1
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Verheyden NA, Klostermann M, Brüggemann M, Steede HM, Scholz A, Amr S, Lichtenthaeler C, Münch C, Schmid T, Zarnack K, Krueger A. A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match. Nucleic Acids Res 2024; 52:8515-8533. [PMID: 38783381 DOI: 10.1093/nar/gkae416] [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: 09/14/2023] [Revised: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) in target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs are expected to predominantly occur in the 3' untranslated region and involve perfect base-pairing of the miRNA seed. Here, we generate a high-resolution map of miR-181a/b-1 (miR-181) MREs to define the targeting rules of miR-181 in developing murine T cells. By combining a multi-omics approach with computational high-resolution analyses, we uncover novel miR-181 targets and demonstrate that miR-181 acts predominantly through RNA destabilization. Importantly, we discover an alternative seed match and identify a distinct set of targets with repeat elements in the coding sequence which are targeted by miR-181 and mediate translational inhibition. In conclusion, deep profiling of MREs in primary cells is critical to expand physiologically relevant targetomes and establish context-dependent miRNA targeting rules.
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Affiliation(s)
- Nikita A Verheyden
- Molecular Immunology, Justus Liebig University Gießen, 35392 Gießen, Germany
| | - Melina Klostermann
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Hanna M Steede
- Molecular Immunology, Justus Liebig University Gießen, 35392 Gießen, Germany
| | - Anica Scholz
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Shady Amr
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Chiara Lichtenthaeler
- Institute of Molecular Medicine, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Andreas Krueger
- Molecular Immunology, Justus Liebig University Gießen, 35392 Gießen, Germany
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2
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von Ehr J, Oberstrass L, Yazgan E, Schnaubelt LI, Blümel N, McNicoll F, Weigand JE, Zarnack K, Müller-McNicoll M, Korn SM, Schlundt A. Arid5a uses disordered extensions of its core ARID domain for distinct DNA- and RNA-recognition and gene regulation. J Biol Chem 2024; 300:107457. [PMID: 38866324 PMCID: PMC11262183 DOI: 10.1016/j.jbc.2024.107457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/23/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024] Open
Abstract
AT-rich interacting domain (ARID)-containing proteins, Arids, are a heterogeneous DNA-binding protein family involved in transcription regulation and chromatin processing. For the member Arid5a, no exact DNA-binding preference has been experimentally defined so far. Additionally, the protein binds to mRNA motifs for transcript stabilization, supposedly through the DNA-binding ARID domain. To date, however, no unbiased RNA motif definition and clear dissection of nucleic acid-binding through the ARID domain have been undertaken. Using NMR-centered biochemistry, we here define the Arid5a DNA preference. Further, high-throughput in vitro binding reveals a consensus RNA-binding motif engaged by the core ARID domain. Finally, transcriptome-wide binding (iCLIP2) reveals that Arid5a has a weak preference for (A)U-rich regions in pre-mRNA transcripts of factors related to RNA processing. We find that the intrinsically disordered regions flanking the ARID domain modulate the specificity and affinity of DNA binding, while they appear crucial for RNA interactions. Ultimately, our data suggest that Arid5a uses its extended ARID domain for bifunctional gene regulation and that the involvement of IDR extensions is a more general feature of Arids in interacting with different nucleic acids at the chromatin-mRNA interface.
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Affiliation(s)
- Julian von Ehr
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany; IMPRS on Cellular Biophysics, Frankfurt, Germany
| | - Lasse Oberstrass
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg, Germany
| | - Ege Yazgan
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Lara Ina Schnaubelt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
| | - Nicole Blümel
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Francois McNicoll
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Julia E Weigand
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg, Germany
| | - Kathi Zarnack
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany; Max-Planck Institute for Biophysics, Frankfurt, Germany
| | - Sophie Marianne Korn
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany; University of Greifswald, Institute of Biochemistry, Greifswald, Germany.
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3
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Klostermann M, Zarnack K. racoon_clip-a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data. BIOINFORMATICS ADVANCES 2024; 4:vbae084. [PMID: 38948010 PMCID: PMC11213630 DOI: 10.1093/bioadv/vbae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/07/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
Motivation A vast variety of biological questions connected to RNA-binding proteins can be tackled with UV crosslinking and immunoprecipitation (CLIP) experiments. However, the processing and analysis of CLIP data are rather complex. Moreover, different types of CLIP experiments like iCLIP or eCLIP are often processed in different ways, reducing comparability between multiple experiments. Therefore, we aimed to build an easy-to-use computational tool for the processing of CLIP data that can be used for both iCLIP and eCLIP data, as well as data from other truncation-based CLIP methods. Results Here, we introduce racoon_clip, a sustainable and fully automated pipeline for the complete processing of iCLIP and eCLIP data to extract RNA binding signal at single-nucleotide resolution. racoon_clip is easy to install and execute, with multiple pre-settings and fully customizable parameters, and outputs a conclusive summary report with visualizations and statistics for all analysis steps. Availability and implementation racoon_clip is implemented as a Snakemake-powered command line tool (Snakemake version ≥7.22, Python version ≥3.9). The latest release can be downloaded from GitHub (https://github.com/ZarnackGroup/racoon_clip/tree/main) and installed via pip. A detailed documentation, including installation, usage, and customization, can be found at https://racoon-clip.readthedocs.io/en/latest/. The example datasets can be downloaded from the Short Read Archive (SRA; iCLIP: SRR5646576, SRR5646577, SRR5646578) or the ENCODE Project (eCLIP: ENCSR202BFN).
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Affiliation(s)
- Melina Klostermann
- Faculty of Biosciences, Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main 60438, Germany
| | - Kathi Zarnack
- Faculty of Biosciences, Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main 60438, Germany
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4
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Carvalho L, Lasek AW. It is not just about transcription: involvement of brain RNA splicing in substance use disorders. J Neural Transm (Vienna) 2024; 131:495-503. [PMID: 38396082 PMCID: PMC11055753 DOI: 10.1007/s00702-024-02740-y] [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: 09/16/2023] [Accepted: 01/04/2024] [Indexed: 02/25/2024]
Abstract
Alternative splicing is a co-transcriptional process that significantly contributes to the molecular landscape of the cell. It plays a multifaceted role in shaping gene transcription, protein diversity, and functional adaptability in response to environmental cues. Recent studies demonstrate that drugs of abuse have a profound impact on alternative splicing patterns within different brain regions. Drugs like alcohol and cocaine modify the expression of genes responsible for encoding splicing factors, thereby influencing alternative splicing of crucial genes involved in neurotransmission, neurogenesis, and neuroinflammation. Notable examples of these alterations include alcohol-induced changes in splicing factors such as HSPA6 and PCBP1, as well as cocaine's impact on PTBP1 and SRSF11. Beyond the immediate effects of drug exposure, recent research has shed light on the role of alternative splicing in contributing to the risk of substance use disorders (SUDs). This is exemplified by exon skipping events in key genes like ELOVL7, which can elevate the risk of alcohol use disorder. Lastly, drugs of abuse can induce splicing alterations through epigenetic modifications. For example, cocaine exposure leads to alterations in levels of trimethylated lysine 36 of histone H3, which exhibits a robust association with alternative splicing and serves as a reliable predictor for exon exclusion. In summary, alternative splicing has emerged as a critical player in the complex interplay between drugs of abuse and the brain, offering insights into the molecular underpinnings of SUDs.
