluorouracil-Induced-Catalytic-Crosslinking-Sequencing (FICC-Seq), in order to identify the relevant enzymatic targets. We demonstrate that TRMT2A is responsible for the majority of m5U present in human RNA, and that it commonly targets U54 of cytosolic tRNAs. By comparison to current methods, we show that FICC-Seq is a particularly robust method for accurate and reliable detection of relevant enzymatic target sites. Our associated finding of extensive irreversible TRMT2A-tRNA crosslinking in vivo following 5-Fluorouracil exposure is also intriguing, as it suggests a tangible mechanism for a previously suspected RNA-dependent route of Fluorouracil-mediated cytotoxicity.
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Affiliation(s)
- Jean-Michel Carter
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Warren Emmett
- The Francis-Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,University College London Genetics Institute, Gower Street, London, WC1E 6BT, UK
| | - Igor Rdl Mozos
- The Francis-Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Annika Kotter
- Johannes Gutenberg-Universität, Institut für Pharmazie und Biochemie, Staudinger Weg 5, 55128 Mainz, Germany
| | - Mark Helm
- Johannes Gutenberg-Universität, Institut für Pharmazie und Biochemie, Staudinger Weg 5, 55128 Mainz, Germany
| | - Jernej Ule
- The Francis-Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Shobbir Hussain
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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46
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Weirick T, Militello G, Hosen MR, John D, Moore JB, Uchida S. Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins. High Throughput 2019; 8:ht8040019. [PMID: 31795425 PMCID: PMC6970233 DOI: 10.3390/ht8040019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/08/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022] Open
Abstract
Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNA Editor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affect the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncovered that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands were examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, human antigen R [HuR; encoded by ELAV-like protein 1 (ELAV1)], was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) compared to the control-suggesting that the presence of RNA editing islands influence HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP-RNA interactions-a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.
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Affiliation(s)
- Tyler Weirick
- Cardiovascular Innovation Institute, University of Louisville, Louisville, KY 40202, USA
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Giuseppe Militello
- Cardiovascular Innovation Institute, University of Louisville, Louisville, KY 40202, USA
- Department of Molecular Cellular and Developmental Biology, Yale University, Yale Science Building-260 Whitney Avenue, New Haven, CT 06511, USA;
| | - Mohammed Rabiul Hosen
- Department of Internal Medicine-II, Molecular Cardiology, Biomedical Center (BMZ), University of Bonn, Sigmund-Freud-Str. 25, Bonn 53127, Germany;
| | - David John
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main 60590, Germany;
| | - Joseph B. Moore
- The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, KY 40202, USA;
- Diabetes and Obesity Center, University of Louisville, Louisville, KY 40202, USA
| | - Shizuka Uchida
- Cardiovascular Innovation Institute, University of Louisville, Louisville, KY 40202, USA
- The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, KY 40202, USA;
- Diabetes and Obesity Center, University of Louisville, Louisville, KY 40202, USA
- Correspondence: ; Tel.: +1-502-854-0570
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47
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Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant JY, Zarnack K, König J, Beli P. The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol 2019; 20:216. [PMID: 31640799 PMCID: PMC6805484 DOI: 10.1186/s13059-019-1814-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and proteins. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products. Translating ribosomes that encounter poly(A) sequences are terminally stalled, followed by ribosome recycling and decay of the truncated nascent polypeptide via ribosome-associated quality control. RESULTS Here, we demonstrate that the conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) promotes ribosome stalling at poly(A) sequences during ribosome-associated quality control. We show that MKRN1 directly binds to the cytoplasmic poly(A)-binding protein (PABPC1) and associates with polysomes. MKRN1 is positioned upstream of poly(A) tails in mRNAs in a PABPC1-dependent manner. Ubiquitin remnant profiling and in vitro ubiquitylation assays uncover PABPC1 and ribosomal protein RPS10 as direct ubiquitylation substrates of MKRN1. CONCLUSIONS We propose that MKRN1 mediates the recognition of poly(A) tails to prevent the production of erroneous proteins from prematurely polyadenylated transcripts, thereby maintaining proteome integrity.
