1
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Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material. Front Zool 2022; 19:27. [DOI: 10.1186/s12983-022-00472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Recent technological advances opened the opportunity to simultaneously study gene expression for thousands of individual cells on a genome-wide scale. The experimental accessibility of such single-cell RNA sequencing (scRNAseq) approaches allowed gaining insights into the cell type composition of heterogeneous tissue samples of animal model systems and emerging models alike. A major prerequisite for a successful application of the method is the dissociation of complex tissues into individual cells, which often requires large amounts of input material and harsh mechanical, chemical and temperature conditions. However, the availability of tissue material may be limited for small animals, specific organs, certain developmental stages or if samples need to be acquired from collected specimens. Therefore, we evaluated different dissociation protocols to obtain single cells from small tissue samples of Drosophila melanogaster eye-antennal imaginal discs.
Results
We show that a combination of mechanical and chemical dissociation resulted in sufficient high-quality cells. As an alternative, we tested protocols for the isolation of single nuclei, which turned out to be highly efficient for fresh and frozen tissue samples. Eventually, we performed scRNAseq and single-nuclei RNA sequencing (snRNAseq) to show that the best protocols for both methods successfully identified relevant cell types. At the same time, snRNAseq resulted in less artificial gene expression that is caused by rather harsh dissociation conditions needed to obtain single cells for scRNAseq. A direct comparison of scRNAseq and snRNAseq data revealed that both datasets share biologically relevant genes among the most variable genes, and we showed differences in the relative contribution of the two approaches to identified cell types.
Conclusion
We present two dissociation protocols that allow isolating single cells and single nuclei, respectively, from low input material. Both protocols resulted in extraction of high-quality RNA for subsequent scRNAseq or snRNAseq applications. If tissue availability is limited, we recommend the snRNAseq procedure of fresh or frozen tissue samples as it is perfectly suited to obtain thorough insights into cellular diversity of complex tissue.
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2
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Quiquand M, Rimesso G, Qiao N, Suo S, Zhao C, Slattery M, White KP, Han JJ, Baker NE. New regulators of Drosophila eye development identified from temporal transcriptome changes. Genetics 2021; 217:6117222. [PMID: 33681970 DOI: 10.1093/genetics/iyab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 12/28/2020] [Indexed: 11/12/2022] Open
Abstract
In the last larval instar, uncommitted progenitor cells in the Drosophila eye primordium start to adopt individual retinal cell fates, arrest their growth and proliferation, and initiate terminal differentiation into photoreceptor neurons and other retinal cell types. To explore the regulation of these processes, we have performed mRNA-Seq studies of the larval eye and antennal primordial at multiple developmental stages. A total of 10,893 fly genes were expressed during these stages and could be adaptively clustered into gene groups, some of whose expression increases or decreases in parallel with the cessation of proliferation and onset of differentiation. Using in situ hybridization of a sample of 98 genes to verify spatial and temporal expression patterns, we estimate that 534 genes or more are transcriptionally upregulated during retinal differentiation, and 1367 or more downregulated as progenitor cells differentiate. Each group of co-expressed genes is enriched for regulatory motifs recognized by co-expressed transcription factors, suggesting that they represent coherent transcriptional regulatory programs. Using available mutant strains, we describe novel roles for the transcription factors SoxNeuro (SoxN), H6-like homeobox (Hmx), CG10253, without children (woc), Structure specific recognition protein (Ssrp), and multisex combs (mxc).