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Affiliation(s)
- Luana Carvalho
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 1220 E. Broad ST, Box 980613, Richmond, VA, 23298, USA.
| | - Amy W Lasek
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 1220 E. Broad ST, Box 980613, Richmond, VA, 23298, USA
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5
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Shah K, He S, Turner DJ, Corbo J, Rebbani K, Dominguez D, Bateman JM, Cheloufi S, Igreja C, Valkov E, Murn J. Regulation by the RNA-binding protein Unkempt at its effector interface. Nat Commun 2024; 15:3159. [PMID: 38605040 PMCID: PMC11009413 DOI: 10.1038/s41467-024-47449-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/28/2024] [Indexed: 04/13/2024] Open
Abstract
How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here, we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of 'dual-purpose' peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for the reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface.
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Affiliation(s)
- Kriti Shah
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA
| | - Shiyang He
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA
| | - David J Turner
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Joshua Corbo
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
| | - Khadija Rebbani
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 5 Cutcombe Road, SE5 9RX, London, UK
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Cátia Igreja
- Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, D-72076, Tübingen, Germany
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA.
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA.
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6
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Feichtner A, Enzler F, Kugler V, Hoppe K, Mair S, Kremser L, Lindner H, Huber RG, Stelzl U, Stefan E, Torres-Quesada O. Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA-protein interactions. Cell Mol Life Sci 2024; 81:162. [PMID: 38568213 PMCID: PMC10991009 DOI: 10.1007/s00018-024-05204-4] [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: 08/18/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modulates kinase signal transmission is the cyclic-adenosine monophosphate (cAMP). The main proteinogenic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal propagation which is indispensable for numerous cell-type specific functions. Here we present evidence that TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, represents a novel nuclear PKA substrate. In cross-linking and immunoprecipitation experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that undergo RNA-binding dynamics upon phosphorylation. We observed that the activation of the cAMP-PKA signaling axis caused a change in the composition of a collection of RNA species that interact with TAF15. This observation appears to be a broader principle in the regulation of molecular interactions, as we identified a significant enrichment of RNA-binding proteins within endogenous PKA complexes. We assume that phosphorylation of RNA-binding domains adds another layer of regulation to binary protein-RNAs interactions with consequences to RNA features including binding specificities, localization, abundance and composition.
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Affiliation(s)
- Andreas Feichtner
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
| | - Valentina Kugler
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Katharina Hoppe
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Sophia Mair
- Department of Cardiac Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
- Vascage, Center of Clinical Stroke Research, 6020, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, 138671, Singapore
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Omar Torres-Quesada
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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7
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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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8
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Lewinski M, Steffen A, Kachariya N, Elgner M, Schmal C, Messini N, Köster T, Reichel M, Sattler M, Zarnack K, Staiger D. Arabidopsis thaliana GLYCINE RICH RNA-BINDING PROTEIN 7 interaction with its iCLIP target LHCB1.1 correlates with changes in RNA stability and circadian oscillation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:203-224. [PMID: 38124335 DOI: 10.1111/tpj.16601] [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: 08/25/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The importance of RNA-binding proteins (RBPs) for plant responses to environmental stimuli and development is well documented. Insights into the portfolio of RNAs they recognize, however, clearly lack behind the understanding gathered in non-plant model organisms. Here, we characterize binding of the circadian clock-regulated Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 7 (AtGRP7) to its target transcripts. We identified novel RNA targets from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) data using an improved bioinformatics pipeline that will be broadly applicable to plant RBP iCLIP data. 2705 transcripts with binding sites were identified in plants expressing AtGRP7-GFP that were not recovered in plants expressing an RNA-binding dead variant or GFP alone. A conserved RNA motif enriched in uridine residues was identified at the AtGRP7 binding sites. NMR titrations confirmed the preference of AtGRP7 for RNAs with a central U-rich motif. Among the bound RNAs, circadian clock-regulated transcripts were overrepresented. Peak abundance of the LHCB1.1 transcript encoding a chlorophyll-binding protein was reduced in plants overexpressing AtGRP7 whereas it was elevated in atgrp7 mutants, indicating that LHCB1.1 was regulated by AtGRP7 in a dose-dependent manner. In plants overexpressing AtGRP7, the LHCB1.1 half-life was shorter compared to wild-type plants whereas in atgrp7 mutant plants, the half-life was significantly longer. Thus, AtGRP7 modulates circadian oscillations of its in vivo binding target LHCB1.1 by affecting RNA stability.
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Affiliation(s)
- Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Alexander Steffen
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Nitin Kachariya
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University of Munich, TUM School of Natural Sciences, Garching, 85747, Germany
| | - Mareike Elgner
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Niki Messini
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University of Munich, TUM School of Natural Sciences, Garching, 85747, 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
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University of Munich, TUM School of Natural Sciences, Garching, 85747, 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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9
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Arnold B, Riegger RJ, Okuda EK, Slišković I, Keller M, Bakisoglu C, McNicoll F, Zarnack K, Müller-McNicoll M. hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates. J Cell Biol 2024; 223:e202304030. [PMID: 38108808 PMCID: PMC10726014 DOI: 10.1083/jcb.202304030] [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: 04/12/2023] [Revised: 09/18/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023] Open
Abstract
Nuclear RNA binding proteins (RBPs) are difficult to study because they often belong to large protein families and form extensive networks of auto- and crossregulation. They are highly abundant and many localize to condensates with a slow turnover, requiring long depletion times or knockouts that cannot distinguish between direct and indirect or compensatory effects. Here, we developed a system that is optimized for the rapid degradation of nuclear RBPs, called hGRAD. It comes as a "one-fits-all" plasmid, and integration into any cell line with endogenously GFP-tagged proteins allows for an inducible, rapid, and complete knockdown. We show that the nuclear RBPs SRSF3, SRSF5, SRRM2, and NONO are completely cleared from nuclear speckles and paraspeckles within 2 h. hGRAD works in various cell types, is more efficient than previous methods, and does not require the expression of exogenous ubiquitin ligases. Combining SRSF5 hGRAD degradation with Nascent-seq uncovered transient transcript changes, compensatory mechanisms, and an effect of SRSF5 on transcript stability.
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Affiliation(s)
- Benjamin Arnold
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ricarda J. Riegger
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ellen Kazumi Okuda
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- International Max Planck Research School for Cellular Biophysics, Frankfurt am Main, Germany
| | - Irena Slišković
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mario Keller
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Cem Bakisoglu
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - François McNicoll
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kathi Zarnack
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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10
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Hayashi M, Lodmell JS. Characterization of RVFV Nucleocapsid Protein Binding Sites on RNA by iCLIP-seq. Methods Mol Biol 2024; 2824:319-334. [PMID: 39039420 DOI: 10.1007/978-1-0716-3926-9_19] [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: 07/24/2024]
Abstract
The nucleocapsid protein (N) in Rift Valley fever virus is an RNA-binding protein that functions in viral transcription, replication, and packaging. In this chapter, the method for studying protein-RNA interactions in context of viral infection using individual nucleotide resolution, cross-linking, immunoprecipitation, and sequencing (iCLIP-seq) is explained. The method is useful for identifying the interactions between both host and viral RNAs with N and can identify RNA motifs that interact with the protein of interest.
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Affiliation(s)
- Miyuki Hayashi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, USA
| | - J Stephen Lodmell
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, USA.