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Affiliation(s)
- Andrea Hildebrandt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Cornelia Rücklé
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susan Boerner
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Martin M Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | | | - Anica Scholz
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Annabelle Dold
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Tobias Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Génopode Building, CH-1015, Lausanne, Switzerland
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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48
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Polishchuk M, Paz I, Yakhini Z, Mandel-Gutfreund Y. SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data. Nucleic Acids Res 2019; 46:W221-W228. [PMID: 29800452 PMCID: PMC6030986 DOI: 10.1093/nar/gky453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/13/2018] [Indexed: 01/24/2023] Open
Abstract
Gene expression regulation is highly dependent on binding of RNA-binding proteins (RBPs) to their RNA targets. Growing evidence supports the notion that both RNA primary sequence and its local secondary structure play a role in specific Protein-RNA recognition and binding. Despite the great advance in high-throughput experimental methods for identifying sequence targets of RBPs, predicting the specific sequence and structure binding preferences of RBPs remains a major challenge. We present a novel webserver, SMARTIV, designed for discovering and visualizing combined RNA sequence and structure motifs from high-throughput RNA-binding data, generated from in-vivo experiments. The uniqueness of SMARTIV is that it predicts motifs from enriched k-mers that combine information from ranked RNA sequences and their predicted secondary structure, obtained using various folding methods. Consequently, SMARTIV generates Position Weight Matrices (PWMs) in a combined sequence and structure alphabet with assigned P-values. SMARTIV concisely represents the sequence and structure motif content as a single graphical logo, which is informative and easy for visual perception. SMARTIV was examined extensively on a variety of high-throughput binding experiments for RBPs from different families, generated from different technologies, showing consistent and accurate results. Finally, SMARTIV is a user-friendly webserver, highly efficient in run-time and freely accessible via http://smartiv.technion.ac.il/.
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Affiliation(s)
- Maya Polishchuk
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Vavilov Institute of General Genetics, Russian Academy of Science, 11933 Moscow, Russia
| | - Inbal Paz
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Zohar Yakhini
- School of Computer Science, Herzliya Interdisciplinary Center, Herzliya 46150, Israel.,Department of Computer Science, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yael Mandel-Gutfreund
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Department of Computer Science, Technion-Israel Institute of Technology, Haifa 32000, Israel
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49
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Královicová J, Ševcíková I, Stejskalová E, Obuca M, Hiller M, Stanek D, Vorechovský I. PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM. Nucleic Acids Res 2019; 46:6166-6187. [PMID: 29788428 PMCID: PMC6093180 DOI: 10.1093/nar/gky389] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/01/2018] [Indexed: 12/27/2022] Open
Abstract
PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.
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Affiliation(s)
- Jana Královicová
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Ivana Ševcíková
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Eva Stejskalová
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Mina Obuca
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics and Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - David Stanek
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Igor Vorechovský
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK
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50
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Singh NN, Singh RN. How RNA structure dictates the usage of a critical exon of spinal muscular atrophy gene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194403. [PMID: 31323435 DOI: 10.1016/j.bbagrm.2019.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022]
Abstract
Role of RNA structure in pre-mRNA splicing has been implicated for several critical exons associated with genetic disorders. However, much of the structural studies linked to pre-mRNA splicing regulation are limited to terminal stem-loop structures (hairpins) sequestering splice sites. In few instances, role of long-distance interactions is implicated as the major determinant of splicing regulation. With the recent surge of reports of circular RNA (circRNAs) generated by backsplicing, role of Alu-associated RNA structures formed by long-range interactions are taking central stage. Humans contain two nearly identical copies of Survival Motor Neuron (SMN) genes, SMN1 and SMN2. Deletion or mutation of SMN1 coupled with the inability of SMN2 to compensate for the loss of SMN1 due to exon 7 skipping causes spinal muscular atrophy (SMA), one of the leading genetic diseases of children. In this review, we describe how structural elements formed by both local and long-distance interactions are being exploited to modulate SMN2 exon 7 splicing as a potential therapy for SMA. We also discuss how Alu-associated secondary structure modulates generation of a vast repertoire of SMN circRNAs. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Natalia N Singh
- Department of Biomedical Science, Iowa State University, Ames, IA 50011, United States of America
| | - Ravindra N Singh
- Department of Biomedical Science, Iowa State University, Ames, IA 50011, United States of America.
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