Microarray Comparison of Anterior and Posterior<i>Drosophila</i>Wing Imaginal Disc Cells Identifies Novel Wing Genes

Ibrahim, Daniel M.; Biehs, Brian; Kornberg, Thomas B.; Klebes, Ansgar

doi:10.1534/g3.113.006569

Cited by 19 publications

(16 citation statements)

References 45 publications

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“…Stubble (Sb) (Ibrahim et al, 2013) were detected at higher levels in Epi_3, whereas Angiotensin converting enzyme (Ance) (Siviter et al, 2002) was specifically in Epi_2, we inferred that Epi_3 was positioned in the anterior lateral notum near the hinge and Epi_2 was in the anterior medial notum. The markers for Epi_15 were four-jointed (fj) and tailup (tup), which localize to the prospective notum (Cho and Irvine, 2004;de Navascues and Modolell, 2007).…”

Section: Cells In the Epithelial Clusters Map To Spatially Distinct Rmentioning

confidence: 69%

A single-cell transcriptome atlas of the adult muscle precursors uncovers early events in fiber-type divergence inDrosophila

et al. 2019

Preprint

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In Drosophila, the wing disc-associated adult muscle precursors (AMPs) give rise to the fibrillar indirect flight muscles (IFM) and the tubular direct flight muscles (DFM). To understand early transcriptional events underlying this muscle diversification, we performed single cell RNA-sequencing experiments and built a cell atlas of AMPs associated with third instar larval wing disc. Our analysis identified distinct transcriptional signatures for IFM and DFM precursors that underlie the molecular basis of their divergence. The atlas further revealed various states of differentiation of AMPs, thus illustrating previously unappreciated spatial and temporal heterogeneity among them. We identified and validated novel markers for both IFM and DFM precursors at various states of differentiation by immunofluorescence and genetic tracing experiments. Finally, we performed a systematic genetic screen using a panel of markers from the reference cell atlas as an entry point and found a novel gene, Ama, which is functionally important in muscle development. Thus, our work provides a framework of leveraging scRNA-seq for gene discovery and therefore, this strategy can be applied to other scRNA-seq datasets.

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Section: Cells In the Epithelial Clusters Map To Spatially Distinct Rmentioning

confidence: 69%

A single-cell transcriptome atlas of the adult muscle precursors uncovers early events in fiber-type divergence inDrosophila

et al. 2019

Preprint

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“…DmStubble and M. sexta haemolymph protease-1 (MsHP-1, CLIPD subfamily) are some of the few proteases of the CLIPD subfamily that have been characterized. DmStubble functions in neuronal projection, cytoskeleton organization and possibly wing disc development in D. melanogaster (Appel et al, 1993;Sepp et al, 2008;Ibrahim et al, 2013). MsHP-1 participates in the prophenoloxidase-activating system of M. sexta (Yang et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

“…D. melanogaster CG9372 was identified in a genome-wide RNA interference (RNAi) screen and was shown to be implicated in neuronal projection (Sepp et al, 2008). DmStubble encodes a clip domain SP that functions in cytoskeleton organization and possibly wing disc development (Appel et al, 1993;Ibrahim et al, 2013). It is suggested that CLIPs may play roles in insect developments.…”

Section: Introductionmentioning

confidence: 99%

A clip domain serine protease involved in moulting in the silkworm, Bombyx mori: cloning, characterization, expression patterns and functional analysis

Liu

Wang

Meng

et al. 2017

Insect Molecular Biology

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Clip domain serine proteases (CLIPs), characterized by one or more conserved clip domains, are essential components of extracellular signalling cascades in various biological processes, especially in innate immunity and the embryonic development of insects. Additionally, CLIPs may have additional non-immune functions in insect development. In the present study, the clip domain serine protease gene Bombyx mori serine protease 95 (BmSP95), which encodes a 527-residue protein, was cloned from the integument of B. mori. Bioinformatics analysis indicated that BmSP95 is a typical CLIP of the subfamily D and possesses a clip domain at the N terminus, a trypsin-like serine protease (tryp_spc) domain at the C terminus and a conserved proline-rich motif between these two domains. At the transcriptional level, BmSP95 is expressed in the integument during moulting and metamorphosis, and the expression pattern is consistent with the fluctuating 20-hydroxyecdysone (20E) titre in B. mori. At the translational level, BmSP95 protein is synthesized in the epidermal cells, secreted as a zymogen and activated in the moulting fluid. Immunofluorescence revealed that BmSP95 is distributed into the old endocuticle in the moulting stage. The expression of BmSP95 was upregulated by 20E. Moreover, expression of BmSP95 was downregulated by pathogen infection. RNA interference-mediated silencing of BmSP95 led to delayed moulting from pupa to moth. These results suggest that BmSP95 is involved in integument remodelling during moulting and metamorphosis.

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“…The other two data sets were collected by microarray expression analysis of anterior and posterior (A/P) wing disc cells in our own laboratory (N Simigdala, unpubl.) or by others (Ibrahim et al 2013). Of all genes in clusters 4b and 5b combined, 12.4% (54/435) showed a compartmentally restricted expression pattern, which is about fivefold higher than for all remaining genes (2.6%, 373/14,505) ( Table 3).…”

Section: Cell Autonomy Of Bivalent Marksmentioning

confidence: 92%

“…( * ) P < 0.05; ( * * ) P < 0.01; ( * * * ) P < 0.001; Fisher's exact test. Butler et al (2003), Ibrahim et al (2013), and N Simigdala (unpubl. ).…”

Section: Cell Autonomy Of Bivalent Marksmentioning

confidence: 99%

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

et al. 2015

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Transcription factors (TFs) are key regulators of cell fate. The estimated 755 genes that encode DNA binding domain-containing proteins comprise ∼5% of all Drosophila genes. However, the majority has remained uncharacterized so far due to the lack of proper genetic tools. We generated 594 site-directed transgenic Drosophila lines that contain integrations of individual UAS-TF constructs to facilitate spatiotemporally controlled misexpression in vivo. All transgenes were expressed in the developing wing, and two-thirds induced specific phenotypic defects. In vivo knockdown of the same genes yielded a phenotype for 50%, with both methods indicating a great potential for misexpression to characterize novel functions in wing growth, patterning, and development. Thus, our UAS-TF library provides an important addition to the genetic toolbox of Drosophila research, enabling the identification of several novel wing development-related TFs. In parallel, we established the chromatin landscape of wing imaginal discs by ChIP-seq analyses of five chromatin marks and RNA Pol II. Subsequent clustering revealed six distinct chromatin states, with two clusters showing enrichment for both active and repressive marks. TFs that carry such “bivalent” chromatin are highly enriched for causing misexpression phenotypes in the wing, and analysis of existing expression data shows that these TFs tend to be differentially expressed across the wing disc. Thus, bivalently marked chromatin can be used as a marker for spatially regulated TFs that are functionally relevant in a developing tissue.

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Microarray Comparison of Anterior and PosteriorDrosophilaWing Imaginal Disc Cells Identifies Novel Wing Genes

Cited by 19 publications

References 45 publications

A single-cell transcriptome atlas of the adult muscle precursors uncovers early events in fiber-type divergence inDrosophila

A single-cell transcriptome atlas of the adult muscle precursors uncovers early events in fiber-type divergence inDrosophila

A clip domain serine protease involved in moulting in the silkworm, Bombyx mori: cloning, characterization, expression patterns and functional analysis

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

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