1
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Choi DY, Mo HH, Park Y. Different development and fecundity between Spodoptera frugiperda USA and China populations, influenced by ecdysone-related genes. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22074. [PMID: 38288488 DOI: 10.1002/arch.22074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 02/01/2024]
Abstract
The fall armyworm (FAW), Spodoptera frugiperda, is one of the most harmful plant pests in the world and is globally distributed from the American continent to the Asian region. The FAW USA population (Sf-USA) and China population (Sf-CHN), which belong to corn strain, showed different developmental periods and fecundity rates in lab conditions. Sf-USA had faster development and higher fecundity compared with Sf-CHN. To examine these differences, transcriptomic data from two FAW populations were analyzed and compared. Twelve gigabytes of transcripts were read from each sample and 21,258 differentially expressed genes (DEGs) were detected. DEGs with log2 fold change ≥ 2 were identified and compared in two populations. In comparison to the Sf-CHN, we discovered that 3471 and 3851 individual DEGs upregulated and downregulated, respectively. Comparing transcriptome profiles for differential gene expression revealed several DEGs, including 39 of ecdysone (E)-, 25 of juvenile hormone-, and 15 of insulin-related genes. We selected six of E-related genes, such as Neverland, Shade, Ecdysone receptor, Ecdysone-inducible protein 74 (E74), E75, and E78 from DEGs. Gene expressions were suppressed by RNA interference to confirm the physiological functions of the selected genes from Sf-USA. The Sf-USA showed developmental retardation and a decrease in fecundity rate by suppression of E-related genes. These findings show that biological characteristics between Sf-USA and Sf-CHN are influenced by E-related genes.
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Affiliation(s)
- Du-Yeol Choi
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Hyoung-Ho Mo
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Youngjin Park
- Department of Plant Medicals, Andong National University, Andong, Korea
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2
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Uygun S, Azodi CB, Shiu SH. Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity. PLANT PHYSIOLOGY 2019; 181:1739-1751. [PMID: 31551359 PMCID: PMC6878017 DOI: 10.1104/pp.19.00653] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/11/2019] [Indexed: 05/08/2023]
Abstract
Multicellular organisms have diverse cell types with distinct roles in development and responses to the environment. At the transcriptional level, the differences in the environmental response between cell types are due to differences in regulatory programs. In plants, although cell-type environmental responses have been examined, it is unclear how these responses are regulated. Here, we identify a set of putative cis-regulatory elements (pCREs) enriched in the promoters of genes responsive to high-salinity stress in six Arabidopsis (Arabidopsis thaliana) root cell types. We then use these pCREs to establish cis-regulatory codes (i.e. models predicting whether a gene is responsive to high salinity for each cell type with machine learning). These pCRE-based models outperform models using in vitro binding data of 758 Arabidopsis transcription factors. Surprisingly, organ pCREs identified based on the whole-root high-salinity response can predict cell-type responses as well as pCREs derived from cell-type data, because organ and cell-type pCREs predict complementary subsets of high-salinity response genes. Our findings not only advance our understanding of the regulatory mechanisms of the plant spatial transcriptional response through cis-regulatory codes but also suggest broad applicability of the approach to any species, particularly those with little or no trans-regulatory data.
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Affiliation(s)
- Sahra Uygun
- Genetics Program, Michigan State University, East Lansing, Michigan 48824
| | - Christina B Azodi
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Genetics Program, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Computational, Mathematics, Science, and Engineering, Michigan State University, East Lansing, Michigan 48824
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3
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Policastro RA, Zentner GE. Enzymatic methods for genome-wide profiling of protein binding sites. Brief Funct Genomics 2019; 17:138-145. [PMID: 29028882 DOI: 10.1093/bfgp/elx030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Genome-wide mapping of protein-DNA interactions is a staple approach in many areas of modern molecular biology. Genome-wide profiles of protein-binding sites are most commonly generated by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). Although ChIP-seq has played a central role in studying genome-wide protein binding, recent work has highlighted systematic biases in the technique that warrant technical and interpretive caution and underscore the need for orthogonal techniques to both confirm the results of ChIP-seq studies and uncover new insights not accessible to ChIP. Several such techniques, based on genetic or immunological targeting of enzymatic activity to specific genomic loci, have been developed. Here, we review the development, applications and future prospects of these methods as complements to ChIP-based approaches and as powerful techniques in their own right.
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4
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A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells. G3-GENES GENOMES GENETICS 2019; 9:403-412. [PMID: 30530643 PMCID: PMC6385967 DOI: 10.1534/g3.118.200872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The small interfering RNA (siRNA) pathway is the main and best studied invertebrate antiviral response. Other poorly characterized protein based antiviral mechanisms also contribute to the control of viral replication in insects. In addition, it remains unclear whether tissue specific factors contribute to RNA and protein-based antiviral immunity mechanisms. In vivo screens to identify such factors are challenging and time consuming. In addition, the scored phenotype is usually limited to survival and/or viral load. Transgenic viral replicons are valuable tools to overcome these limitations and screen for novel antiviral factors. Here we describe transgenic Drosophila melanogaster lines encoding a Flock House Virus-derived replicon (FHV∆B2eGFP), expressing GFP as a reporter of viral replication. This replicon is efficiently controlled by the siRNA pathway in most somatic tissues, with GFP fluorescence providing a reliable marker for the activity of antiviral RNAi. Interestingly, in follicular somatic cells (FSC) of ovaries, this replicon is still partially repressed in an siRNA independent manner. We did not detect replicon derived Piwi-interacting RNAs in FSCs and identified 31 differentially expressed genes between restrictive and permissive FSCs. Altogether, our results uncovered a yet unidentified RNAi-independent mechanism controlling FHV replication in FSCs of ovaries and validate the FHV∆B2eGFP replicon as a tool to screen for novel tissue specific antiviral mechanisms.
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5
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Zhou K, Zhou F, Jiang S, Huang J, Yang Q, Yang L, Jiang S. Ecdysone inducible gene E75 from black tiger shrimp Penaeus monodon: Characterization and elucidation of its role in molting. Mol Reprod Dev 2019; 86:265-277. [PMID: 30618055 DOI: 10.1002/mrd.23101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/11/2018] [Accepted: 12/20/2018] [Indexed: 11/10/2022]
Abstract
Molting is controlled by ecdysteroids, which are synthesized and secreted by the Y-organ in crustaceans. Ecdysone inducible gene, E75, is an early-response gene in the 20-hydroxyecdysone (20E) signaling pathway, with crucial roles in arthropod development. Complementary DNA (cDNA) encoding Penaeus monodon E75 (PmE75) was cloned using RT-PCR and RACE. PmE75 cDNA was 3526 bp long and encoded a 799-amino acid protein. Tissue distribution analysis showed that PmE75 was expressed ubiquitously in selected tissues, and was relatively abundant in the epidermis, muscle, and hepatopancreas. Developmental expression revealed that PmE75 was expressed throughout its life cycle. Silencing PmE75 significantly decreased PmE75 expression. Shrimps injected with PBS and dsGFP started molting on Day 7 and had almost completed molting on Day 9, whereas dsPmE75-injected shrimp presented no signs of molting. These results suggested that PmE75 might be involved in molting. In situ hybridization results support this hypothesis. To explore the role of 20E and eyestalks in the regulation of molting in P. monodon, exogenous 20E injection and eyestalk ablation (ESA) were performed, and showed that 20E can induce the transcription and expression of PmE75 in the hepatopancreas, epidermis, and muscle, which were significantly elevated after ESA. These results provide further insights into our understanding of molting.
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Affiliation(s)
- Kaimin Zhou
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Falin Zhou
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Song Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Jianhua Huang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Qibin Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Lishi Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Shigui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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6
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Peng J, Santiago IJ, Pecot MY. Purification of Low-abundant Cells in the Drosophila Visual System. J Vis Exp 2018. [PMID: 30320761 DOI: 10.3791/58474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Recent improvements in the sensitivity of next generation sequencing have facilitated the application of transcriptomic and genomic analyses to small numbers of cells. Utilizing this technology to study development in the Drosophila visual system, which boasts a wealth of cell type-specific genetic tools, provides a powerful approach for addressing the molecular basis of development with precise cellular resolution. For such an approach to be feasible, it is crucial to have the capacity to reliably and efficiently purify cells present at low abundance within the brain. Here, we present a method that allows efficient purification of single cell clones in genetic mosaic experiments. With this protocol, we consistently achieve a high cellular yield after purification using fluorescence activated cell sorting (FACS) (~25% of all labeled cells), and successfully performed transcriptomics analyses on single cell clones generated through mosaic analysis with a repressible cell marker (MARCM). This protocol is ideal for applying transcriptomic and genomic analyses to specific cell types in the visual system, across different stages of development and in the context of different genetic manipulations.
