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Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

Li, Hongjie; Janssens, Jasper; De Waegeneer, Maxime; Kolluru, Sai Saroja; Davie, Kristofer; Gardeux, Vincent; Saelens, Wouter; David, Fabrice P A; Brbić, Maria; Spanier, Katina; Leskovec, Jure; McLaughlin, Colleen N; Xie, Qijing; Jones, Robert C; Brueckner, Katja; Shim, Jiwon; Tattikota, Sudhir Gopal; Schnorrer, Frank; Rust, Katja; Nystul, Todd G; Carvalho-Santos, Zita; Ribeiro, Carlos; Pal, Soumitra; Mahadevaraju, Sharvani; Przytycka, Teresa M; Allen, Aaron M; Goodwin, Stephen F; Berry, Cameron W; Fuller, Margaret T; White-Cooper, Helen; Matunis, Erika L; DiNardo, Stephen; Galenza, Anthony; O'Brien, Lucy Erin; Dow, Julian A T; Jasper, Heinrich; Oliver, Brian; Perrimon, Norbert; Deplancke, Bart; Quake, Stephen R; Luo, Liqun; Aerts, Stein; Agarwal, Devika; Ahmed-Braimah, Yasir; Arbeitman, Michelle; Ariss, Majd M; Augsburger, Jordan; Ayush, Kumar; Baker, Catherine C; Banisch, Torsten; Birker, Katja; Bodmer, Rolf; Bolival, Benjamin; Brantley, Susanna E; Brill, Julie A; Brown, Nora C; Buehner, Norene A; Cai, Xiaoyu Tracy; Cardoso-Figueiredo, Rita; Casares, Fernando; Chang, Amy; Clandinin, Thomas R; Crasta, Sheela; Desplan, Claude; Detweiler, Angela M; Dhakan, Darshan B; Donà, Erika; Engert, Stefanie; Floc'hlay, Swann; George, Nancy; González-Segarra, Amanda J; Groves, Andrew K; Gumbin, Samantha; Guo, Yanmeng; Harris, Devon E; Heifetz, Yael; Holtz, Stephen L; Horns, Felix; Hudry, Bruno; Hung, Ruei-Jiun; Jan, Yuh Nung; Jaszczak, Jacob S; Jefferis, Gregory S X E; Karkanias, Jim; Karr, Timothy L; Katheder, Nadja Sandra; Kezos, James; Kim, Anna A; Kim, Seung K; Kockel, Lutz; Konstantinides, Nikolaos; Kornberg, Thomas B; Krause, Henry M; Labott, Andrew Thomas; Laturney, Meghan; Lehmann, Ruth; Leinwand, Sarah; Li, Jiefu; Li, Joshua Shing Shun; Li, Kai; Li, Ke; Li, Liying; Li, Tun; Litovchenko, Maria; Liu, Han-Hsuan; Liu, Yifang; Lu, Tzu-Chiao; Manning, Jonathan; Mase, Anjeli; Matera-Vatnick, Mikaela; Matias, Neuza Reis; McDonough-Goldstein, Caitlin E; McGeever, Aaron; McLachlan, Alex D; Moreno-Roman, Paola; Neff, Norma; Neville, Megan; Ngo, Sang; Nielsen, Tanja; O'Brien, Caitlin E; Osumi-Sutherland, David; Özel, Mehmet Neset; Papatheodorou, Irene; Petkovic, Maja; Pilgrim, Clare; Pisco, Angela Oliveira; Reisenman, Carolina; Sanders, Erin Nicole; Dos Santos, Gilberto; Scott, Kristin; Sherlekar, Aparna; Shiu, Philip; Sims, David; Sit, Rene V; Slaidina, Maija; Smith, Harold E; Sterne, Gabriella; Su, Yu-Han; Sutton, Daniel; Tamayo, Marco; Tan, Michelle; Tastekin, Ibrahim; Treiber, Christoph; Vacek, David; Vogler, Georg; Waddell, Scott; Wang, Wanpeng; Wilson, Rachel I; Wolfner, Mariana F; Wong, Yiu-Cheung E; Xie, Anthony; Xu, Jun; Yamamoto, Shinya; Yan, Jia; Yao, Zepeng; Yoda, Kazuki; Zhu, Ruijun; Zinzen, Robert P
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

Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation

Gebert, Daniel; Neubert, Lena K; Lloyd, Catrin; Gui, Jinghua; Lehmann, Ruth; Teixeira, Felipe Karam
PIWI proteins and their guiding Piwi-interacting small RNAs (piRNAs) are crucial for fertility and transposon defense in the animal germline. In most species, the majority of piRNAs are produced from distinct large genomic loci, called piRNA clusters. It is assumed that germline-expressed piRNA clusters, particularly in Drosophila, act as principal regulators to control transposons dispersed across the genome. Here, using synteny analysis, we show that large clusters are evolutionarily labile, arise at loci characterized by recurrent chromosomal rearrangements, and are mostly species-specific across the Drosophila genus. By engineering chromosomal deletions in D. melanogaster, we demonstrate that the three largest germline clusters, which account for the accumulation of >40% of all transposon-targeting piRNAs in ovaries, are neither required for fertility nor for transposon regulation in trans. We provide further evidence that dispersed elements, rather than the regulatory action of large Drosophila germline clusters in trans, may be central for transposon defense.
PMID: 34352205
ISSN: 1097-4164
CID: 5026562