- Division of Biological Sciences, University of Montana, Missoula, MT, USA.
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11
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Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J, Beli P. K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell 2023; 83:4272-4289.e10. [PMID: 37951215 DOI: 10.1016/j.molcel.2023.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
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Affiliation(s)
- Aldwin Suryo Rahmanto
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | | | | | | | | | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Anna Orekhova
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | | | | | - Nils Krapoth
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yajie Zhu
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany.
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12
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Hartstock K, Kueck NA, Spacek P, Ovcharenko A, Hüwel S, Cornelissen NV, Bollu A, Dieterich C, Rentmeister A. MePMe-seq: antibody-free simultaneous m 6A and m 5C mapping in mRNA by metabolic propargyl labeling and sequencing. Nat Commun 2023; 14:7154. [PMID: 37935679 PMCID: PMC10630376 DOI: 10.1038/s41467-023-42832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Internal modifications of mRNA have emerged as widespread and versatile regulatory mechanism to control gene expression at the post-transcriptional level. Most of these modifications are methyl groups, making S-adenosyl-L-methionine (SAM) a central metabolic hub. Here we show that metabolic labeling with a clickable metabolic precursor of SAM, propargyl-selenohomocysteine (PSH), enables detection and identification of various methylation sites. Propargylated A, C, and G nucleosides form at detectable amounts via intracellular generation of the corresponding SAM analogue. Integration into next generation sequencing enables mapping of N6-methyladenosine (m6A) and 5-methylcytidine (m5C) sites in mRNA with single nucleotide precision (MePMe-seq). Analysis of the termination profiles can be used to distinguish m6A from 2'-O-methyladenosine (Am) and N1-methyladenosine (m1A) sites. MePMe-seq overcomes the problems of antibodies for enrichment and sequence-motifs for evaluation, which was limiting previous methodologies. Metabolic labeling via clickable SAM facilitates the joint evaluation of methylation sites in RNA and potentially DNA and proteins.
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Affiliation(s)
- Katja Hartstock
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nadine A Kueck
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Spacek
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Amarnath Bollu
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany.
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13
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Das A, Liu T, Li H, Husain S. The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei. mSphere 2023; 8:e0027323. [PMID: 37581443 PMCID: PMC10654194 DOI: 10.1128/msphere.00273-23] [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: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 08/16/2023] Open
Abstract
RNA-binding proteins (RBPs) are key players in coordinated post-transcriptional regulation of functionally related genes, defined as RNA regulons. RNA regulons play particularly critical roles in parasitic trypanosomes, which exhibit unregulated co-transcription of long unrelated gene arrays. In this report, we present a systematic analysis of an essential RBP, RBP42, in the mammalian-infective bloodstream form of African trypanosome and show that RBP42 is a key regulator of parasite's central carbon and energy metabolism. Using individual-nucleotide resolution UV cross-linking and immunoprecipitation to identify genome-wide RBP42-RNA interactions, we show that RBP42 preferentially binds within the coding region of mRNAs encoding core metabolic enzymes. Global quantitative transcriptomic and proteomic analyses reveal that loss of RBP42 reduces the abundance of target mRNA-encoded proteins, but not target mRNA, suggesting a positive translational regulatory role of RBP42. Significant changes in central carbon metabolic intermediates, following loss of RBP42, further support its critical role in cellular energy metabolism. Trypanosoma brucei infection, transmitted through the bite of blood-feeding tsetse flies, causes deadly diseases in humans and livestock. This disease, if left untreated, is almost always fatal. Existing therapies are toxic and difficult to administer. During T. brucei's lifecycle in two different host environments, the parasite progresses through distinctive life stages with major morphological and metabolic changes, requiring precise alteration of parasite gene expression program. In the absence of regulated transcription, post-transcriptional processes mediated by RNA-binding proteins play critical roles in T. brucei gene regulation. In this study, we show that the RNA-binding protein RBP42 plays crucial roles in cellular energy metabolic regulation of this important human pathogen. Metabolic dysregulation observed in RBP42 knockdown cells offers a breadth of potential interest to researchers studying parasite biology and can also impact research in general eukaryotic biology.
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Affiliation(s)
- Anish Das
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Tong Liu
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Seema Husain
- Genomics Center, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
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14
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Shah K, He S, Turner DJ, Corbo J, Rebbani K, Bateman JM, Cheloufi S, Igreja C, Valkov E, Murn J. A paradigm for regulation at the effector interface with RNA-binding proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558714. [PMID: 37790431 PMCID: PMC10542489 DOI: 10.1101/2023.09.20.558714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
RNA-binding proteins (RBPs) are key regulators of gene expression, but how RBPs convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a deeply conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of 'dual-purpose' peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by the recruiting RBP. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface, with implications for the evolution and function of RBP-operated regulatory networks.
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Affiliation(s)
- Kriti Shah
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- These authors contributed equally
| | - Shiyang He
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- These authors contributed equally
| | - David J. Turner
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
- These authors contributed equally
| | - Joshua Corbo
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, U.S.A
| | - Khadija Rebbani
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Joseph M. Bateman
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, 5 Cutcombe Road, London, SE5 9RX, U.K
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA 92521, U.S.A
| | - Cátia Igreja
- Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, D-72076 Tübingen, Germany
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- Lead contact
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15
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Singh V, Walter V, Elcheva I, Imamura Kawasawa Y, Spiegelman VS. Global role of IGF2BP1 in controlling the expression of Wnt/β-catenin-regulated genes in colorectal cancer cells. Front Cell Dev Biol 2023; 11:1236356. [PMID: 37829185 PMCID: PMC10565211 DOI: 10.3389/fcell.2023.1236356] [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] [Received: 06/07/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Introduction: Wnt/β-catenin signaling controls cell division and lineage specification during embryonic development, and is crucial for stem cells maintenance and gut tissue regeneration in adults. Aberrant activation of Wnt/β-catenin signaling is also essential for the pathogenesis of a variety of malignancies. The RNA-binding protein IGF2BP1 is a transcriptional target of Wnt/β-catenin signaling, normally expressed during development and often reactivated in cancer cells, where it regulates the stability of oncogenic mRNA. Methods: In this study, we employed iCLIP and RNA sequencing techniques to investigate the role of IGF2BP1 in the post-transcriptional regulation of Wnt/β-catenin-induced genes at a global level within colorectal cancer (CRC) cells characterized by constitutively active Wnt/β-catenin signaling. Results and Discussion: In our study, we show that, in contrast to normal cells, CRC cells exhibit a much stronger dependency on IGF2BP1 expression for Wnt/β-catenin-regulated genes. We show that both untransformed and CRC cells have their unique subsets of Wnt/β-catenin-regulated genes that IGF2BP1 directly controls through binding to their mRNA. Our iCLIP analysis revealed a significant change in the IGF2BP1-binding sites throughout the target transcriptomes and a significant change in the enrichment of 6-mer motifs associated with IGF2BP1 binding in response to Wnt/β-catenin signaling. Our study also revealed a signature of IGF2BP1-regulated genes that are significantly associated with colon cancer-free survival in humans, as well as potential targets for CRC treatment. Overall, this study highlights the complex and context-dependent regulation of Wnt/β-catenin signaling target genes by IGF2BP1 in non-transformed and CRC cells and identifies potential targets for colon cancer treatment.