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Affiliation(s)
- Jing Peng
- Department of Neurobiology, Harvard Medical School
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7
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Ghartey-Kwansah G, Li Z, Feng R, Wang L, Zhou X, Chen FZ, Xu MM, Jones O, Mu Y, Chen S, Bryant J, Isaacs WB, Ma J, Xu X. Comparative analysis of FKBP family protein: evaluation, structure, and function in mammals and Drosophila melanogaster. BMC DEVELOPMENTAL BIOLOGY 2018; 18:7. [PMID: 29587629 PMCID: PMC5870485 DOI: 10.1186/s12861-018-0167-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/12/2018] [Indexed: 12/19/2022]
Abstract
Background FK506-binding proteins (FKBPs) have become the subject of considerable interest in several fields, leading to the identification of several cellular and molecular pathways in which FKBPs impact prenatal development and pathogenesis of many human diseases. Main body This analysis revealed differences between how mammalian and Drosophila FKBPs mechanisms function in relation to the immunosuppressant drugs, FK506 and rapamycin. Differences that could be used to design insect-specific pesticides. (1) Molecular phylogenetic analysis of FKBP family proteins revealed that the eight known Drosophila FKBPs share homology with the human FKBP12. This indicates a close evolutionary relationship, and possible origination from a common ancestor. (2) The known FKBPs contain FK domains, that is, a prolyl cis/trans isomerase (PPIase) domain that mediates immune suppression through inhibition of calcineurin. The dFKBP59, CG4735/Shutdown, CG1847, and CG5482 have a Tetratricopeptide receptor domain at the C-terminus, which regulates transcription and protein transportation. (3) FKBP51 and FKBP52 (dFKBP59), along with Cyclophilin 40 and protein phosphatase 5, function as Hsp90 immunophilin co-chaperones within steroid receptor-Hsp90 heterocomplexes. These immunophilins are potential drug targets in pathways associated with normal physiology and may be used to treat a variety of steroid-based diseases by targeting exocytic/endocytic cycling and vesicular trafficking. (4) By associating with presinilin, a critical component of the Notch signaling pathway, FKBP14 is a downstream effector of Notch activation at the membrane. Meanwhile, Shutdown associates with transposons in the PIWI-interacting RNA pathway, playing a crucial role in both germ cells and ovarian somas. Mutations in or silencing of dFKBPs lead to early embryonic lethality in Drosophila. Therefore, further understanding the mechanisms of FK506 and rapamycin binding to immunophilin FKBPs in endocrine, cardiovascular, and neurological function in both mammals and Drosophila would provide prospects in generating unique, insect specific therapeutics targeting the above cellular signaling pathways. Conclusion This review will evaluate the functional roles of FKBP family proteins, and systematically summarize the similarities and differences between FKBP proteins in Drosophila and Mammals. Specific therapeutics targeting cellular signaling pathways will also be discussed.
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Affiliation(s)
- George Ghartey-Kwansah
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Zhongguang Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Rui Feng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Liyang Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Xin Zhou
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China.,Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Meng Meng Xu
- Department of Pharmacology, Duke University Medical Center, Durham, NC, USA
| | - Odell Jones
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yulian Mu
- State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Joseph Bryant
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Jianjie Ma
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Xuehong Xu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China. .,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China.
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8
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The nuclear receptor E75 from the swimming crab, Portunus trituberculatus: cDNA cloning, transcriptional analysis, and putative roles on expression of ecdysteroid-related genes. Comp Biochem Physiol B Biochem Mol Biol 2016; 200:69-77. [DOI: 10.1016/j.cbpb.2016.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 01/24/2023]
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9
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Marshall OJ, Southall TD, Cheetham SW, Brand AH. Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing. Nat Protoc 2016; 11:1586-98. [PMID: 27490632 DOI: 10.1038/nprot.2016.084] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This protocol is an extension to: Nat. Protoc. 2, 1467-1478 (2007); doi:10.1038/nprot.2007.148; published online 7 June 2007The ability to profile transcription and chromatin binding in a cell-type-specific manner is a powerful aid to understanding cell-fate specification and cellular function in multicellular organisms. We recently developed targeted DamID (TaDa) to enable genome-wide, cell-type-specific profiling of DNA- and chromatin-binding proteins in vivo without cell isolation. As a protocol extension, this article describes substantial modifications to an existing protocol, and it offers additional applications. TaDa builds upon DamID, a technique for detecting genome-wide DNA-binding profiles of proteins, by coupling it with the GAL4 system in Drosophila to enable both temporal and spatial resolution. TaDa ensures that Dam-fusion proteins are expressed at very low levels, thus avoiding toxicity and potential artifacts from overexpression. The modifications to the core DamID technique presented here also increase the speed of sample processing and throughput, and adapt the method to next-generation sequencing technology. TaDa is robust, reproducible and highly sensitive. Compared with other methods for cell-type-specific profiling, the technique requires no cell-sorting, cross-linking or antisera, and binding profiles can be generated from as few as 10,000 total induced cells. By profiling the genome-wide binding of RNA polymerase II (Pol II), TaDa can also identify transcribed genes in a cell-type-specific manner. Here we describe a detailed protocol for carrying out TaDa experiments and preparing the material for next-generation sequencing. Although we developed TaDa in Drosophila, it should be easily adapted to other organisms with an inducible expression system. Once transgenic animals are obtained, the entire experimental procedure-from collecting tissue samples to generating sequencing libraries-can be accomplished within 5 d.
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Affiliation(s)
- Owen J Marshall
- The Gurdon Institute, University of Cambridge, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Tony D Southall
- The Gurdon Institute, University of Cambridge, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Seth W Cheetham
- The Gurdon Institute, University of Cambridge, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Andrea H Brand
- The Gurdon Institute, University of Cambridge, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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10
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Vogel MJ, Peric-Hupkes D, van Steensel B. Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing. Nat Protoc 2016; 2:1467-78. [PMID: 17545983 DOI: 10.1038/nprot.2007.148] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This protocol is an extension to: Nat. Protoc. 2, 1467-1478 (2007); doi:10.1038/nprot.2007.148; published online 7 June 2007The ability to profile transcription and chromatin binding in a cell-type-specific manner is a powerful aid to understanding cell-fate specification and cellular function in multicellular organisms. We recently developed targeted DamID (TaDa) to enable genome-wide, cell-type-specific profiling of DNA- and chromatin-binding proteins in vivo without cell isolation. As a protocol extension, this article describes substantial modifications to an existing protocol, and it offers additional applications. TaDa builds upon DamID, a technique for detecting genome-wide DNA-binding profiles of proteins, by coupling it with the GAL4 system in Drosophila to enable both temporal and spatial resolution. TaDa ensures that Dam-fusion proteins are expressed at very low levels, thus avoiding toxicity and potential artifacts from overexpression. The modifications to the core DamID technique presented here also increase the speed of sample processing and throughput, and adapt the method to next-generation sequencing technology. TaDa is robust, reproducible and highly sensitive. Compared with other methods for cell-type-specific profiling, the technique requires no cell-sorting, cross-linking or antisera, and binding profiles can be generated from as few as 10,000 total induced cells. By profiling the genome-wide binding of RNA polymerase II (Pol II), TaDa can also identify transcribed genes in a cell-type-specific manner. Here we describe a detailed protocol for carrying out TaDa experiments and preparing the material for next-generation sequencing. Although we developed TaDa in Drosophila, it should be easily adapted to other organisms with an inducible expression system. Once transgenic animals are obtained, the entire experimental procedure-from collecting tissue samples to generating sequencing libraries-can be accomplished within 5 d.
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Affiliation(s)
- Maartje J Vogel
- Division of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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11
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Lim RSM, Osato M, Kai T. Isolation of Undifferentiated Female Germline Cells from Adult Drosophila Ovaries. ACTA ACUST UNITED AC 2015; 34:2E.3.1-2E.3.15. [PMID: 26237568 DOI: 10.1002/9780470151808.sc02e03s34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This unit describes a method for isolating undifferentiated, stem cell-like germline cells from adult Drosophila ovaries. Here, we demonstrate that this population of cells can be effectively purified from hand-dissected ovaries in considerably large quantities. Tumor ovaries with expanded populations of undifferentiated germline cells are first removed from fly abdomens and dissociated into a cell suspension with the aid of protease treatment. The target cells, which express Vasa-green fluorescent protein (GFP) fusion protein under the control of the germline-specific vasa promoter, are specifically selected from the suspension via fluorescence-activated cell sorting (FACS). These protocols can be adapted to isolate other cell types from fly ovaries, such as somatic follicle cells or escort cells, by driving GFP expression in the respective target cells.
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Affiliation(s)
- Robyn Su May Lim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Toshie Kai
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
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12
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Abstract
The study of Drosophila oogenesis provides invaluable information about signaling pathway regulation and cell cycle programming. During Drosophila oogenesis, a string of egg chambers in each ovariole progressively develops toward maturity. Egg chamber development consists of 14 stages. From stage 1 to stage 6 (mitotic cycle), main-body follicle cells undergo mitotic divisions. From stage 7 to stage 10a (endocycle), follicle cells cease mitosis but continue three rounds of endoreduplication. From stage 10b to stage 13 (gene amplification), instead of whole genome duplication, follicle cells selectively amplify specific genomic regions, mostly for chorion production. So far, Drosophila oogenesis is one of the most well studied model systems used to understand cell cycle switches, which furthers our knowledge about cell cycle control machinery and sheds new light on potential cancer treatments. Here, we give a brief summary of cell cycle switches, the associated signaling pathways and factors, and the detailed experimental procedures used to study the cell cycle switches.
