Gastrulation in Drosophila melanogaster: Genetic control, cellular basis and biomechanics

Gheisari, Elham; Aakhte, Mostafa; Müller, H.‐Arno J.

doi:10.1016/j.mod.2020.103629

Cited by 40 publications

(30 citation statements)

References 194 publications

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“…Many of the DRC genes were previously reported to be important for mesoderm development [ 53 , 62 ] and their interactions suggest functional relationships. For instance, genes that interact with T48 might contribute to fog -independent ventral furrow formation [ 63 ]. The edge between Notch and wingless was identified most frequently in the combined DRC network.…”

Section: Resultsmentioning

confidence: 99%

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

Overton

Sims

Owen

et al. 2020

Cancers

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Cell identity is governed by gene expression, regulated by transcription factor (TF) binding at cis-regulatory modules. Decoding the relationship between TF binding patterns and gene regulation is nontrivial, remaining a fundamental limitation in understanding cell decision-making. We developed the NetNC software to predict functionally active regulation of TF targets; demonstrated on nine datasets for the TFs Snail, Twist, and modENCODE Highly Occupied Target (HOT) regions. Snail and Twist are canonical drivers of epithelial to mesenchymal transition (EMT), a cell programme important in development, tumour progression and fibrosis. Predicted “neutral” (non-functional) TF binding always accounted for the majority (50% to 95%) of candidate target genes from statistically significant peaks and HOT regions had higher functional binding than most of the Snail and Twist datasets examined. Our results illuminated conserved gene networks that control epithelial plasticity in development and disease. We identified new gene functions and network modules including crosstalk with notch signalling and regulation of chromatin organisation, evidencing networks that reshape Waddington’s epigenetic landscape during epithelial remodelling. Expression of orthologous functional TF targets discriminated breast cancer molecular subtypes and predicted novel tumour biology, with implications for precision medicine. Predicted invasion roles were validated using a tractable cell model, supporting our approach.

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Section: Resultsmentioning

confidence: 99%

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

Overton

Sims

Owen

et al. 2020

Cancers

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“…The MT-SPIM imaging of provides an excellent method to study the dynamic changes in the distribution of GFP-tagged proteins in the context of early Drosophila embryos. A whole range of different morphogenetic movements have been well studied during gastrulation and the actomyosin cytoskeleton was shown to be involved in most of these events [24]. The simultaneous imaging of MyoII-GFP in the embryo at the mesoscale has provided important information about the relationship of mechanical forces in instructing cell flows during gastrulation movements in Drosophila [25].…”

Section: D Dynamic Imaging Of Myoii-gfp Distribution During Selected Morphogenetic Movements In the Drosophila Gastrulamentioning

confidence: 99%

Multiview tiling light sheet microscopy for 3D high resolution live imaging

Aakhte

Mueller

2021

Preprint

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Light sheet or selective plane illumination microscopy (SPIM) is ideally suited for in toto imaging of living specimens at high temporal-spatial resolution. In SPIM, the light scattering that occurs during imaging of opaque specimens brings about limitations in terms of resolution and the imaging field of view. To ameliorate this shortcoming, the illumination beam can be engineered into a highly confined light sheet over a large field of view and multi-view imaging can be performed by applying multiple lenses combined with mechanical rotation of the sample. Here, we present a Multiview tiling SPIM (MT-SPIM) that combines the Multi-view SPIM (M-SPIM) with a confined, multi-tiled light sheet. The MT-SPIM provides high-resolution, robust and rotation-free imaging of living specimens. We applied the MT-SPIM to image nuclei and Myosin II from the cellular to subcellular spatial scale in early Drosophila embryogenesis. We show that the MT-SPIM improves the axial-resolution relative to the conventional M-SPIM by a factor of two. We further demonstrate that this axial resolution enhancement improves the automated segmentation of Myosin II distribution and of nuclear volumes and shapes.

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“…Drosophila gastrulae has been an excellent model system for studying multicellular morphogenesis for decades (Gheisari et al, 2020; Martin, 2020; Wieschaus and Nüsslein-Volhard, 2016). The fertilized egg undergoes 13 rounds of nuclear division and then forms a single layer of the epithelial sheet covering the entire embryo, the so-called blastoderm.…”

Section: Introductionmentioning

confidence: 99%

Single-cell transcriptome atlas of Drosophila gastrula 2.0

Sakaguchi

Okochi

Tanegashima

et al. 2021

Preprint

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During development, positional information directs cells to specific fates, leading them to differentiate with their own transcriptomes and express specific behaviors and functions. However, the mechanisms underlying these processes in a genome-wide view remain ambiguous, partly because the single-cell transcriptomic data of early developing embryos containing both accurate spatial and lineage information is still lacking. Here, we report a new single-cell transcriptome atlas of Drosophila gastrulae, divided into 65 transcriptomically distinct clusters. We found that the expression profiles of plasma-membrane-related genes, but not those of transcription factor genes, represented each germ layer, supporting the nonequivalent contribution of each transcription factor mRNA level to effector gene expression profiles at the transcriptome level. We also reconstructed the spatial expression patterns of all genes at the single-cell stripe level as the smallest unit. This atlas is an important resource for the genome-wide understanding of the mechanisms by which genes cooperatively orchestrate Drosophila gastrulation.

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Gastrulation in Drosophila melanogaster: Genetic control, cellular basis and biomechanics

Cited by 40 publications

References 194 publications

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

Multiview tiling light sheet microscopy for 3D high resolution live imaging

Single-cell transcriptome atlas of Drosophila gastrula 2.0

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