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Affiliation(s)
- Vikash Singh
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
| | - Vonn Walter
- Department of Public Health Science, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
| | - Irina Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
| | - Yuka Imamura Kawasawa
- Department of Pharmacology, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
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16
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García-Vílchez R, Añazco-Guenkova AM, Dietmann S, López J, Morón-Calvente V, D'Ambrosi S, Nombela P, Zamacola K, Mendizabal I, García-Longarte S, Zabala-Letona A, Astobiza I, Fernández S, Paniagua A, Miguel-López B, Marchand V, Alonso-López D, Merkel A, García-Tuñón I, Ugalde-Olano A, Loizaga-Iriarte A, Lacasa-Viscasillas I, Unda M, Azkargorta M, Elortza F, Bárcena L, Gonzalez-Lopez M, Aransay AM, Di Domenico T, Sánchez-Martín MA, De Las Rivas J, Guil S, Motorin Y, Helm M, Pandolfi PP, Carracedo A, Blanco S. METTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer. Mol Cancer 2023; 22:119. [PMID: 37516825 PMCID: PMC10386714 DOI: 10.1186/s12943-023-01809-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/17/2023] [Indexed: 07/31/2023] Open
Abstract
Newly growing evidence highlights the essential role that epitranscriptomic marks play in the development of many cancers; however, little is known about the role and implications of altered epitranscriptome deposition in prostate cancer. Here, we show that the transfer RNA N7-methylguanosine (m7G) transferase METTL1 is highly expressed in primary and advanced prostate tumours. Mechanistically, we find that METTL1 depletion causes the loss of m7G tRNA methylation and promotes the biogenesis of a novel class of small non-coding RNAs derived from 5'tRNA fragments. 5'tRNA-derived small RNAs steer translation control to favour the synthesis of key regulators of tumour growth suppression, interferon pathway, and immune effectors. Knockdown of Mettl1 in prostate cancer preclinical models increases intratumoural infiltration of pro-inflammatory immune cells and enhances responses to immunotherapy. Collectively, our findings reveal a therapeutically actionable role of METTL1-directed m7G tRNA methylation in cancer cell translation control and tumour biology.
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Affiliation(s)
- Raquel García-Vílchez
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Ana M Añazco-Guenkova
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Sabine Dietmann
- Washington University School of Medicine in St. Louis, 660S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Judith López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Virginia Morón-Calvente
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Silvia D'Ambrosi
- Present Address: Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Paz Nombela
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Kepa Zamacola
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Isabel Mendizabal
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, 48011, Bilbao, Spain
| | - Saioa García-Longarte
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Amaia Zabala-Letona
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ianire Astobiza
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Sonia Fernández
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Alejandro Paniagua
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
| | - Borja Miguel-López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Virginie Marchand
- Université de Lorraine, UAR2008 IBSLor CNRS-UL-INSERM, Biopôle UL, 9, Avenue de La Forêt de Haye, 54505, Vandoeuvre-Les-Nancy, France
| | - Diego Alonso-López
- Bioinformatics Unit, Cancer Research Center (CIC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), 37007, Salamanca, Spain
| | - Angelika Merkel
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Barcelona, Catalonia, Spain
- Germans Trias I Pujol Health Science Research Institute, Badalona, 08916, Barcelona, Catalonia, Spain
| | - Ignacio García-Tuñón
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
| | | | - Ana Loizaga-Iriarte
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Urology, Basurto University Hospital, 48013, Bilbao, Spain
- Traslational Prostate Cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Avenida Montevideo 18, 48013, Bilbao, Spain
| | | | - Miguel Unda
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Urology, Basurto University Hospital, 48013, Bilbao, Spain
- Traslational Prostate Cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Avenida Montevideo 18, 48013, Bilbao, Spain
| | - Mikel Azkargorta
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
| | - Félix Elortza
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Laura Bárcena
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Ana M Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Tomás Di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Manuel A Sánchez-Martín
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, 37007, Salamanca, Spain
| | - Javier De Las Rivas
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
| | - Sònia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Barcelona, Catalonia, Spain
- Germans Trias I Pujol Health Science Research Institute, Badalona, 08916, Barcelona, Catalonia, Spain
| | - Yuri Motorin
- Université de Lorraine, UAR2008 IBSLor CNRS-UL-INSERM, Biopôle UL, 9, Avenue de La Forêt de Haye, 54505, Vandoeuvre-Les-Nancy, France
- Université de Lorraine, UMR7365 IMoPA CNRS-UL, Biopôle UL, 9, Avenue de La Forêt de Haye, 54505, Vandoeuvre-Les-Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Pier Paolo Pandolfi
- Molecular Biotechnology Center (MBC), Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126, Turin, TO, Italy
- William N. Pennington Cancer Center, Renown Health, Nevada System of Higher Education, Reno, NV, 89502, USA
| | - Arkaitz Carracedo
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, 48011, Bilbao, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Pathology, Basurto University Hospital, 48013, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080, Bilbao, Spain
| | - Sandra Blanco
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain.
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17
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Ebersberger S, Hipp C, Mulorz MM, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, Zarnack K, Ebersberger I, Legewie S, Luck K, Sattler M, König J. FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns. Mol Cell 2023:S1097-2765(23)00516-6. [PMID: 37506698 DOI: 10.1016/j.molcel.2023.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/19/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023]
Abstract
Splicing of pre-mRNAs critically contributes to gene regulation and proteome expansion in eukaryotes, but our understanding of the recognition and pairing of splice sites during spliceosome assembly lacks detail. Here, we identify the multidomain RNA-binding protein FUBP1 as a key splicing factor that binds to a hitherto unknown cis-regulatory motif. By collecting NMR, structural, and in vivo interaction data, we demonstrate that FUBP1 stabilizes U2AF2 and SF1, key components at the 3' splice site, through multivalent binding interfaces located within its disordered regions. Transcriptional profiling and kinetic modeling reveal that FUBP1 is required for efficient splicing of long introns, which is impaired in cancer patients harboring FUBP1 mutations. Notably, FUBP1 interacts with numerous U1 snRNP-associated proteins, suggesting a unique role for FUBP1 in splice site bridging for long introns. We propose a compelling model for 3' splice site recognition of long introns, which represent 80% of all human introns.
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Affiliation(s)
| | - Clara Hipp
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Dalmira Hubrich
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Santiago Martínez-Lumbreras
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Panajot Kristofori
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany
| | | | | | - Jonas Schönfeld
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Cem Bakisoglu
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kerstin Tretow
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Mareen Welzel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Martin M Möckel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; CardioPulmonary Institute (CPI), 35392 Gießen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Center (S-BIK-F), 60325 Frankfurt am Main, Germany; LOEWE Center for Translational Biodiversity Genomics (TBG), 60325 Frankfurt am Main, Germany
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, 70569 Stuttgart, Germany
| | - Katja Luck
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
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18
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Klein T, Funke F, Rossbach O, Lehmann G, Vockenhuber M, Medenbach J, Suess B, Meister G, Babinger P. Investigating the Prevalence of RNA-Binding Metabolic Enzymes in E. coli. Int J Mol Sci 2023; 24:11536. [PMID: 37511294 PMCID: PMC10380284 DOI: 10.3390/ijms241411536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
An open research field in cellular regulation is the assumed crosstalk between RNAs, metabolic enzymes, and metabolites, also known as the REM hypothesis. High-throughput assays have produced extensive interactome data with metabolic enzymes frequently found as hits, but only a few examples have been biochemically validated, with deficits especially in prokaryotes. Therefore, we rationally selected nineteen Escherichia coli enzymes from such datasets and examined their ability to bind RNAs using two complementary methods, iCLIP and SELEX. Found interactions were validated by EMSA and other methods. For most of the candidates, we observed no RNA binding (12/19) or a rather unspecific binding (5/19). Two of the candidates, namely glutamate-5-kinase (ProB) and quinone oxidoreductase (QorA), displayed specific and previously unknown binding to distinct RNAs. We concentrated on the interaction of QorA to the mRNA of yffO, a grounded prophage gene, which could be validated by EMSA and MST. Because the physiological function of both partners is not known, the biological relevance of this interaction remains elusive. Furthermore, we found novel RNA targets for the MS2 phage coat protein that served us as control. Our results indicate that RNA binding of metabolic enzymes in procaryotes is less frequent than suggested by the results of high-throughput studies, but does occur.