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Affiliation(s)
- Dongyu Jia
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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13
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Matts JA, Sytnikova Y, Chirn GW, Igloi GL, Lau NC. Small RNA library construction from minute biological samples. Methods Mol Biol 2014; 1093:123-36. [PMID: 24178561 DOI: 10.1007/978-1-62703-694-8_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Increasingly, the discovery and characterization of small regulatory RNAs from a variety of organisms have all required deep-sequencing methodologies. However, the crux to successful deep-sequencing analysis depends upon optimal construction of a cDNA library compatible for the high-throughput sequencing platform. Challenges to small RNA library constructions arise when dealing with minute tissue samples because certain structural RNA fragments can dominate and mask the desired characterization of regulatory small RNAs like microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs), and Piwi-interacting RNAs (piRNAs). Here, we describe methods that improve the chances of constructing a successful library from small RNAs isolated from minute tissues such as enriched follicle cells from the Drosophila ovarium. Because the ribosomal RNA (rRNA) fragments are frequently the major contaminants in small RNA preparations from minute amounts of tissue, we demonstrate the utility of antisense oligonucleotide depletion and an acryloylaminophenylboronic acid (APB) polyacrylamide gel system for separating the abundant 2S rRNA in Drosophila from endo-siRNAs and piRNAs. Finally, our methodology generates libraries amenable to multiplex sequencing on the Illumina Hi-Seq platform.
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Affiliation(s)
- Jessica A Matts
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA, USA
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14
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Hudson AM, Cooley L. Methods for studying oogenesis. Methods 2014; 68:207-17. [PMID: 24440745 DOI: 10.1016/j.ymeth.2014.01.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 01/02/2014] [Indexed: 12/31/2022] Open
Abstract
Drosophila oogenesis is an excellent system for the study of developmental cell biology. Active areas of research include stem cell maintenance, gamete development, pattern formation, cytoskeletal regulation, intercellular communication, intercellular transport, cell polarity, cell migration, cell death, morphogenesis, cell cycle control, and many more. The large size and relatively simple organization of egg chambers make them ideally suited for microscopy of both living and fixed whole mount tissue. A wide range of tools is available for oogenesis research. Newly available shRNA transgenic lines provide an alternative to classic loss-of-function F2 screens and clonal screens. Gene expression can be specifically controlled in either germline or somatic cells using the Gal4/UAS system. Protein trap lines provide fluorescent tags of proteins expressed at endogenous levels for live imaging and screening backgrounds. This review provides information on many available reagents and key methods for research in oogenesis.
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Affiliation(s)
- Andrew M Hudson
- Department of Genetics, Yale University School of Medicine, United States
| | - Lynn Cooley
- Department of Genetics, Yale University School of Medicine, United States; Department of Cell Biology, Yale University School of Medicine, United States; Department of Molecular, Cellular & Developmental Biology, Yale University, United States.
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15
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Southall TD, Gold KS, Egger B, Davidson CM, Caygill EE, Marshall OJ, Brand AH. Cell-type-specific profiling of gene expression and chromatin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells. Dev Cell 2013; 26:101-12. [PMID: 23792147 PMCID: PMC3714590 DOI: 10.1016/j.devcel.2013.05.020] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/20/2013] [Accepted: 05/24/2013] [Indexed: 12/20/2022]
Abstract
Cell-type-specific transcriptional profiling often requires the isolation of specific cell types from complex tissues. We have developed “TaDa,” a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation, or affinity purification. The method is simple, sensitive, highly reproducible, and transferable to any model system. We show that TaDa can be used to identify transcribed genes in a cell-type-specific manner with considerable temporal precision, enabling the identification of differential gene expression between neuroblasts and the neuroepithelial cells from which they derive. We profile the genome-wide binding of RNA polymerase II in these adjacent, clonally related stem cells within intact Drosophila brains. Our data reveal expression of specific metabolic genes in neuroepithelial cells, but not in neuroblasts, and highlight gene regulatory networks that may pattern neural stem cell fates. TaDa is a method for cell-type-specific profiling of chromatin binding proteins TaDa does not require cell sorting, fixation, or affinity purification This is a highly sensitive and robust technique for transcriptional profiling We report differential RNA Pol II binding in clonally related stem cells
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Affiliation(s)
- Tony D Southall
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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16
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Tamori Y, Deng WM. Tissue repair through cell competition and compensatory cellular hypertrophy in postmitotic epithelia. Dev Cell 2013; 25:350-63. [PMID: 23685249 DOI: 10.1016/j.devcel.2013.04.013] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 02/19/2013] [Accepted: 04/23/2013] [Indexed: 12/14/2022]
Abstract
In multicellular organisms, tissue integrity and organ size are maintained through removal of aberrant or damaged cells and compensatory proliferation. Little is known, however, about this homeostasis system in postmitotic tissues, where tissue-intrinsic genetic programs constrain cell division and new cells no longer arise from stem cells. Here we show that, in postmitotic Drosophila follicular epithelia, aberrant but viable cells are eliminated through cell competition, and the resulting loss of local tissue volume triggers sporadic cellular hypertrophy to repair the tissue. This "compensatory cellular hypertrophy" is implemented by acceleration of the endocycle, a variant cell cycle composed of DNA synthesis and gap phases without mitosis, dependent on activation of the insulin/IGF-like signaling pathway. These results reveal a remarkable homeostatic mechanism in postmitotic epithelia that ensures not only elimination of aberrant cells through cell competition but also proper organ-size control that involves compensatory cellular hypertrophy induced by physical parameters.
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Affiliation(s)
- Yoichiro Tamori
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
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17
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Akkouche A, Grentzinger T, Fablet M, Armenise C, Burlet N, Braman V, Chambeyron S, Vieira C. Maternally deposited germline piRNAs silence the tirant retrotransposon in somatic cells. EMBO Rep 2013; 14:458-64. [PMID: 23559065 DOI: 10.1038/embor.2013.38] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 02/27/2013] [Accepted: 03/01/2013] [Indexed: 01/17/2023] Open
Abstract
Transposable elements (TEs), whose propagation can result in severe damage to the host genome, are silenced in the animal gonad by Piwi-interacting RNAs (piRNAs). piRNAs produced in the ovaries are deposited in the embryonic germline and initiate TE repression in the germline progeny. Whether the maternally transmitted piRNAs play a role in the silencing of somatic TEs is however unknown. Here we show that maternally transmitted piRNAs from the tirant retrotransposon in Drosophila are required for the somatic silencing of the TE and correlate with an increase in histone H3K9 trimethylation an active tirant copy.
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Affiliation(s)
- Abdou Akkouche
- Université de Lyon, Université Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
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18
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Following the 'tracks': Tramtrack69 regulates epithelial tube expansion in the Drosophila ovary through Paxillin, Dynamin, and the homeobox protein Mirror. Dev Biol 2013; 378:154-69. [PMID: 23545328 DOI: 10.1016/j.ydbio.2013.03.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 03/05/2013] [Accepted: 03/16/2013] [Indexed: 11/21/2022]
Abstract
Epithelial tubes are the infrastructure for organs and tissues, and tube morphogenesis requires precise orchestration of cell signaling, shape, migration, and adhesion. Follicle cells in the Drosophila ovary form a pair of epithelial tubes whose lumens act as molds for the eggshell respiratory filaments, or dorsal appendages (DAs). DA formation is a robust and accessible model for studying the patterning, formation, and expansion of epithelial tubes. Tramtrack69 (TTK69), a transcription factor that exhibits a variable embryonic DNA-binding preference, controls DA lumen volume and shape by promoting tube expansion; the tramtrack mutation twin peaks (ttk(twk)) reduces TTK69 levels late in oogenesis, inhibiting this expansion. Microarray analysis of wild-type and ttk(twk) ovaries, followed by in situ hybridization and RNAi of candidate genes, identified the Phospholipase B-like protein Lamina ancestor (LAMA), the scaffold protein Paxillin, the endocytotic regulator Shibire (Dynamin), and the homeodomain transcription factor Mirror, as TTK69 effectors of DA-tube expansion. These genes displayed enriched expression in DA-tube cells, except lama, which was expressed in all follicle cells. All four genes showed reduced expression in ttk(twk) mutants and exhibited RNAi phenotypes that were enhanced in a ttk(twk)/+ background, indicating ttk(twk) genetic interactions. Although previous studies show that Mirror patterns the follicular epithelium prior to DA tubulogenesis, we show that Mirror has an independent, novel role in tube expansion, involving positive regulation of Paxillin. Thus, characterization of ttk(twk)-differentially expressed genes expands the network of TTK69 effectors, identifies novel epithelial tube-expansion regulators, and significantly advances our understanding of this vital developmental process.
