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Zhang T, Xue Y, Su S, Altouma V, Ho K, Martindale JL, Lee SK, Shen W, Park A, Zhang Y, De S, Gorospe M, Wang W. RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames. Nucleic Acids Res 2024; 52:885-905. [PMID: 38000373 PMCID: PMC10810208 DOI: 10.1093/nar/gkad1122] [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: 06/20/2023] [Revised: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
RNA-binding proteins (RBPs) with intrinsically disordered regions (IDRs) are linked to multiple human disorders, but their mechanisms of action remain unclear. Here, we report that one such protein, Nocte, is essential for Drosophila eye development by regulating a critical gene expression cascade at translational level. Knockout of nocte in flies leads to lethality, and its eye-specific depletion impairs eye size and morphology. Nocte preferentially enhances translation of mRNAs with long upstream open reading frames (uORFs). One of the key Nocte targets, glass mRNA, encodes a transcription factor critical for differentiation of photoreceptor neurons and accessory cells, and re-expression of Glass largely rescued the eye defects caused by Nocte depletion. Mechanistically, Nocte counteracts long uORF-mediated translational suppression by promoting translation reinitiation downstream of the uORF. Nocte interacts with translation factors eIF3 and Rack1 through its BAT2 domain, and a Nocte mutant lacking this domain fails to promote translation of glass mRNA. Notably, de novo mutations of human orthologs of Nocte have been detected in schizophrenia patients. Our data suggest that Nocte family of proteins can promote translation reinitiation to overcome long uORFs-mediated translational suppression, and disruption of this function can lead to developmental defects and neurological disorders.
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Affiliation(s)
- Tianyi Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Valerie Altouma
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Katherine Ho
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung-Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Aaron Park
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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Jean‐Guillaume CB, Kumar JP. Development of the ocellar visual system in Drosophila melanogaster. FEBS J 2022; 289:7411-7427. [PMID: 35490409 PMCID: PMC9805374 DOI: 10.1111/febs.16468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 01/14/2023]
Abstract
The adult visual system of the fruit fly, Drosophila melanogaster, contains seven eyes-two compound eyes, a pair of Hofbauer-Buchner eyelets, and three ocelli. Each of these eye types has a specialized and essential role to play in visual and/or circadian behavior. As such, understanding how each is specified, patterned, and wired is of primary importance to vision biologists. Since the fruit fly is amenable to manipulation by an enormous array of genetic and molecular tools, its development is one of the best and most studied model systems. After more than a century of experimental investigations, our understanding of how each eye type is specified and patterned is grossly uneven. The compound eye has been the subject of several thousand studies; thus, our knowledge of its development is the deepest. By comparison, very little is known about the specification and patterning of the other two visual systems. In this Viewpoint article, we will describe what is known about the function and development of the Drosophila ocelli.
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Bravo González‐Blas C, Quan X, Duran‐Romaña R, Taskiran II, Koldere D, Davie K, Christiaens V, Makhzami S, Hulselmans G, de Waegeneer M, Mauduit D, Poovathingal S, Aibar S, Aerts S. Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics. Mol Syst Biol 2020; 16:e9438. [PMID: 32431014 PMCID: PMC7237818 DOI: 10.15252/msb.20209438] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 01/02/2023] Open
Abstract
Single-cell technologies allow measuring chromatin accessibility and gene expression in each cell, but jointly utilizing both layers to map bona fide gene regulatory networks and enhancers remains challenging. Here, we generate independent single-cell RNA-seq and single-cell ATAC-seq atlases of the Drosophila eye-antennal disc and spatially integrate the data into a virtual latent space that mimics the organization of the 2D tissue using ScoMAP (Single-Cell Omics Mapping into spatial Axes using Pseudotime ordering). To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~ 85% of enhancers in which chromatin accessibility and enhancer activity are coupled. Next, we infer enhancer-to-gene relationships in the virtual space, finding that genes are mostly regulated by multiple, often redundant, enhancers. Exploiting cell type-specific enhancers, we deconvolute cell type-specific effects of bulk-derived chromatin accessibility QTLs. Finally, we discover that Prospero drives neuronal differentiation through the binding of a GGG motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue.
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Affiliation(s)
| | - Xiao‐Jiang Quan
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | | | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Duygu Koldere
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | | | - Valerie Christiaens
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Samira Makhzami
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Maxime de Waegeneer
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - David Mauduit
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | | | - Sara Aibar
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Stein Aerts
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
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