Model organism databases are in jeopardy

Bellen, Hugo J; Hubbard, E J A; Lehmann, Ruth; Madhani, Hiten D; Solnica-Krezel, Lila; Southard-Smith, E Michelle
PMID: 35231122
ISSN: 1477-9129
CID: 5174352

A single-cell atlas reveals unanticipated cell type complexity in Drosophila ovaries

Slaidina, Maija; Gupta, Selena; Banisch, Torsten U; Lehmann, Ruth
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.
PMID: 34389661
ISSN: 1549-5469
CID: 5061022

A transitory signaling center controls timing of primordial germ cell differentiation

Banisch, Torsten U; Slaidina, Maija; Gupta, Selena; Ho, Megan; Gilboa, Lilach; Lehmann, Ruth
Organogenesis requires exquisite spatiotemporal coordination of cell morphogenesis, migration, proliferation, and differentiation of multiple cell types. For gonads, this involves complex interactions between somatic and germline tissues. During Drosophila ovary morphogenesis, primordial germ cells (PGCs) either are sequestered in stem cell niches and are maintained in an undifferentiated germline stem cell state or transition directly toward differentiation. Here, we identify a mechanism that links hormonal triggers of somatic tissue morphogenesis with PGC differentiation. An early ecdysone pulse initiates somatic swarm cell (SwC) migration, positioning these cells close to PGCs. A second hormone peak activates Torso-like signal in SwCs, which stimulates the Torso receptor tyrosine kinase (RTK) signaling pathway in PGCs promoting their differentiation by de-repression of the differentiation gene, bag of marbles. Thus, systemic temporal cues generate a transitory signaling center that coordinates ovarian morphogenesis with stem cell self-renewal and differentiation programs, highlighting a more general role for such centers in reproductive and developmental biology.
PMID: 34081907
ISSN: 1878-1551
CID: 4891912

In Memoriam: Kathryn V. Anderson (1952-2020)

Joyner, Alex; Lehmann, Ruth; Niswander, Lee
PMID: 33618188
ISSN: 1095-564x
CID: 4794302

Angelika Amon (1967-2020)

Lehmann, Ruth; Peters, Jan-Michael
PMID: 33417858
ISSN: 1097-4172
CID: 4739462


Lehmann, Ruth
PMID: 33021825
ISSN: 1530-8995
CID: 4626792

Collectively stabilizing and orienting posterior migratory forces disperses cell clusters in vivo

Lin, B; Luo, J; Lehmann, R
Individual cells detach from cohesive ensembles during development and can inappropriately separate in disease. Although much is known about how cells separate from epithelia, it remains unclear how cells disperse from clusters lacking apical-basal polarity, a hallmark of advanced epithelial cancers. Here, using live imaging of the developmental migration program of Drosophila primordial germ cells (PGCs), we show that cluster dispersal is accomplished by stabilizing and orienting migratory forces. PGCs utilize a G protein coupled receptor (GPCR), Tre1, to guide front-back migratory polarity radially from the cluster toward the endoderm. Posteriorly positioned myosin-dependent contractile forces pull on cell-cell contacts until cells release. Tre1 mutant cells migrate randomly with transient enrichment of the force machinery but fail to separate, indicating a temporal contractile force threshold for detachment. E-cadherin is retained on the cell surface during cell separation and augmenting cell-cell adhesion does not impede detachment. Notably, coordinated migration improves cluster dispersal efficiency by stabilizing cell-cell interfaces and facilitating symmetric pulling. We demonstrate that guidance of inherent migratory forces is sufficient to disperse cell clusters under physiological settings and present a paradigm for how such events could occur across development and disease.
PMID: 32901019
ISSN: 2041-1723
CID: 4614672

Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters

Trcek, Tatjana; Douglas, Tyler E; Grosch, Markus; Yin, Yandong; Eagle, Whitby V I; Gavis, Elizabeth R; Shroff, Hari; Rothenberg, Eli; Lehmann, Ruth
mRNAs enriched in membraneless condensates provide functional compartmentalization within cells. The mechanisms that recruit transcripts to condensates are under intense study; however, how mRNAs organize once they reach a granule remains poorly understood. Here, we report on a self-sorting mechanism by which multiple mRNAs derived from the same gene assemble into discrete homotypic clusters. We demonstrate that in vivo mRNA localization to granules and self-assembly within granules are governed by different mRNA features: localization is encoded by specific RNA regions, whereas self-assembly involves the entire mRNA, does not involve sequence-specific, ordered intermolecular RNA:RNA interactions, and is thus RNA sequence independent. We propose that the ability of mRNAs to self-sort into homotypic assemblies is an inherent property of an messenger ribonucleoprotein (mRNP) that is augmented under conditions that increase RNA concentration, such as upon enrichment in RNA-protein granules, a process that appears conserved in diverse cellular contexts and organisms.
PMID: 32464092
ISSN: 1097-4164
CID: 4451882