1
|
Corrales M, Cocanougher BT, Kohn AB, Wittenbach JD, Long XS, Lemire A, Cardona A, Singer RH, Moroz LL, Zlatic M. A single-cell transcriptomic atlas of complete insect nervous systems across multiple life stages. Neural Dev 2022; 17:8. [PMID: 36002881 PMCID: PMC9404646 DOI: 10.1186/s13064-022-00164-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/10/2022] [Indexed: 12/15/2022] Open
Abstract
Molecular profiles of neurons influence neural development and function but bridging the gap between genes, circuits, and behavior has been very difficult. Here we used single cell RNAseq to generate a complete gene expression atlas of the Drosophila larval central nervous system composed of 131,077 single cells across three developmental stages (1 h, 24 h and 48 h after hatching). We identify 67 distinct cell clusters based on the patterns of gene expression. These include 31 functional mature larval neuron clusters, 1 ring gland cluster, 8 glial clusters, 6 neural precursor clusters, and 13 developing immature adult neuron clusters. Some clusters are present across all stages of larval development, while others are stage specific (such as developing adult neurons). We identify genes that are differentially expressed in each cluster, as well as genes that are differentially expressed at distinct stages of larval life. These differentially expressed genes provide promising candidates for regulating the function of specific neuronal and glial types in the larval nervous system, or the specification and differentiation of adult neurons. The cell transcriptome Atlas of the Drosophila larval nervous system is a valuable resource for developmental biology and systems neuroscience and provides a basis for elucidating how genes regulate neural development and function.
Collapse
Affiliation(s)
- Marc Corrales
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA.,Department of Physiology, Development, and Neuroscience, Cambridge University, Cambridge, UK
| | - Benjamin T Cocanougher
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA.,Department of Zoology, Cambridge University, Cambridge, UK
| | - Andrea B Kohn
- Department of Neuroscience and Whitney Laboratory for Marine Biosciences, University of Florida, Gainesville/St. Augustine, FL, 32080, USA
| | - Jason D Wittenbach
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Xi S Long
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Andrew Lemire
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Albert Cardona
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA.,Department of Physiology, Development, and Neuroscience, Cambridge University, Cambridge, UK.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Robert H Singer
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA.,Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Leonid L Moroz
- Department of Neuroscience and Whitney Laboratory for Marine Biosciences, University of Florida, Gainesville/St. Augustine, FL, 32080, USA.
| | - Marta Zlatic
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA. .,Department of Zoology, Cambridge University, Cambridge, UK. .,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK.
| |
Collapse
|
2
|
Son W, Choi KW. The Classic Lobe Eye Phenotype of Drosophila Is Caused by Transposon Insertion-Induced Misexpression of a Zinc-Finger Transcription Factor. Genetics 2020; 216:117-134. [PMID: 32641295 PMCID: PMC7463288 DOI: 10.1534/genetics.120.303486] [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: 08/02/2019] [Accepted: 07/06/2020] [Indexed: 11/18/2022] Open
Abstract
Drosophila Lobe (L) alleles were first discovered ∼100 years ago as spontaneous dominant mutants with characteristic developmental eye defects. However, the molecular basis for L dominant eye phenotypes has not been clearly understood. A previous work reported identification of CG10109/PRAS40 as the L gene, but subsequent analyses suggested that PRAS40 may not be related to L Here, we revisited the L gene to clarify this discrepancy and understand the basis for the dominance of L mutations. Genetic analysis localized the L gene to Oaz, which encodes a homolog of the vertebrate zinc finger protein 423 (Zfp423) family transcriptional regulators. We demonstrate that RNAi knockdown of Oaz almost completely restores all L dominant alleles tested. Lrev6-3 , a revertant allele of the L2 dominant eye phenotype, has an inframe deletion in the Oaz coding sequence. Molecular analysis of L dominant mutants identified allele-specific insertions of natural transposons (roo[ ]L1 , hopper[ ]L5 , and roo[ ]Lr ) or alterations of a preexisting transposon (L2 -specific mutations in roo[ ]Mohr) in the Oaz region. In addition, we generated additional L2 -reversion alleles by CRISPR targeting at Oaz These new loss-of-function Oaz mutations suppress the dominant L eye phenotype. Oaz protein is not expressed in wild-type eye disc but is expressed ectopically in L2/+ mutant eye disc. We induced male recombination between Oaz-GAL4 insertions and the L2 mutation through homologous recombination. By using the L2 -recombined GAL4 reporters, we show that Oaz-GAL4 is expressed ectopically in L2 eye imaginal disc. Taken together, our data suggest that neomorphic L eye phenotypes are likely due to misregulation of Oaz by spontaneous transposon insertions.