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Affiliation(s)
- Thomas Klein
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Franziska Funke
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Faculty of Biology and Chemistry, University of Giessen, D-35392 Giessen, Germany
| | - Gerhard Lehmann
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Michael Vockenhuber
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Jan Medenbach
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Beatrix Suess
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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19
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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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20
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Feng Q, Lin Z, Deng Y, Ran Y, Yu R, Xiang AP, Ye C, Yao C. The U1 antisense morpholino oligonucleotide (AMO) disrupts U1 snRNP structure to promote intronic PCPA modification of pre-mRNAs. J Biol Chem 2023; 299:104854. [PMID: 37224962 PMCID: PMC10404622 DOI: 10.1016/j.jbc.2023.104854] [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: 02/27/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/26/2023] Open
Abstract
Functional depletion of the U1 small nuclear ribonucleoprotein (snRNP) with a 25 nt U1 AMO (antisense morpholino oligonucleotide) may lead to intronic premature cleavage and polyadenylation of thousands of genes, a phenomenon known as U1 snRNP telescripting; however, the underlying mechanism remains elusive. In this study, we demonstrated that U1 AMO could disrupt U1 snRNP structure both in vitro and in vivo, thereby affecting the U1 snRNP-RNAP polymerase II interaction. By performing chromatin immunoprecipitation sequencing for phosphorylation of Ser2 and Ser5 of the C-terminal domain of RPB1, the largest subunit of RNAP polymerase II, we showed that transcription elongation was disturbed upon U1 AMO treatment, with a particular high phosphorylation of Ser2 signal at intronic cryptic polyadenylation sites (PASs). In addition, we showed that core 3'processing factors CPSF/CstF are involved in the processing of intronic cryptic PAS. Their recruitment accumulated toward cryptic PASs upon U1 AMO treatment, as indicated by chromatin immunoprecipitation sequencing and individual-nucleotide resolution CrossLinking and ImmunoPrecipitation sequencing analysis. Conclusively, our data suggest that disruption of U1 snRNP structure mediated by U1 AMO provides a key for understanding the U1 telescripting mechanism.
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Affiliation(s)
- Qiumin Feng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zejin Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Yanhui Deng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yi Ran
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Rui Yu
- Department of Biochemistry, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China; Advanced Medical Technology Center, The first Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China; Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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21
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Chakrabarti AM, Capitanchik C, Ule J, Luscombe NM. clipplotr-a comparative visualization and analysis tool for CLIP data. RNA (NEW YORK, N.Y.) 2023; 29:715-723. [PMID: 36894192 PMCID: PMC10187674 DOI: 10.1261/rna.079326.122] [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: 09/12/2022] [Accepted: 02/09/2023] [Indexed: 05/18/2023]
Abstract
CLIP technologies are now widely used to study RNA-protein interactions and many data sets are now publicly available. An important first step in CLIP data exploration is the visual inspection and assessment of processed genomic data on selected genes or regions and performing comparisons: either across conditions within a particular project, or incorporating publicly available data. However, the output files produced by data processing pipelines or preprocessed files available to download from data repositories are often not suitable for direct comparison and usually need further processing. Furthermore, to derive biological insight it is usually necessary to visualize a CLIP signal alongside other data such as annotations, or orthogonal functional genomic data (e.g., RNA-seq). We have developed a simple, but powerful, command-line tool: clipplotr, which facilitates these visual comparative and integrative analyses with normalization and smoothing options for CLIP data and the ability to show these alongside reference annotation tracks and functional genomic data. These data can be supplied as input to clipplotr in a range of file formats, which will output a publication quality figure. It is written in R and can both run on a laptop computer independently or be integrated into computational workflows on a high-performance cluster. Releases, source code, and documentation are freely available at https://github.com/ulelab/clipplotr.
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Affiliation(s)
| | | | - Jernej Ule
- The Francis Crick Institute, London, NW1 4AT, United Kingdom
- UK Dementia Research Institute at King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, United Kingdom
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, NW1 4AT, United Kingdom
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
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22
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Molitor L, Klostermann M, Bacher S, Merl-Pham J, Spranger N, Burczyk S, Ketteler C, Rusha E, Tews D, Pertek A, Proske M, Busch A, Reschke S, Feederle R, Hauck S, Blum H, Drukker M, Fischer-Posovszky P, König J, Zarnack K, Niessing D. Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies. Nucleic Acids Res 2023; 51:1297-1316. [PMID: 36651277 PMCID: PMC9943675 DOI: 10.1093/nar/gkac1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
The RNA-binding protein PURA has been implicated in the rare, monogenetic, neurodevelopmental disorder PURA Syndrome. PURA binds both DNA and RNA and has been associated with various cellular functions. Only little is known about its main cellular roles and the molecular pathways affected upon PURA depletion. Here, we show that PURA is predominantly located in the cytoplasm, where it binds to thousands of mRNAs. Many of these transcripts change abundance in response to PURA depletion. The encoded proteins suggest a role for PURA in immune responses, mitochondrial function, autophagy and processing (P)-body activity. Intriguingly, reduced PURA levels decrease the expression of the integral P-body components LSM14A and DDX6 and strongly affect P-body formation in human cells. Furthermore, PURA knockdown results in stabilization of P-body-enriched transcripts, whereas other mRNAs are not affected. Hence, reduced PURA levels, as reported in patients with PURA Syndrome, influence the formation and composition of this phase-separated RNA processing machinery. Our study proposes PURA Syndrome as a new model to study the tight connection between P-body-associated RNA regulation and neurodevelopmental disorders.