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19
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Davis MB, Li T. Genomic analysis of the ecdysone steroid signal at metamorphosis onset using ecdysoneless and EcRnullDrosophila melanogaster mutants. Genes Genomics 2013; 35:21-46. [PMID: 23482860 PMCID: PMC3585846 DOI: 10.1007/s13258-013-0061-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 07/23/2012] [Indexed: 12/13/2022]
Abstract
Steroid hormone gene regulation is often depicted as a linear transduction of the signal, from molecule release to the gene level, by activation of a receptor protein after being bound by its steroid ligand. Such an action would require that the hormone be present and bound to the receptor in order to have target gene response. Here, we present data that presents a novel perspective of hormone gene regulation, where the hormone molecule and its receptor have exclusive target gene regulation function, in addition to the traditional direct target genes. Our study is the first genome-wide analysis of conditional mutants simultaneously modeling the steroid and steroid receptor gene expression regulation. We have integrated classical genetic mutant experiments with functional genomics techniques in the Drosophila melanogaster model organism, where we interrogate the 20-hydroxyecdysone signaling response at the onset of metamorphosis. Our novel catalog of ecdysone target genes illustrates the separable transcriptional responses among the hormone, the pre-hormone receptor and the post-hormone receptor. We successfully detected traditional ecdysone target genes as common targets and also identified novel sets of target genes which where exclusive to each mutant condition. Around 12 % of the genome responds to the ecdysone hormone signal at the onset of metamorphosis and over half of these are independent of the receptor. In addition, a significant portion of receptor regulated genes are differentially regulated by the receptor, depending on its ligand state. Gene ontology enrichment analyses confirm known ecdysone regulated biological functions and also validate implicated pathways that have been indirectly associated with ecdysone signaling.
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Affiliation(s)
- Melissa B Davis
- Department of Genetics, Coverdell Biomedical Research Center, University of Georgia, 500 DW Brooks Dr S 270C, Athens, GA 30602 USA
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20
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Lim RSM, Osato M, Kai T. Isolation of undifferentiated female germline cells from adult Drosophila ovaries. ACTA ACUST UNITED AC 2013; Chapter 2:Unit2E.3. [PMID: 22872426 DOI: 10.1002/9780470151808.sc02e03s22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This unit describes a method for isolating undifferentiated, stem cell-like germline cells from adult Drosophila ovaries. Here, we demonstrate that this population of cells can be effectively purified from hand-dissected ovaries in considerably large quantities. Tumor ovaries with expanded populations of undifferentiated germline cells are first removed from fly abdomens and dissociated into a cell suspension with the aid of protease treatment. The target cells, which express Vasa-green fluorescent protein (GFP) fusion protein under the control of the germline-specific vasa promoter, are specifically selected from the suspension via fluorescence-activated cell sorting (FACS). These protocols can be adapted to isolate other cell types from fly ovaries, such as somatic follicle cells or escort cells, by driving GFP expression in the respective target cells.
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Affiliation(s)
- Robyn Su May Lim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore
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21
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Asprer J. An excitingly predictable 'omic future. Development 2012; 139:3675-6. [DOI: 10.1242/dev.088450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Joanna Asprer
- Life Technologies, 5781 Van Allen Way, Carlsbad, CA 92008, USA
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Berger C, Harzer H, Burkard T, Steinmann J, van der Horst S, Laurenson AS, Novatchkova M, Reichert H, Knoblich J. FACS purification and transcriptome analysis of drosophila neural stem cells reveals a role for Klumpfuss in self-renewal. Cell Rep 2012; 2:407-18. [PMID: 22884370 PMCID: PMC3828055 DOI: 10.1016/j.celrep.2012.07.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 06/27/2012] [Accepted: 07/23/2012] [Indexed: 12/05/2022] Open
Abstract
Drosophila neuroblasts (NBs) have emerged as a model for stem cell biology that is ideal for genetic analysis but is limited by the lack of cell-type-specific gene expression data. Here, we describe a method for isolating large numbers of pure NBs and differentiating neurons that retain both cell-cycle and lineage characteristics. We determine transcriptional profiles by mRNA sequencing and identify 28 predicted NB-specific transcription factors that can be arranged in a network containing hubs for Notch signaling, growth control, and chromatin regulation. Overexpression and RNA interference for these factors identify Klumpfuss as a regulator of self-renewal. We show that loss of Klumpfuss function causes premature differentiation and that overexpression results in the formation of transplantable brain tumors. Our data represent a valuable resource for investigating Drosophila developmental neurobiology, and the described method can be applied to other invertebrate stem cell lineages as well.
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Affiliation(s)
- Christian Berger
- Institute of Molecular Biotechnology of the Austrian Academy of Science, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Heike Harzer
- Institute of Molecular Biotechnology of the Austrian Academy of Science, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Thomas R. Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Jonas Steinmann
- Institute of Molecular Biotechnology of the Austrian Academy of Science, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Suzanne van der Horst
- Institute of Molecular Biotechnology of the Austrian Academy of Science, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | | | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Science, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Heinrich Reichert
- University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Juergen A. Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Corresponding author
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23
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Cash AC, Andrews J. Fine scale analysis of gene expression in Drosophila melanogaster gonads reveals Programmed cell death 4 promotes the differentiation of female germline stem cells. BMC DEVELOPMENTAL BIOLOGY 2012; 12:4. [PMID: 22252300 PMCID: PMC3322342 DOI: 10.1186/1471-213x-12-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/17/2012] [Indexed: 11/10/2022]
Abstract
Background Germline stem cells (GSCs) are present in the gonads of Drosophila females and males, and their proper maintenance, as well as their correct differentiation, is essential for fertility and fecundity. The molecular characterization of factors involved in maintenance and differentiation is a major goal both in Drosophila and stem cell research. While genetic studies have identified many of these key factors, the use of genome-wide expression studies holds the potential to greatly increase our knowledge of these pathways. Results Here we report a genome-wide expression study that uses laser cutting microdissection to isolate germline stem cells, somatic niche cells, and early differentiating germ cells from female and male gonads. Analysis of this data, in association with two previously published genome-wide GSC data sets, revealed sets of candidate genes as putatively expressed in specific cell populations. Investigation of one of these genes, CG10990 the Drosophila ortholog of mammalian Programmed cell death 4 (Pdcd4), reveals expression in female and male germline stem cells and early differentiating daughter cells. Functional analysis demonstrates that while it is not essential for oogenesis or spermatogenesis, it does function to promote the differentiation of GSCs in females. Furthermore, in females, Pdcd4 genetically interacts with the key differentiation gene bag of marbles (bam) and the stem cell renewal factor eIF4A, suggesting a possible pathway for its function in differentiation. Conclusions We propose that Pdcd4 promotes the differentiation of GSC daughter cells by relieving the eIF4A-mediated inhibition of Bam.
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Affiliation(s)
- Amy C Cash
- Department of Biology, Indiana University, Myers Hall, 915 East Third St,, Bloomington, IN 47403, USA
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24
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Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression. Genes Dev 2011; 25:1384-98. [PMID: 21724831 DOI: 10.1101/gad.2043111] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In metazoans, how replication origins are specified and subsequently activated is not well understood. Drosophila amplicons in follicle cells (DAFCs) are genomic regions that undergo rereplication to increase DNA copy number. We identified all DAFCs by comparative genomic hybridization, uncovering two new amplicons in addition to four known previously. The complete identification of all DAFCs enabled us to investigate these in vivo replicons with respect to parameters of transcription, localization of the origin recognition complex (ORC), and histone acetylation, yielding important insights into gene amplification as a metazoan replication model. Significantly, ORC is bound across domains spanning 10 or more kilobases at the DAFC rather than at a specific site. Additionally, ORC is bound at many regions that do not undergo amplification, and, in contrast to cell culture, these regions do not correlate with high gene expression. As a developmental strategy, gene amplification is not the predominant means of achieving high expression levels, even in cells capable of amplification. Intriguingly, we found that, in some strains, a new amplicon, DAFC-22B, does not amplify, a consequence of distant repression of ORC binding and origin activation. This repression is alleviated when a fragment containing the origin is placed in different genomic contexts.
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25
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Priya TJ, Li F, Zhang J, Yang C, Xiang J. Molecular characterization of an ecdysone inducible gene E75 of Chinese shrimp Fenneropenaeus chinensis and elucidation of its role in molting by RNA interference. Comp Biochem Physiol B Biochem Mol Biol 2010; 156:149-57. [DOI: 10.1016/j.cbpb.2010.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2009] [Revised: 02/06/2010] [Accepted: 02/08/2010] [Indexed: 11/24/2022]
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Pemberton TJ, Kay JE. Identification and comparative analysis of the peptidyl-prolyl cis/trans isomerase repertoires of H. sapiens, D. melanogaster, C. elegans, S. cerevisiae and Sz. pombe. Comp Funct Genomics 2010; 6:277-300. [PMID: 18629211 PMCID: PMC2447506 DOI: 10.1002/cfg.482] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 05/01/2005] [Accepted: 05/26/2005] [Indexed: 11/11/2022] Open
Abstract
The peptidyl-prolyl cis/trans isomerase (PPIase) class of proteins comprises three
member families that are found throughout nature and are present in all the major
compartments of the cell. Their numbers appear to be linked to the number of genes in
their respective genomes, although we have found the human repertoire to be smaller
than expected due to a reduced cyclophilin repertoire. We show here that whilst the
members of the cyclophilin family (which are predominantly found in the nucleus
and cytoplasm) and the parvulin family (which are predominantly nuclear) are
largely conserved between different repertoires, the FKBPs (which are predominantly
found in the cytoplasm and endoplasmic reticulum) are not. It therefore appears
that the cyclophilins and parvulins have evolved to perform conserved functions,
while the FKBPs have evolved to fill ever-changing niches within the constantly
evolving organisms. Many orthologous subgroups within the different PPIase families
appear to have evolved from a distinct common ancestor, whereas others, such as the
mitochondrial cyclophilins, appear to have evolved independently of one another. We
have also identified a novel parvulin within Drosophila melanogaster that is unique to
the fruit fly, indicating a recent evolutionary emergence. Interestingly, the fission yeast
repertoire, which contains no unique cyclophilins and parvulins, shares no PPIases
solely with the budding yeast but it does share a majority with the higher eukaryotes
in this study, unlike the budding yeast. It therefore appears that, in comparison with
Schizosaccharomyces pombe, Saccharomyces cerevisiae is a poor representation of the
higher eukaryotes for the study of PPIases.