Collapse
Affiliation(s)
- Wonseok Son
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Kwang-Wook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| |
Collapse
|
3
|
Lecheta MC, Awde DN, O’Leary TS, Unfried LN, Jacobs NA, Whitlock MH, McCabe E, Powers B, Bora K, Waters JS, Axen HJ, Frietze S, Lockwood BL, Teets NM, Cahan SH. Integrating GWAS and Transcriptomics to Identify the Molecular Underpinnings of Thermal Stress Responses in Drosophila melanogaster. Front Genet 2020; 11:658. [PMID: 32655626 PMCID: PMC7324644 DOI: 10.3389/fgene.2020.00658] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022] Open
Abstract
Thermal tolerance of an organism depends on both the ability to dynamically adjust to a thermal stress and preparatory developmental processes that enhance thermal resistance. However, the extent to which standing genetic variation in thermal tolerance alleles influence dynamic stress responses vs. preparatory processes is unknown. Here, using the model species Drosophila melanogaster, we used a combination of Genome Wide Association mapping (GWAS) and transcriptomic profiling to characterize whether genes associated with thermal tolerance are primarily involved in dynamic stress responses or preparatory processes that influence physiological condition at the time of thermal stress. To test our hypotheses, we measured the critical thermal minimum (CTmin) and critical thermal maximum (CTmax) of 100 lines of the Drosophila Genetic Reference Panel (DGRP) and used GWAS to identify loci that explain variation in thermal limits. We observed greater variation in lower thermal limits, with CTmin ranging from 1.81 to 8.60°C, while CTmax ranged from 38.74 to 40.64°C. We identified 151 and 99 distinct genes associated with CTmin and CTmax, respectively, and there was strong support that these genes are involved in both dynamic responses to thermal stress and preparatory processes that increase thermal resistance. Many of the genes identified by GWAS were involved in the direct transcriptional response to thermal stress (72/151 for cold; 59/99 for heat), and overall GWAS candidates were more likely to be differentially expressed than other genes. Further, several GWAS candidates were regulatory genes that may participate in the regulation of stress responses, and gene ontologies related to development and morphogenesis were enriched, suggesting many of these genes influence thermal tolerance through effects on development and physiological status. Overall, our results suggest that thermal tolerance alleles can influence both dynamic plastic responses to thermal stress and preparatory processes that improve thermal resistance. These results also have utility for directly comparing GWAS and transcriptomic approaches for identifying candidate genes associated with thermal tolerance.
Collapse
Affiliation(s)
- Melise C. Lecheta
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - David N. Awde
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Thomas S. O’Leary
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Laura N. Unfried
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Nicholas A. Jacobs
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Miles H. Whitlock
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Eleanor McCabe
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Beck Powers
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Katie Bora
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - James S. Waters
- Department of Biology, Providence College, Providence, RI, United States
| | - Heather J. Axen
- Department of Biology and Biomedical Sciences, Salve Regina College, Providence, RI, United States
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Brent L. Lockwood
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Nicholas M. Teets
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Sara H. Cahan
- Department of Biology, University of Vermont, Burlington, VT, United States
| |
Collapse
|
4
|
Coléno-Costes A, Jang SM, de Vanssay A, Rougeot J, Bouceba T, Randsholt NB, Gibert JM, Le Crom S, Mouchel-Vielh E, Bloyer S, Peronnet F. New partners in regulation of gene expression: the enhancer of Trithorax and Polycomb Corto interacts with methylated ribosomal protein l12 via its chromodomain. PLoS Genet 2012; 8:e1003006. [PMID: 23071455 PMCID: PMC3469418 DOI: 10.1371/journal.pgen.1003006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 08/16/2012] [Indexed: 01/24/2023] Open
Abstract
Chromodomains are found in many regulators of chromatin structure, and most of them recognize methylated lysines on histones. Here, we investigate the role of the Drosophila melanogaster protein Corto's chromodomain. The Enhancer of Trithorax and Polycomb Corto is involved in both silencing and activation of gene expression. Over-expression of the Corto chromodomain (CortoCD) in transgenic flies shows that it is a chromatin-targeting module, critical for Corto function. Unexpectedly, mass spectrometry analysis reveals that polypeptides pulled down by CortoCD from nuclear extracts correspond to ribosomal proteins. Furthermore, real-time interaction analyses demonstrate that CortoCD binds with high affinity RPL12 tri-methylated on lysine 3. Corto and RPL12 co-localize with active epigenetic marks on polytene chromosomes, suggesting that both are involved in fine-tuning transcription of genes in open chromatin. RNA-seq based transcriptomes of wing imaginal discs over-expressing either CortoCD or RPL12 reveal that both factors deregulate large sets of common genes, which are enriched in heat-response and ribosomal protein genes, suggesting that they could be implicated in dynamic coordination of ribosome biogenesis. Chromatin immunoprecipitation experiments show that Corto and RPL12 bind hsp70 and are similarly recruited on gene body after heat shock. Hence, Corto and RPL12 could be involved together in regulation of gene transcription. We discuss whether pseudo-ribosomal complexes composed of various ribosomal proteins might participate in regulation of gene expression in connection with chromatin regulators.