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Affiliation(s)
| | | | - Sabrina Bacher
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Juliane Merl-Pham
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Nadine Spranger
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Sandra Burczyk
- Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Carolin Ketteler
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Ejona Rusha
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Daniel Tews
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, 89070 Ulm, Germany
| | - Anna Pertek
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Marcel Proske
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands
| | - Pamela Fischer-Posovszky
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, 89070 Ulm, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Kathi Zarnack
- Correspondence may also be addressed to Kathi Zarnack. Tel: +49 69 798 42506; Fax: +49 69 798 763 42506;
| | - Dierk Niessing
- To whom correspondence should be addressed. Tel: +49 731 50 23160; Fax: +49 731 50 23169;
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23
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de Oliveira Freitas Machado C, Schafranek M, Brüggemann M, Hernández Cañás M, Keller M, Di Liddo A, Brezski A, Blümel N, Arnold B, Bremm A, Wittig I, Jaé N, McNicoll F, Dimmeler S, Zarnack K, Müller-McNicoll M. Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia. Nucleic Acids Res 2023; 51:870-890. [PMID: 36620874 PMCID: PMC9881134 DOI: 10.1093/nar/gkac1225] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 01/10/2023] Open
Abstract
Hypoxia induces massive changes in alternative splicing (AS) to adapt cells to the lack of oxygen. Here, we identify the splicing factor SRSF6 as a key factor in the AS response to hypoxia. The SRSF6 level is strongly reduced in acute hypoxia, which serves a dual purpose: it allows for exon skipping and triggers the dispersal of nuclear speckles. Our data suggest that cells use dispersal of nuclear speckles to reprogram their gene expression during hypoxic adaptation and that SRSF6 plays an important role in cohesion of nuclear speckles. Down-regulation of SRSF6 is achieved through inclusion of a poison cassette exon (PCE) promoted by SRSF4. Removing the PCE 3' splice site using CRISPR/Cas9 abolishes SRSF6 reduction in hypoxia. Aberrantly high SRSF6 levels in hypoxia attenuate hypoxia-mediated AS and impair dispersal of nuclear speckles. As a consequence, proliferation and genomic instability are increased, while the stress response is suppressed. The SRSF4-PCE-SRSF6 hypoxia axis is active in different cancer types, and high SRSF6 expression in hypoxic tumors correlates with a poor prognosis. We propose that the ultra-conserved PCE of SRSF6 acts as a tumor suppressor and that its inclusion in hypoxia is crucial to reduce SRSF6 levels. This may prevent tumor cells from entering the metastatic route of hypoxia adaptation.
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Affiliation(s)
- Camila de Oliveira Freitas Machado
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - Michal Schafranek
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Mirko Brüggemann
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | | | - Mario Keller
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Antonella Di Liddo
- Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Andre Brezski
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Nicole Blümel
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Benjamin Arnold
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Anja Bremm
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Nicolas Jaé
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - François McNicoll
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
| | - Kathi Zarnack
- Correspondence may also be addressed to Kathi Zarnack.
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24
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Sobeh AM, Eichhorn CD. C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition. Biophys Chem 2023; 292:106928. [PMID: 36427363 PMCID: PMC9768861 DOI: 10.1016/j.bpc.2022.106928] [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: 05/12/2022] [Revised: 10/13/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022]
Abstract
The 7SK ribonucleoprotein (RNP) is a critical regulator of eukaryotic transcription. Recently, RNA binding motif 7 (RBM7) containing an RNA recognition motif (RRM) was reported to associate with 7SK RNA and core 7SK RNP protein components in response to DNA damage. However, little is known about the mode of RBM7-7SK RNA recognition. Here, we found that RRM constructs containing extended C-termini have increased solubility compared to a minimal RRM construct, although these constructs aggregate in a temperature and concentration-dependent manner. Using solution NMR dynamics experiments, we identified additional structural features observed previously in crystal but not in solution structures. To identify potential RBM7-7SK RNA binding sites, we analyzed deposited data from in cellulo crosslinking experiments and found that RBM7 primarily crosslinks to the distal region of 7SK stem-loop 3 (SL3). Electrophoretic mobility shift assays and NMR chemical shift perturbation experiments showed weak binding to 7SK SL3 constructs in vitro. Together, these results provide new insights into RBM7 RRM folding and recognition of 7SK RNA.
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Affiliation(s)
- Amr M Sobeh
- Department of Chemistry, University of Nebraska, 639 North 12th St, Lincoln, NE 68588, USA
| | - Catherine D Eichhorn
- Department of Chemistry, University of Nebraska, 639 North 12th St, Lincoln, NE 68588, USA.
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25
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Splicing factor BUD31 promotes ovarian cancer progression through sustaining the expression of anti-apoptotic BCL2L12. Nat Commun 2022; 13:6246. [PMID: 36271053 PMCID: PMC9587234 DOI: 10.1038/s41467-022-34042-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Dysregulated expression of splicing factors has important roles in cancer development and progression. However, it remains a challenge to identify the cancer-specific splicing variants. Here we demonstrate that spliceosome component BUD31 is increased in ovarian cancer, and its higher expression predicts worse prognosis. We characterize the BUD31-binding motif and find that BUD31 preferentially binds exon-intron regions near splicing sites. Further analysis reveals that BUD31 inhibition results in extensive exon skipping and a reduced production of long isoforms containing full coding sequence. In particular, we identify BCL2L12, an anti-apoptotic BCL2 family member, as one of the functional splicing targets of BUD31. BUD31 stimulates the inclusion of exon 3 to generate full-length BCL2L12 and promotes ovarian cancer progression. Knockdown of BUD31 or splice-switching antisense oligonucleotide treatment promotes exon 3 skipping and results in a truncated isoform of BCL2L12 that undergoes nonsense-mediated mRNA decay, and the cells subsequently undergo apoptosis. Our findings reveal BUD31-regulated exon inclusion as a critical factor for ovarian cancer cell survival and cancer progression.
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26
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Cortés-López M, Schulz L, Enculescu M, Paret C, Spiekermann B, Quesnel-Vallières M, Torres-Diz M, Unic S, Busch A, Orekhova A, Kuban M, Mesitov M, Mulorz MM, Shraim R, Kielisch F, Faber J, Barash Y, Thomas-Tikhonenko A, Zarnack K, Legewie S, König J. High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance. Nat Commun 2022; 13:5570. [PMID: 36138008 PMCID: PMC9500061 DOI: 10.1038/s41467-022-31818-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Following CART-19 immunotherapy for B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the cognate CD19 epitope. Since epitope loss can be caused by aberrant CD19 exon 2 processing, we herein investigate the regulatory code that controls CD19 splicing. We combine high-throughput mutagenesis with mathematical modelling to quantitatively disentangle the effects of all mutations in the region comprising CD19 exons 1-3. Thereupon, we identify ~200 single point mutations that alter CD19 splicing and thus could predispose B-ALL patients to developing CART-19 resistance. Furthermore, we report almost 100 previously unknown splice isoforms that emerge from cryptic splice sites and likely encode non-functional CD19 proteins. We further identify cis-regulatory elements and trans-acting RNA-binding proteins that control CD19 splicing (e.g., PTBP1 and SF3B4) and validate that loss of these factors leads to pervasive CD19 mis-splicing. Our dataset represents a comprehensive resource for identifying predictive biomarkers for CART-19 therapy. Multiple alternative splicing events in CD19 mRNA have been associated with resistance/relapse to CD19 CAR-T therapy in patients with B cell malignancies. Here, by combining patient data and a high-throughput mutagenesis screen, the authors identify single point mutations and RNA-binding proteins that can control CD19 splicing and be associated with CD19 CAR-T therapy resistance.
