Faculty Bibliography
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110
Origin and establishment of the germline in Drosophila melanogaster
The continuity of a species depends on germ cells. Germ cells are different from all the other cell types of the body (somatic cells) as they are solely destined to develop into gametes (sperm or egg) to create the next generation. In this review, we will touch on 4 areas of embryonic germ cell development in Drosophila melanogaster: the assembly and function of germplasm, which houses the determinants for germ cell specification and fate and the mitochondria of the next generation; the process of pole cell formation, which will give rise to primordial germ cells (PGCs); the specification of pole cells toward the PGC fate; and finally, the migration of PGCs to the somatic gonadal precursors, where they, together with somatic gonadal precursors, form the embryonic testis and ovary.
PMID: 40180587
ISSN: 1943-2631
CID: 5819322
Integrator-mediated clustering of poised RNA polymerase II synchronizes histone transcription
UNLABELLED:nurse cells as a model, we find that Pol II forms long-lived, transcriptionally poised clusters distinct from liquid droplets, which contain unbound and paused Pol II. Depletion of the Integrator complex endonuclease module, but not its phosphatase module or Pol II pausing factors disperses these Pol II clusters. Consequently, histone transcription fails to reach peak levels during S-phase and aberrantly continues throughout the cell cycle. We propose that Pol II clustering is a regulatory step occurring near promoters that limits rapid gene activation to defined times. ONE SENTENCE SUMMARY/UNASSIGNED:histone locus as a model, we show that clustered RNA polymerase II is poised for synchronous activation.
PMCID:10592978
PMID: 37873455
ISSN: 2692-8205
CID: 5744062
Direct observation of translational activation by a ribonucleoprotein granule
Biomolecular condensates organize biochemical processes at the subcellular level and can provide spatiotemporal regulation within a cell. Among these, ribonucleoprotein (RNP) granules are storage hubs for translationally repressed mRNA. Whether RNP granules can also activate translation and how this could be achieved remains unclear. Here, using single-molecule imaging, we demonstrate that the germ cell-determining RNP granules in Drosophila embryos are sites for active translation of nanos mRNA. Nanos translation occurs preferentially at the germ granule surface with the 3' UTR buried within the granule. Smaug, a cytosolic RNA-binding protein, represses nanos translation, which is relieved when Smaug is sequestered to the germ granule by the scaffold protein Oskar. Together, our findings uncover a molecular process by which RNP granules achieve localized protein synthesis through the compartmentalized loss of translational repression.
PMCID:11321996
PMID: 38965420
ISSN: 1476-4679
CID: 5726442
Boosting the toolbox for live imaging of translation
Live imaging of translation based on tag recognition by a single-chain antibody is a powerful technique to assess translation regulation in living cells. However, this approach is challenging and requires optimization in terms of expression level and detection sensitivity of the system, especially in a multicellular organism. Here, we improved existing fluorescent tools and developed new ones to image and quantify nascent translation in the living Drosophila embryo and in mammalian cells. We tested and characterized five different green fluorescent protein variants fused to the single-chain fragment variable (scFv) and uncovered photobleaching, aggregation, and intensity disparities. Using different strengths of germline and somatic drivers, we determined that the availability of the scFv is critical in order to detect translation throughout development. We introduced a new translation imaging method based on a nanobody/tag system named ALFA-array, allowing the sensitive and simultaneous detection of the translation of several distinct mRNA species. Finally, we developed a largely improved RNA imaging system based on an MCP-tdStaygold fusion.
PMCID:11404453
PMID: 39060168
ISSN: 1469-9001
CID: 5713952
Juvenile hormones direct primordial germ cell migration to the embryonic gonad
Germ cells are essential to sexual reproduction. Across the animal kingdom, extracellular signaling isoprenoids, such as retinoic acids (RAs) in vertebrates and juvenile hormones (JHs) in invertebrates, facilitate multiple processes in reproduction. Here we investigated the role of these potent signaling molecules in embryonic germ cell development, using JHs in Drosophila melanogaster as a model system. In contrast to their established endocrine roles during larval and adult germline development, we found that JH signaling acts locally during embryonic development. Using an in vivo biosensor, we observed active JH signaling first within and near primordial germ cells (PGCs) as they migrate to the developing gonad. Through in vivo and in vitro assays, we determined that JHs are both necessary and sufficient for PGC migration. Analysis into the mechanisms of this newly uncovered paracrine JH function revealed that PGC migration was compromised when JHs were decreased or increased, suggesting that specific titers or spatiotemporal JH dynamics are required for robust PGC colonization of the gonad. Compromised PGC migration can impair fertility and cause germ cell tumors in many species, including humans. In mammals, retinoids have many roles in development and reproduction. We found that like JHs in Drosophila, RA was sufficient to impact mouse PGC migration in vitro. Together, our study reveals a previously unanticipated role of isoprenoids as local effectors of pre-gonadal PGC development and suggests a broadly shared mechanism in PGC migration.
