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Loedige I, Baranovskii A, Mendonsa S, Dantsuji S, Popitsch N, Breimann L, Zerna N, Cherepanov V, Milek M, Ameres S, Chekulaeva M. mRNA stability and m 6A are major determinants of subcellular mRNA localization in neurons. Mol Cell 2023; 83:2709-2725.e10. [PMID: 37451262 PMCID: PMC10529935 DOI: 10.1016/j.molcel.2023.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
For cells to perform their biological functions, they need to adopt specific shapes and form functionally distinct subcellular compartments. This is achieved in part via an asymmetric distribution of mRNAs within cells. Currently, the main model of mRNA localization involves specific sequences called "zipcodes" that direct mRNAs to their proper locations. However, while thousands of mRNAs localize within cells, only a few zipcodes have been identified, suggesting that additional mechanisms contribute to localization. Here, we assess the role of mRNA stability in localization by combining the isolation of the soma and neurites of mouse primary cortical and mESC-derived neurons, SLAM-seq, m6A-RIP-seq, the perturbation of mRNA destabilization mechanisms, and the analysis of multiple mRNA localization datasets. We show that depletion of mRNA destabilization elements, such as m6A, AU-rich elements, and suboptimal codons, functions as a mechanism that mediates the localization of mRNAs associated with housekeeping functions to neurites in several types of neurons.
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Affiliation(s)
- Inga Loedige
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Artem Baranovskii
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Samantha Mendonsa
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Sayaka Dantsuji
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Niko Popitsch
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Laura Breimann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nadja Zerna
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Vsevolod Cherepanov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Miha Milek
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Stefan Ameres
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany.
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Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J. Structure and dynamics of the quaternary hunchback mRNA translation repression complex. Nucleic Acids Res 2021; 49:8866-8885. [PMID: 34329466 PMCID: PMC8421216 DOI: 10.1093/nar/gkab635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 01/02/2023] Open
Abstract
A key regulatory process during Drosophila development is the localized suppression of the hunchback mRNA translation at the posterior, which gives rise to a hunchback gradient governing the formation of the anterior-posterior body axis. This suppression is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for proper Drosophila development. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins during RNA suppression remains a long-standing open question. Here, we characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos with hunchback mRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternary hunchback mRNA suppression complex comprising the RNA binding domains is flexible with unoccupied nucleotides functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, the presence of the Pum-HD/Nanos-ZnF complex has no effect on the equilibrium RNA binding affinity of the Brat RNA binding domain. This is in accordance with previous studies, which showed that Brat can suppress mRNA independently and is distributed uniformly throughout the embryo.
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Affiliation(s)
- Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Sophie L Winter
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jaelle Foot
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Kathryn Perez
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Miloš T Ivanović
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Inga Loedige
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Frank Gabel
- Institut Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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Reichardt I, Bonnay F, Steinmann V, Loedige I, Burkard TR, Meister G, Knoblich JA. The tumor suppressor Brat controls neuronal stem cell lineages by inhibiting Deadpan and Zelda. EMBO Rep 2017; 19:102-117. [PMID: 29191977 DOI: 10.15252/embr.201744188] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 10/31/2017] [Accepted: 11/10/2017] [Indexed: 11/09/2022] Open
Abstract
The TRIM-NHL protein Brain tumor (Brat) acts as a tumor suppressor in the Drosophila brain, but how it suppresses tumor formation is not completely understood. Here, we combine temperature-controlled brat RNAi with transcriptome analysis to identify the immediate Brat targets in Drosophila neuroblasts. Besides the known target Deadpan (Dpn), our experiments identify the transcription factor Zelda (Zld) as a critical target of Brat. Our data show that Zld is expressed in neuroblasts and required to allow re-expression of Dpn in transit-amplifying intermediate neural progenitors. Upon neuroblast division, Brat is enriched in one daughter cell where its NHL domain directly binds to specific motifs in the 3'UTR of dpn and zld mRNA to mediate their degradation. In brat mutants, both Dpn and Zld continue to be expressed, but inhibition of either transcription factor prevents tumorigenesis. Our genetic and biochemical data indicate that Dpn inhibition requires higher Brat levels than Zld inhibition and suggest a model where stepwise post-transcriptional inhibition of distinct factors ensures sequential generation of fates in a stem cell lineage.
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Affiliation(s)
- Ilka Reichardt
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - François Bonnay
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Victoria Steinmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Inga Loedige
- Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Gunter Meister
- Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
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Abstract
TRIM-NHL proteins are conserved regulators of development and differentiation but their molecular function has remained largely elusive. Here, we report an as yet unrecognized activity for the mammalian TRIM-NHL protein TRIM71 as a repressor of mRNAs. We show that TRIM71 is associated with mRNAs and that it promotes translational repression and mRNA decay. We have identified Rbl1 and Rbl2, two transcription factors whose down-regulation is important for stem cell function, as TRIM71 targets in mouse embryonic stem cells. Furthermore, one of the defining features of TRIM-NHL proteins, the NHL domain, is necessary and sufficient to target TRIM71 to RNA, while the RING domain that confers ubiquitin ligase activity is dispensable for repression. Our results reveal strong similarities between TRIM71 and Drosophila BRAT, the best-studied TRIM-NHL protein and a well-documented translational repressor, suggesting that BRAT and TRIM71 are part of a family of mRNA repressors regulating proliferation and differentiation.
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Affiliation(s)
- Inga Loedige
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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Abstract
MicroRNAs (miRNAs) are a large family of post-transcriptional regulators of gene expression that are approximately 21 nucleotides in length and control many developmental and cellular processes in eukaryotic organisms. Research during the past decade has identified major factors participating in miRNA biogenesis and has established basic principles of miRNA function. More recently, it has become apparent that miRNA regulators themselves are subject to sophisticated control. Many reports over the past few years have reported the regulation of miRNA metabolism and function by a range of mechanisms involving numerous protein-protein and protein-RNA interactions. Such regulation has an important role in the context-specific functions of miRNAs.
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Affiliation(s)
- Jacek Krol
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
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