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Affiliation(s)
- Manon Quiquand
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gerard Rimesso
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nan Qiao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shengbao Suo
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chunyu Zhao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Matthew Slattery
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Kevin P White
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jackie J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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3
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Zelhof AC, Mahato S, Liang X, Rylee J, Bergh E, Feder LE, Larsen ME, Britt SG, Friedrich M. The brachyceran de novo gene PIP82, a phosphorylation target of aPKC, is essential for proper formation and maintenance of the rhabdomeric photoreceptor apical domain in Drosophila. PLoS Genet 2020; 16:e1008890. [PMID: 32579558 PMCID: PMC7340324 DOI: 10.1371/journal.pgen.1008890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/07/2020] [Accepted: 05/27/2020] [Indexed: 11/18/2022] Open
Abstract
The Drosophila apical photoreceptor membrane is defined by the presence of two distinct morphological regions, the microvilli-based rhabdomere and the stalk membrane. The subdivision of the apical membrane contributes to the geometrical positioning and the stereotypical morphology of the rhabdomeres in compound eyes with open rhabdoms and neural superposition. Here we describe the characterization of the photoreceptor specific protein PIP82. We found that PIP82's subcellular localization demarcates the rhabdomeric portion of the apical membrane. We further demonstrate that PIP82 is a phosphorylation target of aPKC. PIP82 localization is modulated by phosphorylation, and in vivo, the loss of the aPKC/Crumbs complex results in an expansion of the PIP82 localization domain. The absence of PIP82 in photoreceptors leads to misshapped rhabdomeres as a result of misdirected cellular trafficking of rhabdomere proteins. Comparative analyses reveal that PIP82 originated de novo in the lineage leading to brachyceran Diptera, which is also characterized by the transition from fused to open rhabdoms. Taken together, these findings define a novel factor that delineates and maintains a specific apical membrane domain, and offers new insights into the functional organization and evolutionary history of the Drosophila retina.
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Affiliation(s)
- Andrew C. Zelhof
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Simpla Mahato
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Xulong Liang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Jonathan Rylee
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Emma Bergh
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Lauren E. Feder
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Matthew E. Larsen
- Department of Neurology and Ophthalmology, Dell Medical School, University of Texas, Austin, Texas, United States of America
| | - Steven G. Britt
- Department of Neurology and Ophthalmology, Dell Medical School, University of Texas, Austin, Texas, United States of America
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
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4
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Chen YC, Desplan C. Gene regulatory networks during the development of the Drosophila visual system. Curr Top Dev Biol 2020; 139:89-125. [PMID: 32450970 DOI: 10.1016/bs.ctdb.2020.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Drosophila visual system integrates input from 800 ommatidia and extracts different features in stereotypically connected optic ganglia. The development of the Drosophila visual system is controlled by gene regulatory networks that control the number of precursor cells, generate neuronal diversity by integrating spatial and temporal information, coordinate the timing of retinal and optic lobe cell differentiation, and determine distinct synaptic targets of each cell type. In this chapter, we describe the known gene regulatory networks involved in the development of the different parts of the visual system and explore general components in these gene networks. Finally, we discuss the advantages of the fly visual system as a model for gene regulatory network discovery in the era of single-cell transcriptomics.
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Affiliation(s)
- Yen-Chung Chen
- Department of Biology, New York University, New York, NY, United States
| | - Claude Desplan
- Department of Biology, New York University, New York, NY, United States.
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5
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Fritsch C, Bernardo-Garcia FJ, Humberg TH, Mishra AK, Miellet S, Almeida S, Frochaux MV, Deplancke B, Huber A, Sprecher SG. Multilevel regulation of the glass locus during Drosophila eye development. PLoS Genet 2019; 15:e1008269. [PMID: 31299050 PMCID: PMC6655844 DOI: 10.1371/journal.pgen.1008269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/24/2019] [Accepted: 06/23/2019] [Indexed: 12/28/2022] Open
Abstract
Development of eye tissue is initiated by a conserved set of transcription factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to control identity of photoreceptor as well as non-photoreceptor cells. Tight control of spatial and temporal gene expression is a critical feature during development, cell-fate determination as well as maintenance of differentiated tissues. The molecular mechanisms that control expression of glass, however, remain largely unknown. We here identify complex regulatory mechanisms controlling expression of the glass locus. All information to recapitulate glass expression are contained in a compact 5.2 kb cis-acting genomic element by combining different cell-type specific and general enhancers with repressor elements. Moreover, the immature RNA of the locus contains an alternative small open reading frame (smORF) upstream of the actual glass translation start, resulting in a small peptide instead of the three possible Glass protein isoforms. CRISPR/Cas9-based mutagenesis shows that the smORF is not required for the formation of functioning photoreceptors, but is able to attenuate effects of glass misexpression. Furthermore, editing the genome to generate glass loci eliminating either one or two isoforms shows that only one of the three proteins is critical for formation of functioning photoreceptors, while removing the two other isoforms did not cause defects in developmental or photoreceptor function. Our results show that eye development and function is largely unaffected by targeted manipulations of critical features of the glass transcript, suggesting a strong selection pressure to allow the formation of a functioning eye.