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Affiliation(s)
- Trevor J Pemberton
- The Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton ,East Sussex BN1 9PX, United Kingdom.
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27
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Anzenbacher, Jr. P, Lubal P, Buček P, Palacios MA, Kozelkova ME. A practical approach to optical cross-reactive sensor arrays. Chem Soc Rev 2010; 39:3954-79. [DOI: 10.1039/b926220m] [Citation(s) in RCA: 272] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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28
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Stuckenholz C, Lu L, Thakur P, Kaminski N, Bahary N. FACS-assisted microarray profiling implicates novel genes and pathways in zebrafish gastrointestinal tract development. Gastroenterology 2009; 137:1321-32. [PMID: 19563808 PMCID: PMC2785077 DOI: 10.1053/j.gastro.2009.06.050] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 06/02/2009] [Accepted: 06/18/2009] [Indexed: 01/26/2023]
Abstract
BACKGROUND & AIMS The zebrafish Danio rerio is an excellent model system for mammalian gastrointestinal development. To identify differentially regulated genes important in gastrointestinal organogenesis, we profiled the transcriptome of the zebrafish developing gastrointestinal tract. METHODS Embryos from a transgenic zebrafish line expressing green fluorescent protein (GFP) in the developing intestine, liver, and pancreas were dissociated at 4 developmental time points, their cells sorted based on GFP expression with fluorescence-activated cell sorting (FACS), and analyzed with microarrays. To improve our analysis, we annotated the Affymetrix Zebrafish GeneChip with human orthologs. RESULTS Transcriptional profiling showed significant differences between GFP(+) and GFP(-) cells. Up-regulated genes and pathways were consistent with mammalian gastrointestinal development, such as hepatic nuclear factor gene networks and cancer. We implicate the phosphatidylinositol 3 kinase (PI3K) pathway and show that inhibition with LY294002 causes gastrointestinal defects in zebrafish. We identified novel genes, such as the microRNAs miR-217 and miR-122, the tight junction protein claudin c, the gene fam136a, and a zebrafish tetraspanin. Novel pathways include genes containing a putative transcription factor binding sequence, GGAANCGGAANY, and a nucleolar gene network. The zebrafish microarrays also identify a set of 32 genes that may mediate the effects of gain of chromosome arm 8q in human colon, liver, and pancreatic cancers. CONCLUSIONS We successfully combine FACS and microarray profiling to follow organogenesis throughout development. These experiments identify novel genes and pathways that probably play a role in mammalian gastrointestinal development and are potential targets for therapeutic intervention in the management of gastrointestinal disease and cancer.
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Affiliation(s)
- Carsten Stuckenholz
- Department of Medicine, Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Lili Lu
- Department of Medicine, Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Prakash Thakur
- Department of Medicine, Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Naftali Kaminski
- Dorothy P. & Richard P. Simmons Center for Interstitial Lung Disease, Pulmonary, Allergy and Critical Care Medicine University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Nathan Bahary
- Department of Medicine, Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania,Department of Microbiology and Molecular Genetics University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
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Abstract
The molting process in arthropods is regulated by steroid hormones acting via nuclear receptor proteins. The most common molting hormone is the ecdysteroid, 20-hydroxyecdysone. The receptors of 20-hydroxyecdysone have also been identified in many arthropod species, and the amino acid sequences determined. The functional molting hormone receptors consist of two members of the nuclear receptor superfamily, namely the ecdysone receptor and the ultraspiracle, although the ecdysone receptor may be functional, in some instances, without the ultraspiracle. Generally, the ecdysone receptor/ultraspiracle heterodimer binds to a number of ecdysone response elements, sequence motifs that reside in the promoter of various ecdysteroid-responsive genes. In the ensuing transcriptional induction, the ecdysone receptor/ultraspiracle complex binds to 20-hydroxyecdysone or to a cognate ligand that, in turn, leads to the release of a corepressor and the recruitment of coactivators. 3D structures of the ligand-binding domains of the ecdysone receptor and the ultraspiracle have been solved for a few insect species. Ecdysone agonists bind to ecdysone receptors specifically, and ligand-ecdysone receptor binding is enhanced in the presence of the ultraspiracle in insects. The basic mode of ecdysteroid receptor action is highly conserved, but substantial functional differences exist among the receptors of individual species. Even though the transcriptional effects are apparently similar for ecdysteroids and nonsteroidal compounds such as diacylhydrazines, the binding shapes are different between them. The compounds having the strongest binding affinity to receptors ordinarily have strong molting hormone activity. The ability of the ecdysone receptor/ultraspiracle complex to manifest the effects of small lipophilic agonists has led to their use as gene switches for medical and agricultural applications.
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Affiliation(s)
- Yoshiaki Nakagawa
- Division of Applied Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-Ku, Kyoto 606-8502, Japan.
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van de Hoef DL, Hughes J, Livne-Bar I, Garza D, Konsolaki M, Boulianne GL. Identifying genes that interact with Drosophila presenilin and amyloid precursor protein. Genesis 2009; 47:246-60. [PMID: 19241393 DOI: 10.1002/dvg.20485] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The gamma-secretase complex is involved in cleaving transmembrane proteins such as Notch and one of the genes targeted in Alzheimer's disease known as amyloid precursor protein (APP). Presenilins function within the catalytic core of gamma-secretase, and mutated forms of presenilins were identified as causative factors in familial Alzheimer's disease. Recent studies show that in addition to Notch and APP, numerous signal transduction pathways are modulated by presenilins, including intracellular calcium signaling. Thus, presenilins appear to have diverse roles. To further understand presenilin function, we searched for Presenilin-interacting genes in Drosophila by performing a genetic modifier screen for enhancers and suppressors of Presenilin-dependent Notch-related phenotypes. We identified 177 modifiers, including known members of the Notch pathway and genes involved in intracellular calcium homeostasis. We further demonstrate that 53 of these modifiers genetically interacted with APP. Characterization of these genes may provide valuable insights into Presenilin function in development and disease.
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Affiliation(s)
- Diana L van de Hoef
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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31
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Zhang Z, Mascheri N, Dharmakumar R, Fan Z, Paunesku T, Woloschak G, Li D. Superparamagnetic iron oxide nanoparticle-labeled cells as an effective vehicle for tracking the GFP gene marker using magnetic resonance imaging. Cytotherapy 2009; 11:43-51. [PMID: 18956269 DOI: 10.1080/14653240802420243] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Detection of a gene using magnetic resonance imaging (MRI) is hindered by the magnetic resonance (MR) targeting gene technique. Therefore it may be advantageous to image gene-expressing cells labeled with superparamagnetic iron oxide (SPIO) nanoparticles by MRI. METHODS The GFP-R3230Ac (GFP) cell line was incubated for 24 h using SPIO nanoparticles at a concentration of 20 microg Fe/mL. Cell samples were prepared for iron content analysis and cell function evaluation. The labeled cells were imaged using fluorescent microscopy and MRI. RESULTS SPIO was used to label GFP cells effectively, with no effects on cell function and GFP expression. Iron-loaded GFP cells were successfully imaged with both fluorescent microscopy and T2*-weighted MRI. Prussian blue staining showed intracellular iron accumulation in the cells. All cells were labeled (100% labeling efficiency). The average iron content per cell was 4.75+/-0.11 pg Fe/cell (P<0.05 versus control). DISCUSSION This study demonstrates that the GFP expression of cells is not altered by the SPIO labeling process. SPIO-labeled GFP cells can be visualized by MRI; therefore, GFP, a gene marker, was tracked indirectly with the SPIO-loaded cells using MRI. The technique holds promise for monitoring the temporal and spatial migration of cells with a gene marker and enhancing the understanding of cell- and gene-based therapeutic strategies.