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Affiliation(s)
| | - Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mihaela Enculescu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Claudia Paret
- Department of Pediatric Hematology/Oncology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany.,German Cancer Consortium (DKTK), site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Bea Spiekermann
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sebastian Unic
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Allmandring 30E, 70569, Stuttgart, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anna Orekhova
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Monika Kuban
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Allmandring 30E, 70569, Stuttgart, Germany
| | - Mikhail Mesitov
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Rawan Shraim
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Fridolin Kielisch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Jörg Faber
- Department of Pediatric Hematology/Oncology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany.,German Cancer Consortium (DKTK), site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. .,Faculty Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany. .,Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Allmandring 30E, 70569, Stuttgart, Germany. .,Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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27
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Ito-Kureha T, Leoni C, Borland K, Cantini G, Bataclan M, Metzger RN, Ammann G, Krug AB, Marsico A, Kaiser S, Canzar S, Feske S, Monticelli S, König J, Heissmeyer V. The function of Wtap in N 6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells. Nat Immunol 2022; 23:1208-1221. [PMID: 35879451 DOI: 10.1038/s41590-022-01268-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022]
Abstract
T cell antigen-receptor (TCR) signaling controls the development, activation and survival of T cells by involving several layers and numerous mechanisms of gene regulation. N6-methyladenosine (m6A) is the most prevalent messenger RNA modification affecting splicing, translation and stability of transcripts. In the present study, we describe the Wtap protein as essential for m6A methyltransferase complex function and reveal its crucial role in TCR signaling in mouse T cells. Wtap and m6A methyltransferase functions were required for the differentiation of thymocytes, control of activation-induced death of peripheral T cells and prevention of colitis by enabling gut RORγt+ regulatory T cell function. Transcriptome and epitranscriptomic analyses reveal that m6A modification destabilizes Orai1 and Ripk1 mRNAs. Lack of post-transcriptional repression of the encoded proteins correlated with increased store-operated calcium entry activity and diminished survival of T cells with conditional genetic inactivation of Wtap. These findings uncover how m6A modification impacts on TCR signal transduction and determines activation and survival of T cells.
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Affiliation(s)
- Taku Ito-Kureha
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Cristina Leoni
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Kayla Borland
- Department of Chemistry, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Giulia Cantini
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany.,Institute for Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marian Bataclan
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Rebecca N Metzger
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Anne B Krug
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Annalisa Marsico
- Institute for Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stefanie Kaiser
- Department of Chemistry, Ludwig-Maximilians-Universität in Munich, Munich, Germany.,Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt am Main, Germany
| | - Stefan Canzar
- Gene Center, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Stefan Feske
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Silvia Monticelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | | | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany. .,Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany.
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28
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Wang Z, Lei X. A web server for identifying circRNA-RBP variable-length binding sites based on stacked generalization ensemble deep learning network. Methods 2022; 205:179-190. [PMID: 35810958 DOI: 10.1016/j.ymeth.2022.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022] Open
Abstract
Circular RNA (circRNA) can exert biological functions by interacting with RNA-binding protein (RBP), and some deep learning-based methods have been developed to predict RBP binding sites on circRNA. However, most of these methods identify circRNA-RBP binding sites are only based on single data resource and cannot provide exact binding sites, only providing the probability value of a sequence fragment. To solve these problems, we propose a binding sites localization algorithm that fuses binding sites from multiple databases, and further design a stacked generalization ensemble deep learning model named CirRBP to identify RBP binding sites on circRNA. The CirRBP is trained by combining the binding sites from multiple databases and makes predictions by weighted aggregating the predictions of each sub-model. The results show that the CirRBP outperforms any sub-model and existing online prediction model. For better access to our research results, we develop an open-source web application called CRWS (CircRNA-RBP Web Server). Its back-end learning model of the CRWS is a stacked generalization ensemble learning model CirRBP based on different deep learning frameworks. Given a full-length circRNA or fragment sequence and a target RBP, the CRWS can analyze and provide the exact potential binding sites of the target RBP on the given sequence through the binding sites localization algorithm, and visualize it. In addition, the CRWS can discover the most widely distributed motif in each RBP dataset. Up to now, CRWS is the first significant online tool that uses multi-source data to train models and predict exact binding sites. CRWS is now publicly and freely available without login requirement at: http://www.bioinformatics.team.
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Affiliation(s)
- Zhengfeng Wang
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China; College of Information Science and Engineering, Guilin University of Technology, Guilin 541004, China; Guangxi Key Laboratory of Embedded Technology and Intelligent System, Guilin University of Technology, Guilin 541004, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China.
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29
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Li L, Krasnykov K, Homolka D, Gos P, Mendel M, Fish RJ, Pandey RR, Pillai RS. The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m 6A recognition. Mol Cell 2022; 82:1678-1690.e12. [PMID: 35305312 DOI: 10.1016/j.molcel.2022.02.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/11/2022]
Abstract
The functional consequence of N6-methyladenosine (m6A) RNA modification is mediated by "reader" proteins of the YTH family. YTH domain-containing 2 (YTHDC2) is essential for mammalian fertility, but its molecular function is poorly understood. Here, we identify U-rich motifs as binding sites of YTHDC2 on 3' UTRs of mouse testicular RNA targets. Although its YTH domain is an m6A-binder in vitro, the YTH point mutant mice are fertile. Significantly, the loss of its 3'→5' RNA helicase activity causes mouse infertility, with the catalytic-dead mutation being dominant negative. Biochemical studies reveal that the weak helicase activity of YTHDC2 is enhanced by its interaction with the 5'→3' exoribonuclease XRN1. Single-cell transcriptomics indicate that Ythdc2 mutant mitotic germ cells transition into meiosis but accumulate a transcriptome with mixed mitotic/meiotic identity that fail to progress further into meiosis. Finally, our demonstration that ythdc2 mutant zebrafish are infertile highlights its conserved role in animal germ cell development.
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Affiliation(s)
- Lingyun Li
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Kyrylo Krasnykov
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - David Homolka
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Pascal Gos
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Mateusz Mendel
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Richard J Fish
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - Radha Raman Pandey
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
| | - Ramesh S Pillai
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
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30
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Jiang Y, Fu X, Zhang Y, Wang SF, Zhu H, Wang WK, Zhang L, Wu P, Wong CCL, Li J, Ma J, Guan JS, Huang Y, Hui J. Rett syndrome linked to defects in forming the MeCP2/Rbfox/LASR complex in mouse models. Nat Commun 2021; 12:5767. [PMID: 34599184 PMCID: PMC8486766 DOI: 10.1038/s41467-021-26084-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/13/2021] [Indexed: 01/01/2023] Open
Abstract
Rett syndrome (RTT) is a severe neurological disorder and a leading cause of intellectual disability in young females. RTT is mainly caused by mutations found in the X-linked gene encoding methyl-CpG binding protein 2 (MeCP2). Despite extensive studies, the molecular mechanism underlying RTT pathogenesis is still poorly understood. Here, we report MeCP2 as a key subunit of a higher-order multiunit protein complex Rbfox/LASR. Defective MeCP2 in RTT mouse models disrupts the assembly of the MeCP2/Rbfox/LASR complex, leading to reduced binding of Rbfox proteins to target pre-mRNAs and aberrant splicing of Nrxns and Nlgn1 critical for synaptic plasticity. We further show that MeCP2 disease mutants display defective condensate properties and fail to promote phase-separated condensates with Rbfox proteins in vitro and in cultured cells. These data link an impaired function of MeCP2 with disease mutation in splicing control to its defective properties in mediating the higher-order assembly of the MeCP2/Rbfox/LASR complex. MeCP2 mutations can cause Rett syndrome, a severe childhood neurological disorder. Here the authors show that MeCP2 mediates the higher-order assembly of a large splicing complex Rbfox/LASR, which is disrupted in the mouse models of Rett syndrome.