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Affiliation(s)
- Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - F. Javier Bernardo-Garcia
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | | | | | - Sara Miellet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Silvia Almeida
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Bart Deplancke
- Laboratory of Systems Biology, IBI, SV, EPFL, Lausanne, Switzerland
| | - Armin Huber
- Institute of Physiology, University of Hohenheim, Hohenheim, Germany
| | - Simon G. Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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6
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Bernardo-Garcia FJ, Syed M, Jékely G, Sprecher SG. Glass confers rhabdomeric photoreceptor identity in Drosophila, but not across all metazoans. EvoDevo 2019; 10:4. [PMID: 30873275 PMCID: PMC6399963 DOI: 10.1186/s13227-019-0117-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/15/2019] [Indexed: 12/14/2022] Open
Abstract
Across metazoans, visual systems employ different types of photoreceptor neurons (PRs) to detect light. These include rhabdomeric PRs, which exist in distantly related phyla and possess an evolutionarily conserved phototransduction cascade. While the development of rhabdomeric PRs has been thoroughly studied in the fruit fly Drosophila melanogaster, we still know very little about how they form in other species. To investigate this question, we tested whether the transcription factor Glass, which is crucial for instructing rhabdomeric PR formation in Drosophila, may play a similar role in other metazoans. Glass homologues exist throughout the animal kingdom, indicating that this protein evolved prior to the metazoan radiation. Interestingly, our work indicates that glass is not expressed in rhabdomeric photoreceptors in the planarian Schmidtea mediterranea nor in the annelid Platynereis dumerilii. Combined with a comparative analysis of the Glass DNA-binding domain, our data suggest that the fate of rhabdomeric PRs is controlled by Glass-dependent and Glass-independent mechanisms in different animal clades.
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Affiliation(s)
- F Javier Bernardo-Garcia
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.,2Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Maryam Syed
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Gáspár Jékely
- 3Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD UK
| | - Simon G Sprecher
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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7
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Davie K, Janssens J, Koldere D, De Waegeneer M, Pech U, Kreft Ł, Aibar S, Makhzami S, Christiaens V, Bravo González-Blas C, Poovathingal S, Hulselmans G, Spanier KI, Moerman T, Vanspauwen B, Geurs S, Voet T, Lammertyn J, Thienpont B, Liu S, Konstantinides N, Fiers M, Verstreken P, Aerts S. A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain. Cell 2018; 174:982-998.e20. [PMID: 29909982 PMCID: PMC6086935 DOI: 10.1016/j.cell.2018.05.057] [Citation(s) in RCA: 437] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/30/2018] [Accepted: 05/25/2018] [Indexed: 02/06/2023]
Abstract
The diversity of cell types and regulatory states in the brain, and how these change during aging, remains largely unknown. We present a single-cell transcriptome atlas of the entire adult Drosophila melanogaster brain sampled across its lifespan. Cell clustering identified 87 initial cell clusters that are further subclustered and validated by targeted cell-sorting. Our data show high granularity and identify a wide range of cell types. Gene network analyses using SCENIC revealed regulatory heterogeneity linked to energy consumption. During aging, RNA content declines exponentially without affecting neuronal identity in old brains. This single-cell brain atlas covers nearly all cells in the normal brain and provides the tools to study cellular diversity alongside other Drosophila and mammalian single-cell datasets in our unique single-cell analysis platform: SCope (http://scope.aertslab.org). These results, together with SCope, allow comprehensive exploration of all transcriptional states of an entire aging brain. A single-cell atlas of the adult fly brain during aging Network inference reveals regulatory states related to oxidative phosphorylation Cell identity is retained during aging despite exponential decline of gene expression SCope: An online tool to explore and compare single-cell datasets across species
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Affiliation(s)
- Kristofer Davie
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Jasper Janssens
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Duygu Koldere
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Maxime De Waegeneer
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Uli Pech
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Łukasz Kreft
- VIB Bioinformatics Core, VIB, Ghent 9052, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Samira Makhzami
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | | | - Gert Hulselmans
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Katina I Spanier
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Thomas Moerman
- ESAT, KU Leuven, Leuven 3001, Belgium; Smart Applications and Innovation Services, IMEC, Leuven 3001, Belgium
| | | | - Sarah Geurs
- Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Thierry Voet
- Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | | | | | - Sha Liu
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | | | - Mark Fiers
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Patrik Verstreken
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium.