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Affiliation(s)
- Z Zhang
- Department of Radiology, Northwestern University, Chicago, Illinois 60611, USA
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32
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Cellular responses to endoplasmic reticulum stress and apoptosis. Apoptosis 2009; 14:996-1007. [PMID: 19360473 DOI: 10.1007/s10495-009-0341-y] [Citation(s) in RCA: 247] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 03/18/2009] [Indexed: 01/08/2023]
Abstract
The endoplasmic reticulum (ER) is the cell organelle where secretory and membrane proteins are synthesized and folded. Correctly folded proteins exit the ER and are transported to the Golgi and other destinations within the cell, but proteins that fail to fold properly-misfolded proteins-are retained in the ER and their accumulation may constitute a form of stress to the cell-ER stress. Several signaling pathways, collectively known as unfolded protein response (UPR), have evolved to detect the accumulation of misfolded proteins in the ER and activate a cellular response that attempts to maintain homeostasis and a normal flux of proteins in the ER. In certain severe situations of ER stress, however, the protective mechanisms activated by the UPR are not sufficient to restore normal ER function and cells die by apoptosis. Most research on the UPR used yeast or mammalian model systems and only recently Drosophila has emerged as a system to study the molecular and cellular mechanisms of the UPR. Here, we review recent advances in Drosophila UPR research, in the broad context of mammalian and yeast literature.
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Yakoby N, Bristow CA, Gong D, Schafer X, Lembong J, Zartman JJ, Halfon MS, Schüpbach T, Shvartsman SY. A combinatorial code for pattern formation in Drosophila oogenesis. Dev Cell 2008; 15:725-37. [PMID: 19000837 PMCID: PMC2822874 DOI: 10.1016/j.devcel.2008.09.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 08/27/2008] [Accepted: 09/17/2008] [Indexed: 10/21/2022]
Abstract
Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.
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Affiliation(s)
- Nir Yakoby
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
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Sun J, Smith L, Armento A, Deng WM. Regulation of the endocycle/gene amplification switch by Notch and ecdysone signaling. ACTA ACUST UNITED AC 2008; 182:885-96. [PMID: 18779369 PMCID: PMC2528591 DOI: 10.1083/jcb.200802084] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The developmental signals that regulate the switch from genome-wide DNA replication to site-specific amplification remain largely unknown. Drosophila melanogaster epithelial follicle cells, which begin synchronized chorion gene amplification after three rounds of endocycle, provide an excellent model for study of the endocycle/gene amplification (E/A) switch. Here, we report that down-regulation of Notch signaling and activation of ecdysone receptor (EcR) are required for the E/A switch in these cells. Extended Notch activity suppresses EcR activation and prevents exit from the endocycle. Tramtrack (Ttk), a zinc-finger protein essential for the switch, is regulated negatively by Notch and positively by EcR. Ttk overexpression stops endoreplication prematurely and alleviates the endocycle exit defect caused by extended Notch activity or removal of EcR function. Our results reveal a developmental pathway that includes down-regulation of Notch, activation of the EcR, up-regulation of Ttk to execute the E/A switch, and, for the first time, the genetic interaction between Notch and ecdysone signaling in regulation of cell cycle programs and differentiation.
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Affiliation(s)
- Jianjun Sun
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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The Drosophila homolog of human tumor suppressor TSC-22 promotes cellular growth, proliferation, and survival. Proc Natl Acad Sci U S A 2008; 105:5414-9. [PMID: 18375761 DOI: 10.1073/pnas.0800945105] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
TSC22D1, which encodes transforming growth factor beta-stimulated clone 22 (TSC-22), is thought to be a tumor suppressor because its expression is lost in many glioblastoma, salivary gland, and prostate cancers. TSC-22 is the founding member of the TSC-22/DIP/Bun family of leucine zipper transcription factors; its functions have not been investigated in a multicellular environment. Genetic studies in the model organism Drosophila melanogaster often provide fundamental insights into mechanisms disrupted in carcinogenesis, because of the strong evolutionary conservation of molecular mechanisms between flies and humans. Whereas humans and mice have four TSC-22 domain genes with numerous isoforms, Drosophila has only one TSC-22 domain gene, bunched (bun), which encodes both large and small protein isoforms. Surprisingly, Drosophila Bun proteins promote cellular growth and proliferation in ovarian follicle cells. Loss of both large isoforms has the strongest phenotypes, including increased apoptosis. Cultured S2 cells depleted for large Bun isoforms show increased apoptosis and less frequent cell division, with decreased cell size. Altogether, these data indicate that Drosophila TSC-22/DIP/Bun proteins are necessary for cellular growth, proliferation, and survival both in culture and in an epithelial context. Previous work demonstrated that bun prevents recruitment of epithelial cells to a migratory fate and, thus, maintains epithelial organization. We speculate that reduced TSC22D1 expression generally reduces cellular fitness and only contributes to carcinogenesis in specific tissue environments.
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Abstract
Flow cytometry is a powerful technique that allows the researcher to measure fluorescence emissions on a per-cell basis, at multiple wavelengths, in populations of thousands of cells. In this chapter, we outline the use of flow cytometry for the analysis of cells from Drosophila's imaginal discs, which are developing epithelial organs that give rise to, but not exclusively, the wings, eyes, and legs of the adult. A variety of classical and transgenic genetic methods can be used to mark cells (e.g., mutant, or overexpressing a gene, or in a particular compartment) in these organs with green fluorescent protein (GFP), which is readily detected by flow cytometry. After dissecting an organ out of the animal and dissociating it into single cells, a flow cytometer can be used to assay the size, DNA content, and other parameters in GFP-marked experimental cells as well as GFP-negative control cells from the same sample. Specific marked cell populations can also be physically sorted, and then used in diverse biochemical assays. This chapter includes protocols for isolation and dissociation of larval imaginal discs and pupal appendages for flow cytometry, and as well as for flow cytometric acquisition and analysis. In addition, we present protocols for performing flow cytometry on fixed or live-cultured Drosophila S2 cells.
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Chapter 19 Cell Type–Specific Analysis of mRNA Synthesis and Decay In Vivo with Uracil Phosphoribosyltransferase and 4‐thiouracil. Methods Enzymol 2008; 448:379-406. [DOI: 10.1016/s0076-6879(08)02619-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Achilles J, Stahl F, Harms H, Müller S. Isolation of intact RNA from cytometrically sorted Saccharomyces cerevisiae for the analysis of intrapopulation diversity of gene expression. Nat Protoc 2007; 2:2203-11. [PMID: 17853877 DOI: 10.1038/nprot.2007.322] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Characterizing and understanding the functional heterogeneity in a given population on the cellular and molecular level is a great challenge in microbiology. Each microorganism contributes differently to the overall performance of the community and responds differently to changing microenvironmental conditions. Here, we present a method for isolation of intact RNA out of small subpopulations of live Saccharomyces cerevisiae cells for differential gene expression analysis. The protocol includes fluorescence staining, flow cytometric analysis and sorting of live yeast cells, subsequent isolation of RNA from the resulting subpopulations and finally RNA quantification and integrity check. The isolated RNA can be transcribed into cDNA and successfully used for microarray analysis. This aids in relating molecular regulation processes within subpopulations with the dynamics and functioning of the entire population. The procedure can be accomplished in 2 d.
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Affiliation(s)
- Jeannette Achilles
- Department of Environmental Microbiology, UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
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Hackney JF, Pucci C, Naes E, Dobens L. Ras signaling modulates activity of the ecdysone receptor EcR during cell migration in the Drosophila ovary. Dev Dyn 2007; 236:1213-26. [PMID: 17436275 DOI: 10.1002/dvdy.21140] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ecdysone Receptor (EcR) mediates effects of the hormone ecdysone during larval molts, pupal metamorphosis, and adult female oogenesis. In the ovary, egg chamber formation requires interactions between the somatic follicle cell (FC) epithelium and the germ line nurse cell/oocyte cyst. Previous work has shown EcR is required in the germ line for egg chamber maturation, and here we examine EcR requirements in the FC at late stages of oogenesis. EcR protein is ubiquitous in the FC but its activity is restricted, visualized by activity of the "ligand sensor" hs-GAL4-EcR ligand binding domain fusion and EcRE-lacZ reporter gene expression. GAL4-EcR is activated in the FC by an ecdysone agonist and repressed by tissue-specific Ras GTPase signals. To determine the significance of restricted sites of EcR activity in the FC, we used targeted misexpression of the dominant negative EcR (EcR-DN) molecules EcR(F645A) and EcR(W650A). EcR-DN expression at stage 10 reduced EcRE-lacZ expression in the nurse cell FC and resulted in abnormal FC migrations, including aberrant centripetal migration and dorsal appendage tube formation, leading to the formation of cup-shaped eggs with shortened, branched dorsal appendages at stage 14. Clones of FC expressing EcR-DN displayed cell-autonomous increases in DE-cadherin expression and abnormal epithelial junction formation. EcR-DN expression caused thin eggshell phenotypes that correlated with both reduced levels of chorion gene expression and reduction in chorion gene amplification. Our results indicate that tissue-specific modulation of EcR activity by the Ras signaling pathway refines temporal ecdysone signals that regulate FC differentiation and cadherin-mediated epithelial cell shape changes.