Collapse
Affiliation(s)
- Anne Coléno-Costes
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Suk Min Jang
- Institut Pasteur, Département de Biologie du Développement, Unité de Régulation Epigénétique, Paris, France
- Centre National de la Recherche Scientifique, URA2578, Paris, France
- INSERM Avenir, Paris, France
| | - Augustin de Vanssay
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Répression Épigénétique et Éléments Transposables, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Répression Épigénétique et Éléments Transposables, Paris, France
| | - Julien Rougeot
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Tahar Bouceba
- Plateforme d'Ingénierie des Protéines, Service d'Interaction des Biomolécules, IFR83, Université Pierre et Marie Curie-Paris 6, UMR7622, Paris, France
| | - Neel B. Randsholt
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Jean-Michel Gibert
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Stéphane Le Crom
- École Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Plateforme Génomique, Paris, France
- INSERM, U1024, Paris, France
- CNRS, UMR 8197, Paris, France
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Analyse des Données à Haut Débit en Génomique Fonctionnelle, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Analyse des Données à Haut Débit en Génomique Fonctionnelle, Paris, France
| | - Emmanuèle Mouchel-Vielh
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Sébastien Bloyer
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Frédérique Peronnet
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| |
Collapse
|
5
|
Seetharam A, Bai Y, Stuart GW. A survey of well conserved families of C2H2 zinc-finger genes in Daphnia. BMC Genomics 2010; 11:276. [PMID: 20433734 PMCID: PMC2889900 DOI: 10.1186/1471-2164-11-276] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 04/30/2010] [Indexed: 12/15/2022] Open
Abstract
Background A recent comparative genomic analysis tentatively identified roughly 40 orthologous groups of C2H2 Zinc-finger proteins that are well conserved in "bilaterians" (i.e. worms, flies, and humans). Here we extend that analysis to include a second arthropod genome from the crustacean, Daphnia pulex. Results Most of the 40 orthologous groups of C2H2 zinc-finger proteins are represented by just one or two proteins within each of the previously surveyed species. Likewise, Daphnia were found to possess a similar number of orthologs for all of these small orthology groups. In contrast, the number of Sp/KLF homologs tends to be greater and to vary between species. Like the corresponding mammalian Sp/KLF proteins, most of the Drosophila and Daphnia homologs can be placed into one of three sub-groups: Class I-III. Daphnia were found to have three Class I proteins that roughly correspond to their Drosophila counterparts, dSP1, btd, CG5669, and three Class II proteins that roughly correspond to Luna, CG12029, CG9895. However, Daphnia have four additional KLF-Class II proteins that are most similar to the vertebrate KLF1/2/4 proteins, a subset not found in Drosophila. Two of these four proteins are encoded by genes linked in tandem. Daphnia also have three KLF-Class III members, one more than Drosophila. One of these is a likely Bteb2 homolog, while the other two correspond to Cabot and KLF13, a vertebrate homolog of Cabot. Conclusion Consistent with their likely roles as fundamental determinants of bilaterian form and function, most of the 40 groups of C2H2 zinc-finger proteins are conserved in kind and number in Daphnia. However, the KLF family includes several additional genes that are most similar to genes present in vertebrates but missing in Drosophila.
Collapse
Affiliation(s)
- Arun Seetharam
- Department of Biology, Indiana State University, Terre Haute, IN 47809, USA
| | | | | |
Collapse
|
6
|
Blitz IL, Cho KWY. Finding partners: how BMPs select their targets. Dev Dyn 2009; 238:1321-31. [PMID: 19441058 DOI: 10.1002/dvdy.21984] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The bone morphogenetic protein (BMP) signaling pathway is a conserved and evolutionarily ancient regulatory module affecting a large variety of cellular behaviors. The evolutionary flexibility in using BMP responses presumably arose by co-option of a canonical BMP signaling cascade to regulate the transcription of diverse batteries of target genes. This begs the question of how seemingly interchangeable BMP signaling components elicit widely different outputs in different cell types, an important issue in the context of understanding how BMP signaling integrates with gene regulatory networks to control development. Because a molecular understanding of how BMP signaling activates different batteries of target genes is an essential prerequisite to comprehending the roles of BMPs in regulating cellular responses, here we review the current knowledge of how BMP-regulated target genes are selected by the signal transduction machinery. We highlight recent studies suggesting the evolutionary conservation of BMP target gene regulation signaling by Schnurri family zinc finger proteins. Developmental Dynamics 238:1321-1331, 2009. (c) 2009 Wiley-Liss, Inc.
Collapse
Affiliation(s)
- Ira L Blitz
- Department of Developmental and Cell Biology and the Developmental Biology Center, University of California, Irvine, California, USA.
| | | |
Collapse
|