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8
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Mishra AK, Bernardo-Garcia FJ, Fritsch C, Humberg TH, Egger B, Sprecher SG. Patterning mechanisms diversify neuroepithelial domains in the Drosophila optic placode. PLoS Genet 2018; 14:e1007353. [PMID: 29677185 PMCID: PMC5937791 DOI: 10.1371/journal.pgen.1007353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 05/07/2018] [Accepted: 04/04/2018] [Indexed: 12/31/2022] Open
Abstract
The central nervous system develops from monolayered neuroepithelial sheets. In a first step patterning mechanisms subdivide the seemingly uniform epithelia into domains allowing an increase of neuronal diversity in a tightly controlled spatial and temporal manner. In Drosophila, neuroepithelial patterning of the embryonic optic placode gives rise to the larval eye primordium, consisting of two photoreceptor (PR) precursor types (primary and secondary), as well as the optic lobe primordium, which during larval and pupal stages develops into the prominent optic ganglia. Here, we characterize a genetic network that regulates the balance between larval eye and optic lobe precursors, as well as between primary and secondary PR precursors. In a first step the proneural factor Atonal (Ato) specifies larval eye precursors, while the orphan nuclear receptor Tailless (Tll) is crucial for the specification of optic lobe precursors. The Hedgehog and Notch signaling pathways act upstream of Ato and Tll to coordinate neural precursor specification in a timely manner. The correct spatial placement of the boundary between Ato and Tll in turn is required to control the precise number of primary and secondary PR precursors. In a second step, Notch signaling also controls a binary cell fate decision, thus, acts at the top of a cascade of transcription factor interactions to define PR subtype identity. Our model serves as an example of how combinatorial action of cell extrinsic and cell intrinsic factors control neural tissue patterning.
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Affiliation(s)
| | | | - Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Boris Egger
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Simon G. Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail:
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9
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Morrison CA, Chen H, Cook T, Brown S, Treisman JE. Glass promotes the differentiation of neuronal and non-neuronal cell types in the Drosophila eye. PLoS Genet 2018; 14:e1007173. [PMID: 29324767 PMCID: PMC5783423 DOI: 10.1371/journal.pgen.1007173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 01/24/2018] [Accepted: 12/29/2017] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulators can specify different cell types from a pool of equivalent progenitors by activating distinct developmental programs. The Glass transcription factor is expressed in all progenitors in the developing Drosophila eye, and is maintained in both neuronal and non-neuronal cell types. Glass is required for neuronal progenitors to differentiate as photoreceptors, but its role in non-neuronal cone and pigment cells is unknown. To determine whether Glass activity is limited to neuronal lineages, we compared the effects of misexpressing it in neuroblasts of the larval brain and in epithelial cells of the wing disc. Glass activated overlapping but distinct sets of genes in these neuronal and non-neuronal contexts, including markers of photoreceptors, cone cells and pigment cells. Coexpression of other transcription factors such as Pax2, Eyes absent, Lozenge and Escargot enabled Glass to induce additional genes characteristic of the non-neuronal cell types. Cell type-specific glass mutations generated in cone or pigment cells using somatic CRISPR revealed autonomous developmental defects, and expressing Glass specifically in these cells partially rescued glass mutant phenotypes. These results indicate that Glass is a determinant of organ identity that acts in both neuronal and non-neuronal cells to promote their differentiation into functional components of the eye.
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Affiliation(s)
- Carolyn A. Morrison
- Skirball Institute for Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Hao Chen
- Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Tiffany Cook
- Center of Molecular Medicine and Genomics and Department of Ophthalmology, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Stuart Brown
- Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Jessica E. Treisman
- Skirball Institute for Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
- * E-mail:
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10
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Larderet I, Fritsch PM, Gendre N, Neagu-Maier GL, Fetter RD, Schneider-Mizell CM, Truman JW, Zlatic M, Cardona A, Sprecher SG. Organization of the Drosophila larval visual circuit. eLife 2017; 6:28387. [PMID: 30726702 PMCID: PMC5577918 DOI: 10.7554/elife.28387] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/07/2017] [Indexed: 11/20/2022] Open
Abstract
Visual systems transduce, process and transmit light-dependent environmental cues. Computation of visual features depends on photoreceptor neuron types (PR) present, organization of the eye and wiring of the underlying neural circuit. Here, we describe the circuit architecture of the visual system of Drosophila larvae by mapping the synaptic wiring diagram and neurotransmitters. By contacting different targets, the two larval PR-subtypes create two converging pathways potentially underlying the computation of ambient light intensity and temporal light changes already within this first visual processing center. Locally processed visual information then signals via dedicated projection interneurons to higher brain areas including the lateral horn and mushroom body. The stratified structure of the larval optic neuropil (LON) suggests common organizational principles with the adult fly and vertebrate visual systems. The complete synaptic wiring diagram of the LON paves the way to understanding how circuits with reduced numerical complexity control wide ranges of behaviors.