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Affiliation(s)
- Jennifer F Hackney
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
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40
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Furriols M, Ventura G, Casanova J. Two distinct but convergent groups of cells trigger Torso receptor tyrosine kinase activation by independently expressing torso-like. Proc Natl Acad Sci U S A 2007; 104:11660-5. [PMID: 17595301 PMCID: PMC1913882 DOI: 10.1073/pnas.0700991104] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell fate determination is often the outcome of specific interactions between adjacent cells. However, cells frequently change positions during development, and thus signaling molecules might be synthesized far from their final site of action. Here, we analyze the regulation of the torso-like gene, which is required to trigger Torso receptor tyrosine kinase activation in the Drosophila embryo. Whereas torso is present in the oocyte, torso-like is expressed in the egg chamber, at the posterior follicle cells and in two separated groups of anterior cells, the border cells and the centripetal cells. We find that JAK/STAT signaling regulates torso-like expression in the posterior follicle cells and border cells but not in the centripetal cells, where torso-like is regulated by a different enhancer. The border and centripetal cells, which are originally apart, converge at the anterior end of the oocyte, and we find that both groups contribute to trigger Torso activation. Our results illustrate how independently acquired expression of a signaling molecule can constitute a mechanism by which distinct groups of cells act together in the activation of a signaling pathway.
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Affiliation(s)
- Marc Furriols
- Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Institut de Recerca Biomèdica de Barcelona, C/Josep Samitier 1-5, 08028 Barcelona, Spain
- *To whom correspondence may be addressed. E-mail: or
| | - Gemma Ventura
- Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Institut de Recerca Biomèdica de Barcelona, C/Josep Samitier 1-5, 08028 Barcelona, Spain
| | - Jordi Casanova
- Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Institut de Recerca Biomèdica de Barcelona, C/Josep Samitier 1-5, 08028 Barcelona, Spain
- *To whom correspondence may be addressed. E-mail: or
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Levine B, Jean-Francois M, Bernardi F, Gargiulo G, Dobens L. Notch signaling links interactions between the C/EBP homolog slow border cells and the GILZ homolog bunched during cell migration. Dev Biol 2007; 305:217-31. [PMID: 17383627 DOI: 10.1016/j.ydbio.2007.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 01/11/2007] [Accepted: 02/09/2007] [Indexed: 10/23/2022]
Abstract
In the follicle cell (FC) epithelium that surrounds the Drosophila egg, a complex set of cell signals specifies two cell fates that pattern the eggshell: the anterior centripetal FC that produce the operculum and the posterior columnar FC that produce the main body eggshell structure. We have previously shown that the long-range morphogen DPP represses the expression of the bunched (bun) gene in the anterior-most centripetal FC. bun, which encodes a homolog of vertebrate TSC-22/GILZ, in turn represses anterior gene expression and antagonizes Notch signaling to restrict centripetal FC fates in posterior cells. From a screen for novel targets of bun repression we have identified the C/EBP homolog slow border cells (slbo). At stage 10A, slbo expression overlaps bun in anterior FC; by stage 10B they repress each other's expression to establish a sharp slbo/bun expression boundary. The precise position of the slbo/bun expression boundary is sensitive to Notch signaling, which is required for both slbo activation and bun repression. As centripetal migration proceeds from stages 10B-14, slbo represses its own expression and both slbo loss-of-function mutations and overexpression approaches reveal that slbo is required to coordinate centripetal migration with nurse cell dumping. We propose that in anterior FC exposed to a Dpp morphogen gradient, high and low levels of slbo and bun, respectively, are established by modulation of Notch signaling to direct threshold cell fates. Interactions among Notch, slbo and bun resemble a conserved signaling cassette that regulates mammalian adipocyte differentiation.
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Affiliation(s)
- Benjamin Levine
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
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42
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Ibrahim SF, van den Engh G. Flow cytometry and cell sorting. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 106:19-39. [PMID: 17728993 DOI: 10.1007/10_2007_073] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Flow cytometry and cell sorting are well-established technologies in clinical diagnostics and biomedical research. Heterogeneous mixtures of cells are placed in suspension and passed single file across one or more laser interrogation points. Light signals emitted from the particles are collected and correlated to entities such as cell morphology, surface and intracellular protein expression, gene expression, and cellular physiology. Based on user-defined parameters, individual cells can then be diverted from the fluid stream and collected into viable, homogeneous fractions at exceptionally high speeds and a purity that approaches 100%. As such, the cell sorter becomes the launching point for numerous downstream studies. Flow cytometry is a cornerstone in clinical diagnostics, and cheaper, more versatile machines are finding their way into widespread and varied uses. In addition, advances in computing and optics have led to a new generation of flow cytometers capable of processing cells at orders of magnitudes faster than their predecessors, and with staggering degrees of complexity, making the cytometer a powerful discovery tool in biotechnology. This chapter will begin with a discussion of basic principles of flow cytometry and cell sorting, including a technical description of factors that contribute to the performance of these instruments. The remaining sections will then be divided into clinical- and research-based applications of flow cytometry and cell sorting, highlighting salient studies that illustrate the versatility of this indispensable technology.
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Affiliation(s)
- Sherrif F Ibrahim
- Department of Dermatology, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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43
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Poulton JS, Deng WM. Dystroglycan down-regulation links EGF receptor signaling and anterior-posterior polarity formation in the Drosophila oocyte. Proc Natl Acad Sci U S A 2006; 103:12775-80. [PMID: 16908845 PMCID: PMC1568923 DOI: 10.1073/pnas.0603817103] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Anterior-posterior axis formation in the Drosophila oocyte requires activation of the EGF receptor (EGFR) pathway in the posterior follicle cells (PFC), where it also redirects them from the default anterior to the posterior cell fate. The relationship between EGFR activity in the PFC and oocyte polarity is unclear, because no EGFR-induced changes in the PFC have been observed that subsequently affect oocyte polarity. Here, we show that an extracellular matrix receptor, Dystroglycan, is down-regulated in the PFC by EGFR signaling, and this down-regulation is necessary for proper localization of posterior polarity determinants in the oocyte. Failure to down-regulate Dystroglycan disrupts apicobasal polarity in the PFC, which includes mislocalization of the extracellular matrix component Laminin. Our data indicate that Dystroglycan links EGFR-induced repression of the anterior follicle cell fate and anterior-posterior polarity formation in the oocyte.
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Affiliation(s)
- John S. Poulton
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370
- *To whom correspondence should be addressed. E-mail:
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44
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Borghese L, Fletcher G, Mathieu J, Atzberger A, Eades WC, Cagan RL, Rørth P. Systematic analysis of the transcriptional switch inducing migration of border cells. Dev Cell 2006; 10:497-508. [PMID: 16580994 PMCID: PMC2955450 DOI: 10.1016/j.devcel.2006.02.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 12/02/2005] [Accepted: 02/07/2006] [Indexed: 02/06/2023]
Abstract
Cell migration within a natural context is tightly controlled, often by specific transcription factors. However, the switch from stationary to migratory behavior is poorly understood. Border cells perform a spatially and temporally controlled invasive migration during Drosophila oogenesis. Slbo, a C/EBP family transcriptional activator, is required for them to become migratory. We purified wild-type and slbo mutant border cells as well as nonmigratory follicle cells and performed comparative whole-genome expression profiling, followed by functional tests of the contributions of identified targets to migration. About 300 genes were significantly upregulated in border cells, many dependent on Slbo. Among these, the microtubule regulator Stathmin was strongly upregulated and was required for normal migration. Actin cytoskeleton regulators were also induced, including, surprisingly, a large cluster of "muscle-specific" genes. We conclude that Slbo induces multiple cytoskeletal effectors, and that each contributes to the behavioral changes in border cells.
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Affiliation(s)
- Lodovica Borghese
- European Molecular Biology Laboratory Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Georgina Fletcher
- European Molecular Biology Laboratory Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Juliette Mathieu
- European Molecular Biology Laboratory Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Ann Atzberger
- European Molecular Biology Laboratory Meyerhofstrasse 1 69117 Heidelberg Germany
| | - William C. Eades
- Washington University School of Medicine 660 South Euclid Avenue St. Louis, Missouri 63110
| | - Ross L. Cagan
- Washington University School of Medicine 660 South Euclid Avenue St. Louis, Missouri 63110
| | - Pernille Rørth
- European Molecular Biology Laboratory Meyerhofstrasse 1 69117 Heidelberg Germany
- Correspondence:
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45
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Keshan B, Hiruma K, Riddiford LM. Developmental expression and hormonal regulation of different isoforms of the transcription factor E75 in the tobacco hornworm Manduca sexta. Dev Biol 2006; 295:623-32. [PMID: 16697364 DOI: 10.1016/j.ydbio.2006.03.049] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 03/12/2006] [Accepted: 03/31/2006] [Indexed: 10/24/2022]
Abstract
E75A and E75B, isoforms of the E75 orphan nuclear receptor, are sequentially up-regulated in the abdominal epidermis of the tobacco hornworm Manduca sexta by 20-hydroxyecdysone (20E) during larval and pupal molts, with E75A also increasing at pupal commitment (Zhou et al., Dev. Biol. 193, 127-138, 1998). We have now cloned E75C and show that little is expressed in the epidermis during larval life with trace amounts seen just before ecdysis. Instead, E75C is found in high amounts during the development of the adult wings as the ecdysteroid titer is rising, and this increase was prevented by juvenile hormone (JH) that prevented adult development. By contrast, E75D is expressed transiently during the larval and pupal molts as the ecdysteroid titer begins to decline and again just before ecdysis, but in the developing adult wings is expressed on the rise of 20E. Removal of the source of JH had little effect on either E75C or E75D mRNA expression during the larval and pupal molts. At the time of pupal commitment, in vitro experiments show that 20E up-regulates E75D and JH prevents this increase. Neither E75A nor E75D mRNA was up-regulated by JH alone. Thus, E75C is primarily involved in adult differentiation whereas E75D has roles both during the molt and pupal commitment.
