1
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He Q, Wang S, Chen S, Chen J. Juvenile hormone signal transducer hairy inhibits Krüppel homolog1 expression. Biochem Biophys Res Commun 2024; 726:150276. [PMID: 38908347 DOI: 10.1016/j.bbrc.2024.150276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
Hairy and Krüppel homolog 1 (Kr-h1) are transcriptional repressors that act synergistically to mediate the gene-repressive action of juvenile hormone (JH). However, whether a regulatory relationship exists between Hairy and Kr-h1 remains unclear. In this study, an inhibitory effect of Hairy on Kr-h1 expression was found. Genetic studies in Drosophila have shown that the simultaneous overexpression of Hairy and Kr-h1 can rescue the defective phenotypes caused by the overexpression of a single factor. Reduced expression of Kr-h1 was observed in Hairy-overexpressing flies and cells, whereas the expression levels of Hairy were unaffected in cells with ectopic expression of Kr-h1. The inhibitory effect of Hairy on Kr-h1 expression was found to occur at the transcriptional level, as Hairy bound directly to the B-box within the Kr-h1 promoter via the bHLH motif and recruited the corepressors C-terminal binding protein (CtBP) and Groucho (Gro) through the PLSLV and WRPW motifs, respectively. Our findings revealed a regulatory relationship between two JH response factors, which advances our understanding of the molecular mechanism of JH signaling.
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Affiliation(s)
- Qianyu He
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China.
| | - Shunxin Wang
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shanshan Chen
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jinxia Chen
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
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2
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Sheloukhova L, Watanabe H. Evolution of glial cells: a non-bilaterian perspective. Neural Dev 2024; 19:10. [PMID: 38907299 PMCID: PMC11193209 DOI: 10.1186/s13064-024-00184-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 06/06/2024] [Indexed: 06/23/2024] Open
Abstract
Nervous systems of bilaterian animals generally consist of two cell types: neurons and glial cells. Despite accumulating data about the many important functions glial cells serve in bilaterian nervous systems, the evolutionary origin of this abundant cell type remains unclear. Current hypotheses regarding glial evolution are mostly based on data from model bilaterians. Non-bilaterian animals have been largely overlooked in glial studies and have been subjected only to morphological analysis. Here, we provide a comprehensive overview of conservation of the bilateral gliogenic genetic repertoire of non-bilaterian phyla (Cnidaria, Placozoa, Ctenophora, and Porifera). We overview molecular and functional features of bilaterian glial cell types and discuss their possible evolutionary history. We then examine which glial features are present in non-bilaterians. Of these, cnidarians show the highest degree of gliogenic program conservation and may therefore be crucial to answer questions about glial evolution.
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Affiliation(s)
- Larisa Sheloukhova
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan
| | - Hiroshi Watanabe
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan.
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3
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Arnosti DN. Soft repression and chromatin modification by conserved transcriptional corepressors. Enzymes 2023; 53:69-96. [PMID: 37748837 DOI: 10.1016/bs.enz.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Transcriptional regulation in eukaryotic cells involves the activity of multifarious DNA-binding transcription factors and recruited corepressor complexes. Together, these complexes interact with the core transcriptional machinery, chromatin, and nuclear environment to effect complex patterns of gene regulation. Much focus has been paid to the action of master regulatory switches that are key to developmental and environmental responses, as these genetic elements have important phenotypic effects. The regulation of widely-expressed metabolic control genes has been less well studied, particularly in cases in which physically-interacting repressors and corepressors have subtle influences on steady-state expression. This latter phenomenon, termed "soft repression" is a topic of increasing interest as genomic approaches provide ever more powerful tools to uncover the significance of this level of control. This review provides an oversight of classic and current approaches to the study of transcriptional repression in eukaryotic systems, with a specific focus on opportunities and challenges that lie ahead in the study of soft repression.
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Affiliation(s)
- David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.
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4
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Hagen JFD, Mendes CC, Booth SR, Figueras Jimenez J, Tanaka KM, Franke FA, Baudouin-Gonzalez L, Ridgway AM, Arif S, Nunes MDS, McGregor AP. Unraveling the Genetic Basis for the Rapid Diversification of Male Genitalia between Drosophila Species. Mol Biol Evol 2021; 38:437-448. [PMID: 32931587 PMCID: PMC7826188 DOI: 10.1093/molbev/msaa232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In the last 240,000 years, males of the Drosophila simulans species clade have evolved striking differences in the morphology of their epandrial posterior lobes and claspers (surstyli). These appendages are used for grasping the female during mating and so their divergence is most likely driven by sexual selection. Mapping studies indicate a highly polygenic and generally additive genetic basis for these morphological differences. However, we have limited understanding of the gene regulatory networks that control the development of genital structures and how they evolved to result in this rapid phenotypic diversification. Here, we used new D. simulans/D. mauritiana introgression lines on chromosome arm 3L to generate higher resolution maps of posterior lobe and clasper differences between these species. We then carried out RNA-seq on the developing genitalia of both species to identify the expressed genes and those that are differentially expressed between the two species. This allowed us to test the function of expressed positional candidates during genital development in D. melanogaster. We identified several new genes involved in the development and possibly the evolution of these genital structures, including the transcription factors Hairy and Grunge. Furthermore, we discovered that during clasper development Hairy negatively regulates tartan (trn), a gene known to contribute to divergence in clasper morphology. Taken together, our results provide new insights into the regulation of genital development and how this has evolved between species.