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Affiliation(s)
- Ivan Larderet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Nanae Gendre
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Richard D Fetter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | | | - James W Truman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Marta Zlatic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Albert Cardona
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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11
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Cerqueira DM, Bodnar AJ, Phua YL, Freer R, Hemker SL, Walensky LD, Hukriede NA, Ho J. Bim gene dosage is critical in modulating nephron progenitor survival in the absence of microRNAs during kidney development. FASEB J 2017; 31:3540-3554. [PMID: 28446592 PMCID: PMC5503708 DOI: 10.1096/fj.201700010r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/11/2017] [Indexed: 12/18/2022]
Abstract
Low nephron endowment at birth has been associated with an increased risk for developing hypertension and chronic kidney disease. We demonstrated in an earlier study that conditional deletion of the microRNA (miRNA)-processing enzyme Dicer from nephron progenitors results in premature depletion of the progenitors and increased expression of the proapoptotic protein Bim (also known as Bcl-2L11). In this study, we generated a compound mouse model with conditional deletion of both Dicer and Bim, to determine the biologic significance of increased Bim expression in Dicer-deficient nephron progenitors. The loss of Bim partially restored the number of nephron progenitors and improved nephron formation. The number of progenitors undergoing apoptosis was significantly reduced in kidneys with loss of a single allele, or both alleles, of Bim compared to mutant kidneys. Furthermore, 2 miRNAs expressed in nephron progenitors (miR-17 and miR-106b) regulated Bim levels in vitro and in vivo Together, these data suggest that miRNA-mediated regulation of Bim controls nephron progenitor survival during nephrogenesis, as one potential means of regulating nephron endowment.-Cerqueira, D. M., Bodnar, A. J., Phua, Y. L., Freer, R., Hemker, S. L., Walensky, L. D., Hukriede, N. A., Ho, J. Bim gene dosage is critical in modulating nephron progenitor survival in the absence of microRNAs during kidney development.
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Affiliation(s)
- Débora M Cerqueira
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Andrew J Bodnar
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yu Leng Phua
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rachel Freer
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Shelby L Hemker
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Loren D Walensky
- Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Neil A Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jacqueline Ho
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA;
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Bernardo-Garcia FJ, Humberg TH, Fritsch C, Sprecher SG. Successive requirement of Glass and Hazy for photoreceptor specification and maintenance in Drosophila. Fly (Austin) 2016; 11:112-120. [PMID: 27723419 PMCID: PMC5406162 DOI: 10.1080/19336934.2016.1244591] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Development of the insect compound eye requires a highly controlled interplay between transcription factors. However, the genetic mechanisms that link early eye field specification to photoreceptor terminal differentiation and fate maintenance remain largely unknown. Here, we decipher the function of 2 transcription factors, Glass and Hazy, which play a central role during photoreceptor development. The regulatory interactions between Glass and Hazy suggest that they function together in a coherent feed-forward loop in all types of Drosophila photoreceptors. While the glass mutant eye lacks the expression of virtually all photoreceptor genes, young hazy mutants correctly express most phototransduction genes. Interestingly, the expression of these genes is drastically reduced in old hazy mutants. This age-dependent loss of the phototransduction cascade correlates with a loss of phototaxis in old hazy mutant flies. We conclude that Glass can either directly or indirectly initiate the expression of most phototransduction proteins in a Hazy-independent manner, and that Hazy is mainly required for the maintenance of functional photoreceptors in adult flies.
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Affiliation(s)
| | | | - Cornelia Fritsch
- a Department of Biology , University of Fribourg , Fribourg , Switzerland
| | - Simon G Sprecher
- a Department of Biology , University of Fribourg , Fribourg , Switzerland
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