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Ichinose T, Kondo S, Kanno M, Shichino Y, Mito M, Iwasaki S, Tanimoto H. Translational regulation enhances distinction of cell types in the nervous system. eLife 2024; 12:RP90713. [PMID: 39010741 PMCID: PMC11251722 DOI: 10.7554/elife.90713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024] Open
Abstract
Multicellular organisms are composed of specialized cell types with distinct proteomes. While recent advances in single-cell transcriptome analyses have revealed differential expression of mRNAs, cellular diversity in translational profiles remains underinvestigated. By performing RNA-seq and Ribo-seq in genetically defined cells in the Drosophila brain, we here revealed substantial post-transcriptional regulations that augment the cell-type distinctions at the level of protein expression. Specifically, we found that translational efficiency of proteins fundamental to neuronal functions, such as ion channels and neurotransmitter receptors, was maintained low in glia, leading to their preferential translation in neurons. Notably, distribution of ribosome footprints on these mRNAs exhibited a remarkable bias toward the 5' leaders in glia. Using transgenic reporter strains, we provide evidence that the small upstream open-reading frames in the 5' leader confer selective translational suppression in glia. Overall, these findings underscore the profound impact of translational regulation in shaping the proteomics for cell-type distinction and provide new insights into the molecular mechanisms driving cell-type diversity.
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Grants
- 21K06369 Ministry of Education, Culture, Sports, Science and Technology
- 21H05713 Ministry of Education, Culture, Sports, Science and Technology
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology
- JP21K15023 Ministry of Education, Culture, Sports, Science and Technology
- 22H05481 Ministry of Education, Culture, Sports, Science and Technology
- 22KK0106 Ministry of Education, Culture, Sports, Science and Technology
- 20H00519 Ministry of Education, Culture, Sports, Science and Technology
- JP20gm1410001 Japan Agency for Medical Research and Development
- Biology of Intracellular Environments RIKEN
- Special Postdoctoral Researchers RIKEN
- Incentive Research Projects RIKEN
- Takeda Science Foundation
- Tohoku University Research Program "Frontier Research in Duo"
- The Uehara Memorial Foundation
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Affiliation(s)
- Toshiharu Ichinose
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku UniversitySendaiJapan
- Graduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Shu Kondo
- Faculty of Advanced Engineering, Tokyo University of SciencesTokyoJapan
| | - Mai Kanno
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku UniversitySendaiJapan
- Graduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, WakoSaitamaJapan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, WakoSaitamaJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, WakoSaitamaJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoKashiwaJapan
| | - Hiromu Tanimoto
- Graduate School of Life Sciences, Tohoku UniversitySendaiJapan
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Salinas-Saavedra M. SABER-FISH in Hydractinia. Methods Mol Biol 2024; 2784:77-85. [PMID: 38502479 DOI: 10.1007/978-1-0716-3766-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
In situ hybridization allows the detection of nucleic acid sequences in fixed cells and tissues. The gelatinous nature of cnidarians and Hydractinia demands extensive and exhausting protocols to detect RNA transcripts with traditional methods (e.g., colorimetric in situ hybridization). Signal amplification by exchange reaction (SABER) fluorescence in situ hybridization (FISH) enables simplifying and multiplex imaging of RNA targets in a rapid and cost-effective manner. In one enzymatic reaction, SABER-FISH uses a strand-displacing polymerase and catalytic DNA hairpin to generate FISH probes with adjustable signal amplification, allowing highly sensitive detection of nucleic acids and reducing the number of required probes. Here I describe the methodology to detect transcripts within the cells of Hydractinia by SABER-FISH in whole-mount samples.
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Ford BL, Wei T, Liu H, Scull CE, Najmi SM, Pitts S, Fan W, Schneider DA, Laiho M. Expression of RNA polymerase I catalytic core is influenced by RPA12. PLoS One 2023; 18:e0285660. [PMID: 37167337 PMCID: PMC10174586 DOI: 10.1371/journal.pone.0285660] [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: 12/30/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
RNA Polymerase I (Pol I) has recently been recognized as a cancer therapeutic target. The activity of this enzyme is essential for ribosome biogenesis and is universally activated in cancers. The enzymatic activity of this multi-subunit complex resides in its catalytic core composed of RPA194, RPA135, and RPA12, a subunit with functions in RNA cleavage, transcription initiation and elongation. Here we explore whether RPA12 influences the regulation of RPA194 in human cancer cells. We use a specific small-molecule Pol I inhibitor BMH-21 that inhibits transcription initiation, elongation and ultimately activates the degradation of Pol I catalytic subunit RPA194. We show that silencing RPA12 causes alterations in the expression and localization of Pol I subunits RPA194 and RPA135. Furthermore, we find that despite these alterations not only does the Pol I core complex between RPA194 and RPA135 remain intact upon RPA12 knockdown, but the transcription of Pol I and its engagement with chromatin remain unaffected. The BMH-21-mediated degradation of RPA194 was independent of RPA12 suggesting that RPA12 affects the basal expression, but not the drug-inducible turnover of RPA194. These studies add to knowledge defining regulatory factors for the expression of this Pol I catalytic subunit.
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Affiliation(s)
- Brittany L. Ford
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Department of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ting Wei
- Department of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Hester Liu
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Catherine E. Scull
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Saman M. Najmi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Stephanie Pitts
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Wenjun Fan
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Marikki Laiho
- Department of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
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Sanchez-Arias JC, Carrier M, Frederiksen SD, Shevtsova O, McKee C, van der Slagt E, Gonçalves de Andrade E, Nguyen HL, Young PA, Tremblay MÈ, Swayne LA. A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy. Front Neuroanat 2021; 15:722443. [PMID: 34949993 PMCID: PMC8691181 DOI: 10.3389/fnana.2021.722443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023] Open
Abstract
The ever-expanding availability and evolution of microscopy tools has enabled ground-breaking discoveries in neurobiology, particularly with respect to the analysis of cell-type density and distribution. Widespread implementation of many of the elegant image processing tools available continues to be impeded by the lack of complete workflows that span from experimental design, labeling techniques, and analysis workflows, to statistical methods and data presentation. Additionally, it is important to consider open science principles (e.g., open-source software and tools, user-friendliness, simplicity, and accessibility). In the present methodological article, we provide a compendium of resources and a FIJI-ImageJ-based workflow aimed at improving the quantification of cell density in mouse brain samples using semi-automated open-science-based methods. Our proposed framework spans from principles and best practices of experimental design, histological and immunofluorescence staining, and microscopy imaging to recommendations for statistical analysis and data presentation. To validate our approach, we quantified neuronal density in the mouse barrel cortex using antibodies against pan-neuronal and interneuron markers. This framework is intended to be simple and yet flexible, such that it can be adapted to suit distinct project needs. The guidelines, tips, and proposed methodology outlined here, will support researchers of wide-ranging experience levels and areas of focus in neuroscience research.
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Affiliation(s)
| | - Micaël Carrier
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada
| | | | - Olga Shevtsova
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Chloe McKee
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Emma van der Slagt
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | | | - Hai Lam Nguyen
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Penelope A Young
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada.,Department of Molecular Medicine, Université de Laval, Québec City, QC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Leigh Anne Swayne
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.,Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, QC, Canada
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