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Affiliation(s)
- Bela Keshan
- Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
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46
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Fakhouri M, Elalayli M, Sherling D, Hall JD, Miller E, Sun X, Wells L, LeMosy EK. Minor proteins and enzymes of the Drosophila eggshell matrix. Dev Biol 2006; 293:127-41. [PMID: 16515779 PMCID: PMC2701256 DOI: 10.1016/j.ydbio.2006.01.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 01/26/2006] [Accepted: 01/27/2006] [Indexed: 11/29/2022]
Abstract
The Drosophila eggshell provides an in vivo model system for extracellular matrix assembly, in which programmed gene expression, cell migrations, extracellular protein trafficking, proteolytic processing, and cross-linking are all required to generate a multi-layered and regionally complex architecture. While abundant structural components of the eggshell are known and are being characterized, less is known about non-abundant structural, regulatory, and enzymatic components that are likely to play critical roles in eggshell assembly. We have used sensitive mass spectrometry-based analyses of fractionated eggshell matrices to validate six previously predicted eggshell proteins and to identify eleven novel components, and have characterized the expression patterns of many of their mRNAs. Among these are several putative structural or regulatory (non-enzymatic) proteins, most larger in mass than the major eggshell proteins and often showing preferential expression in follicle cells overlying specific structural features of the eggshell. Of particular note are the putative enzymes, some likely to be involved in matrix cross-linking (two yellow family members previously implicated in eggshell integrity, a heme peroxidase, and a small-molecule oxidoreductase) and others possibly involved in matrix proteolysis or adhesion (proteins related to cathepsins B and D). This work provides a framework for future molecular studies of eggshell assembly.
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Affiliation(s)
- Mazen Fakhouri
- Department of Cellular Biology and Anatomy, Medical College of Georgia, 1120 15 St., CB2915, Augusta, GA 30912, USA
| | - Maggie Elalayli
- Department of Cellular Biology and Anatomy, Medical College of Georgia, 1120 15 St., CB2915, Augusta, GA 30912, USA
| | | | - Jacklyn D. Hall
- Department of Cellular Biology and Anatomy, Medical College of Georgia, 1120 15 St., CB2915, Augusta, GA 30912, USA
| | | | - Xutong Sun
- Department of Cellular Biology and Anatomy, Medical College of Georgia, 1120 15 St., CB2915, Augusta, GA 30912, USA
| | | | - Ellen K. LeMosy
- Department of Cellular Biology and Anatomy, Medical College of Georgia, 1120 15 St., CB2915, Augusta, GA 30912, USA
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47
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Estrada B, Choe SE, Gisselbrecht SS, Michaud S, Raj L, Busser BW, Halfon MS, Church GM, Michelson AM. An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes. PLoS Genet 2006; 2:e16. [PMID: 16482229 PMCID: PMC1366495 DOI: 10.1371/journal.pgen.0020016] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 12/28/2005] [Indexed: 11/19/2022] Open
Abstract
An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within the tissue of interest. Here, we use an integrated genetic, genomic, and computational strategy to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified. A compendium of gene expression profiles was generated for primary mesodermal cells purified by flow cytometry from appropriately staged wild-type embryos and from 12 genotypes in which myogenesis was selectively and predictably perturbed. A statistical meta-analysis of these pooled datasets--based on expected trends in gene expression and on the relative contribution of each genotype to the detection of known muscle genes--provisionally assigned hundreds of differentially expressed genes to particular myoblast subtypes. Whole embryo in situ hybridizations were then used to validate the majority of these predictions, thereby enabling true-positive detection rates to be estimated for the microarray data. This combined analysis reveals that myoblasts exhibit much greater gene expression heterogeneity and overall complexity than was previously appreciated. Moreover, it implicates the involvement of large numbers of uncharacterized, differentially expressed genes in myogenic specification and subsequent morphogenesis. These findings also underscore a requirement for considerable regulatory specificity for generating diverse myoblast identities. Finally, to illustrate how the developmental functions of newly identified myoblast genes can be efficiently surveyed, a rapid RNA interference assay that can be scored in living embryos was developed and applied to selected genes. This integrated strategy for examining embryonic gene expression and function provides a substantially expanded framework for further studies of this model developmental system.
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Affiliation(s)
- Beatriz Estrada
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Sung E Choe
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Sebastien Michaud
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Lakshmi Raj
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Brian W Busser
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Marc S Halfon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alan M Michelson
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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48
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Yang Z, Edenberg HJ, Davis RL. Isolation of mRNA from specific tissues of Drosophila by mRNA tagging. Nucleic Acids Res 2005; 33:e148. [PMID: 16204451 PMCID: PMC1243647 DOI: 10.1093/nar/gni149] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
To study the function of specific cells or tissues using genomic tools like microarray analyses, it is highly desirable to obtain mRNA from a homogeneous source. However, this is particularly challenging for small organisms, like Caenorhabditis elegans and Drosophila melanogaster. We have optimized and applied a new technique, mRNA tagging, to isolate mRNA from specific tissues of D.melanogaster. A FLAG-tagged poly(A)-binding protein (PABP) is expressed in a specific tissue and mRNA from that tissue is thus tagged by the recombinant PABP and separated from mRNA in other tissues by co-immunoprecipitation with a FLAG-tag specific antibody. The fractionated mRNA is then amplified and used as probe in microarray experiments. As a test system, we employed the procedures to identify genes expressed in Drosophila photoreceptor cells. We found that most known photoreceptor cell-specific mRNAs were identified by mRNA tagging. Furthermore, at least 11 novel genes have been identified as enriched in photoreceptor cells. mRNA tagging is a powerful general method for profiling gene expression in specific tissues and for identifying tissue-specific genes.
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Affiliation(s)
- Zhiyong Yang
- Department of Molecular and Cellular Biology, Baylor College of MedicineHouston, TX 77030, USA
| | - Howard J. Edenberg
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of MedicineHouston, TX 77030, USA
| | - Ronald L. Davis
- Department of Molecular and Cellular Biology, Baylor College of MedicineHouston, TX 77030, USA
- Center for Medical Genomics, Indiana University School of MedicineIndianapolis, IN 46202, USA
- To whom correspondence should be addressed. Tel: +1 713 798 6641; Fax: +1 713 798 8005;
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Jordan KC, Hatfield SD, Tworoger M, Ward EJ, Fischer KA, Bowers S, Ruohola-Baker H. Genome wide analysis of transcript levels after perturbation of the EGFR pathway in the Drosophila ovary. Dev Dyn 2005; 232:709-24. [PMID: 15704171 DOI: 10.1002/dvdy.20318] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Defects in the epidermal growth factor receptor (EGFR) pathway can lead to aggressive tumor formation. Activation of this pathway during normal development produces multiple outcomes at the cellular level, leading to cellular differentiation and cell cycle activation. To elucidate the downstream events induced by this pathway, we used genome-wide cDNA microarray technology to identify potential EGFR targets in Drosophila oogenesis. We focused on genes for which the transcriptional responses due to EGFR pathway activation and inactivation were in opposite directions, as this is expected for genes that are directly regulated by the pathway in this tissue type. We perturbed the EGFR pathway in epithelial follicle cells using seven different genetic backgrounds. To activate the pathway, we overexpressed an activated form of the EGFR (UAS-caEGFR), and an activated form of the signal transducer Raf (UAS-caRaf); we also over- or ectopically expressed the downstream homeobox transcription factor Mirror (UAS-mirr) and the ligand-activating serine protease Rhomboid (UAS-rho). To reduce pathway activity we used loss-of-function mutations in the ligand (gurken) and receptor (torpedo). From microarrays containing 6,255 genes, we found 454 genes that responded in an opposite manner in gain-of-function and loss-of-function conditions among which are many Wingless signaling pathway components. Further analysis of two such components, sugarless and pangolin, revealed a function for these genes in late follicle cell patterning. Of interest, components of other signaling pathways were also enriched in the EGFR target group, suggesting that one reason for the pleiotropic effects seen with EGFR activity in cancer progression and development may be its ability to regulate many other signaling pathways.
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Affiliation(s)
- Katherine C Jordan
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350, USA
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Abstract
Nuclear receptors are ancient ligand-regulated transcription factors that control key metabolic and developmental pathways. The fruitfly Drosophila melanogaster has only 18 nuclear-receptor genes - far fewer than any other genetic model organism and representing all 6 subfamilies of vertebrate receptors. These unique attributes establish the fly as an ideal system for studying the regulation and function of nuclear receptors during development. Here, we review recent breakthroughs in our understanding of D. melanogaster nuclear receptors, and interpret these results in light of findings from their evolutionarily conserved vertebrate homologues.
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Affiliation(s)
- Kirst King-Jones
- Howard Hughes Medical Institute, Department of Human Genetics, University of Utah School of Medicine, 15 North 2030 East, Room 5100, Salt Lake City, Utah 84112-5331, USA.
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