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Affiliation(s)
- Yan Jiang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, 201602, Shanghai, China
| | - Yuhan Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China.,Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, 200092, Shanghai, China
| | - Shen-Fei Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Hong Zhu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Wei-Kang Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Lin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Ping Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210, Shanghai, China
| | - Catherine C L Wong
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210, Shanghai, China.,Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, School of Basic Medical Sciences, Peking University, 100191, Beijing, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Ji-Song Guan
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Ying Huang
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, 200092, Shanghai, China.
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.
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31
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Körtel N, Rücklé C, Zhou Y, Busch A, Hoch-Kraft P, Sutandy FXR, Haase J, Pradhan M, Musheev M, Ostareck D, Ostareck-Lederer A, Dieterich C, Hüttelmaier S, Niehrs C, Rausch O, Dominissini D, König J, Zarnack K. Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning. Nucleic Acids Res 2021; 49:e92. [PMID: 34157120 PMCID: PMC8450095 DOI: 10.1093/nar/gkab485] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of RNA processing. miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is an antibody-based approach to map m6A sites with single-nucleotide resolution. However, due to broad antibody reactivity, reliable identification of m6A sites from miCLIP data remains challenging. Here, we present miCLIP2 in combination with machine learning to significantly improve m6A detection. The optimized miCLIP2 results in high-complexity libraries from less input material. Importantly, we established a robust computational pipeline to tackle the inherent issue of false positives in antibody-based m6A detection. The analyses were calibrated with Mettl3 knockout cells to learn the characteristics of m6A deposition, including m6A sites outside of DRACH motifs. To make our results universally applicable, we trained a machine learning model, m6Aboost, based on the experimental and RNA sequence features. Importantly, m6Aboost allows prediction of genuine m6A sites in miCLIP2 data without filtering for DRACH motifs or the need for Mettl3 depletion. Using m6Aboost, we identify thousands of high-confidence m6A sites in different murine and human cell lines, which provide a rich resource for future analysis. Collectively, our combined experimental and computational methodology greatly improves m6A identification.
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Affiliation(s)
- Nadine Körtel
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - You Zhou
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - F X Reymond Sutandy
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
- Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt 60590, Germany
| | - Jacob Haase
- Institute of Molecular Medicine, Sect. Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Halle 06120, Germany
| | - Mihika Pradhan
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - Dirk Ostareck
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen 52074, Germany
| | - Antje Ostareck-Lederer
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen 52074, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK) - Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Sect. Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Halle 06120, Germany
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Dan Dominissini
- Cancer Research Center and Wohl Institute for Translational Medicine, Chaim Sheba Medical Center, Tel HaShomer, and Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt 60438, Germany
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32
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Wilkins OG, Capitanchik C, Luscombe NM, Ule J. Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer. Wellcome Open Res 2021; 6:141. [PMID: 34286104 PMCID: PMC8287537 DOI: 10.12688/wellcomeopenres.16791.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2021] [Indexed: 01/23/2023] Open
Abstract
Background: The first step of virtually all next generation sequencing analysis involves the splitting of the raw sequencing data into separate files using sample-specific barcodes, a process known as "demultiplexing". However, we found that existing software for this purpose was either too inflexible or too computationally intensive for fast, streamlined processing of raw, single end fastq files containing combinatorial barcodes. Results: Here, we introduce a fast and uniquely flexible demultiplexer, named Ultraplex, which splits a raw FASTQ file containing barcodes either at a single end or at both 5' and 3' ends of reads, trims the sequencing adaptors and low-quality bases, and moves unique molecular identifiers (UMIs) into the read header, allowing subsequent removal of PCR duplicates. Ultraplex is able to perform such single or combinatorial demultiplexing on both single- and paired-end sequencing data, and can process an entire Illumina HiSeq lane, consisting of nearly 500 million reads, in less than 20 minutes. Conclusions: Ultraplex greatly reduces computational burden and pipeline complexity for the demultiplexing of complex sequencing libraries, such as those produced by various CLIP and ribosome profiling protocols, and is also very user friendly, enabling streamlined, robust data processing. Ultraplex is available on PyPi and Conda and via Github.
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Affiliation(s)
- Oscar G Wilkins
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | | | - Nicholas M. Luscombe
- The Francis Crick Institute, London, UK
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
| | - Jernej Ule
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
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33
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Alvelos MI, Brüggemann M, Sutandy FXR, Juan-Mateu J, Colli ML, Busch A, Lopes M, Castela Â, Aartsma-Rus A, König J, Zarnack K, Eizirik DL. The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells. Life Sci Alliance 2021; 4:e202000825. [PMID: 33376132 PMCID: PMC7772782 DOI: 10.26508/lsa.202000825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022] Open
Abstract
In pancreatic β-cells, the expression of the splicing factor SRSF6 is regulated by GLIS3, a transcription factor encoded by a diabetes susceptibility gene. SRSF6 down-regulation promotes β-cell demise through splicing dysregulation of central genes for β-cells function and survival, but how RNAs are targeted by SRSF6 remains poorly understood. Here, we define the SRSF6 binding landscape in the human pancreatic β-cell line EndoC-βH1 by integrating individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) under basal conditions with RNA sequencing after SRSF6 knockdown. We detect thousands of SRSF6 bindings sites in coding sequences. Motif analyses suggest that SRSF6 specifically recognizes a purine-rich consensus motif consisting of GAA triplets and that the number of contiguous GAA triplets correlates with increasing binding site strength. The SRSF6 positioning determines the splicing fate. In line with its role in β-cell function, we identify SRSF6 binding sites on regulated exons in several diabetes susceptibility genes. In a proof-of-principle, the splicing of the susceptibility gene LMO7 is modulated by antisense oligonucleotides. Our present study unveils the splicing regulatory landscape of SRSF6 in immortalized human pancreatic β-cells.
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Affiliation(s)
- Maria Inês Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mirko Brüggemann
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Jonàs Juan-Mateu
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maikel Luis Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Anke Busch
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Miguel Lopes
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ângela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Julian König
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Kathi Zarnack
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Décio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
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Buddika K, Xu J, Ariyapala IS, Sokol NS. I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells. Development 2021; 148:dev196568. [PMID: 33246929 PMCID: PMC7803463 DOI: 10.1242/dev.196568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/19/2021] [Indexed: 12/13/2022]
Abstract
The adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. Here, we describe a new proximity-based profiling method that relies upon a GAL4 driver, termed intestinal-kickout-GAL4 (I-KCKT-GAL4), that is exclusively expressed in intestinal progenitor cells. This method uses UV crosslinked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven by I-KCKT-GAL4 When applied to the general mRNA-binder, poly(A)-binding protein, the RNA profile obtained by this method identifies 98.8% of transcripts found after progenitor cell sorting, and has low background noise despite being derived from whole animal lysate. We also mapped the targets of the more selective RNA binder, Fragile X mental retardation protein (FMRP), using enhanced crosslinking and immunoprecipitation (eCLIP), and report for the first time its binding motif in Drosophila cells. This method will therefore enable the RNA profiling of wild-type and mutant intestinal progenitor cells from intact flies exposed to normal and altered environments, as well as the identification of RNA-protein interactions crucial for stem cell function.
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Affiliation(s)
- Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jingjing Xu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Nicholas S Sokol
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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