PMID: 38215744
ISSN: 1879-0445
CID: 5633172
visMOP "“ A Visual Analytics Approach for Multi-omics Pathways
We present an approach for the visual analysis of multi-omics data obtained using high-throughput methods. The term "omics" denotes measurements of different types of biologically relevant molecules like the products of gene transcription (transcriptomics) or the abundance of proteins (proteomics). Current popular visualization approaches often only support analyzing each of these omics separately. This, however, disregards the interconnectedness of different biologically relevant molecules and processes. Consequently, it describes the actual events in the organism suboptimally or only partially. Our visual analytics approach for multi-omics data provides a comprehensive overview and details-on-demand by integrating the different omics types in multiple linked views. To give an overview, we map the measurements to known biological pathways and use a combination of a clustered network visualization, glyphs, and interactive filtering. To ensure the effectiveness and utility of our approach, we designed it in close collaboration with domain experts and assessed it using an exemplary workflow with real-world transcriptomics, proteomics, and lipidomics measurements from mice.
SCOPUS:85164273496
ISSN: 0167-7055
CID: 5548832
An AMPK phosphoregulated RhoGEF feedback loop tunes cortical flow-driven amoeboid migration in vivo
Development, morphogenesis, immune system function, and cancer metastasis rely on the ability of cells to move through diverse tissues. To dissect migratory cell behavior in vivo, we developed cell type-specific imaging and perturbation techniques for Drosophila primordial germ cells (PGCs). We find that PGCs use global, retrograde cortical actin flows for orientation and propulsion during guided developmental homing. PGCs use RhoGEF2, a RhoA-specific RGS-RhoGEF, as a dose-dependent regulator of cortical flow through a feedback loop requiring its conserved PDZ and PH domains for membrane anchoring and local RhoA activation. This feedback loop is regulated for directional migration by RhoGEF2 availability and requires AMPK rather than canonical Gα12/13 signaling. AMPK multisite phosphorylation of RhoGEF2 near a conserved EB1 microtubule-binding SxIP motif releases RhoGEF2 from microtubule-dependent inhibition. Thus, we establish the mechanism by which global cortical flow and polarized RhoA activation can be dynamically adapted during natural cell navigation in a changing environment.
PMCID:9473612
PMID: 36103538
ISSN: 2375-2548
CID: 5332862
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.
PMID: 35239393
ISSN: 1095-9203
CID: 5174612
Model organism databases are in jeopardy
PMID: 35231122
ISSN: 1477-9129
CID: 5174352
A single-cell atlas reveals unanticipated cell type complexity in Drosophila ovaries
Organ function relies on the spatial organization and functional coordination of numerous cell types. The Drosophila ovary is a widely used model system to study the cellular activities underlying organ function, including stem cell regulation, cell signaling and epithelial morphogenesis. However, the relative paucity of cell type-specific reagents hinders investigation of molecular functions at the appropriate cellular resolution. Here, we used single-cell RNA sequencing to characterize all cell types of the stem cell compartment and early follicles of the Drosophila ovary. We computed transcriptional signatures and identified specific markers for nine states of germ cell differentiation and 23 somatic cell types and subtypes. We uncovered an unanticipated diversity of escort cells, the somatic cells that directly interact with differentiating germline cysts. Three escort cell subtypes reside in discrete anatomical positions and express distinct sets of secreted and transmembrane proteins, suggesting that diverse micro-environments support the progressive differentiation of germ cells. Finally, we identified 17 follicle cell subtypes and characterized their transcriptional profiles. Altogether, we provide a comprehensive resource of gene expression, cell type-specific markers, spatial coordinates, and functional predictions for 34 ovarian cell types and subtypes.
PMCID:8494228
PMID: 34389661
ISSN: 1549-5469
CID: 5061022