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Affiliation(s)
- Joanna F D Hagen
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Cláudia C Mendes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Shamma R Booth
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Javier Figueras Jimenez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Kentaro M Tanaka
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Franziska A Franke
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Luis Baudouin-Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Amber M Ridgway
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Saad Arif
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.,Centre for Functional Genomics, Oxford Brookes University, Oxford, United Kingdom
| | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.,Centre for Functional Genomics, Oxford Brookes University, Oxford, United Kingdom
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.,Centre for Functional Genomics, Oxford Brookes University, Oxford, United Kingdom
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5
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Shokri L, Inukai S, Hafner A, Weinand K, Hens K, Vedenko A, Gisselbrecht SS, Dainese R, Bischof J, Furger E, Feuz JD, Basler K, Deplancke B, Bulyk ML. A Comprehensive Drosophila melanogaster Transcription Factor Interactome. Cell Rep 2020; 27:955-970.e7. [PMID: 30995488 PMCID: PMC6485956 DOI: 10.1016/j.celrep.2019.03.071] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/04/2019] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays. We combined our interactome with prior PPI data to generate an integrated Drosophila TF-TF binary interaction network. Our analysis of ChIP-seq data, integrating PPI and gene expression information, uncovered different modes by which interacting TFs are recruited to DNA. We further demonstrate the utility of our Drosophila interactome in shedding light on human TF-TF interactions. This study reveals how TFs interact to bind regulatory elements in vivo and serves as a resource of Drosophila TF-TF binary PPIs for understanding tissue-specific gene regulation. Combinatorial regulation by transcription factors (TFs) is one mechanism for achieving condition and tissue-specific gene regulation. Shokri et al. mapped TF-TF interactions between most Drosophila TFs, reporting a comprehensive TF-TF network integrated with previously known interactions. They used this network to discern distinct TF-DNA binding modes.
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Affiliation(s)
- Leila Shokri
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sachi Inukai
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Antonina Hafner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Kathryn Weinand
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA
| | - Korneel Hens
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Anastasia Vedenko
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen S Gisselbrecht
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Johannes Bischof
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Edy Furger
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Jean-Daniel Feuz
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Martha L Bulyk
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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6
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Zhang Y, Xin Q, Zhang JY, Wang YY, Cheng JT, Cai WQ, Han ZW, Zhou Y, Cui SZ, Peng XC, Wang XW, Ma Z, Xiang Y, Su XL, Xin HW. Transcriptional Regulation of Latency-Associated Transcripts (LATs) of Herpes Simplex Viruses. J Cancer 2020; 11:3387-3399. [PMID: 32231745 PMCID: PMC7097949 DOI: 10.7150/jca.40186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Herpes simplex viruses (HSVs) cause cold sores and genital herpes and can establish lifelong latent infection in neurons. An engineered oncolytic HSV (oHSV) has recently been approved to treat tumors in clinics. HSV latency-associated transcripts (LATs) are associated with the latent infection, but LAT transcriptional regulation was seldom reported. For a better treatment of HSV infection and tumors, here we sequenced the LAT encoding DNA and LAT transcription regulatory region of our recently isolated new strain HSV-1-LXMW and did comparative analysis of the sequences together with those of other four HSV-1 and two HSV-2 strains. Phylogenetic analysis of LATs revealed that HSV-1-LXMW is evolutionarily close to HSV-1-17 from MRC University, Glasgow, UK. For the first time, Using a weight matrix-based program Match and multi-sequences alignment of the 6 HSV strains, we identified HSV LAT transcription regulatory sequences that bind to 9 transcription factors: AP-1, C-REL, Comp1, E2F, Hairy, HFH-3, Kr, TCF11/MAFG, v-Myb. Interestingly, these transcription regulatory sequences and factors are either conserved or unique among LATs of HSV-1 and HSV-2, suggesting they are potentially functional. Furthermore, literature analysis found that the transcription factors v-myb and AP-1 family member JunD are functional in regulating HSV gene transcription, including LAT transcription. For the first time, we discovered seven novel transcription factors and their corresponding transcription regulatory sequences of HSV LATs. Based on our findings and other reports, we proposed potential mechanisms of the initiation and maintenance of HSV latent infection. Our findings may have significant implication in our understanding of HSV latency and engineering of better oncolytic HSVs.
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Affiliation(s)
- Ying Zhang
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Qiang Xin
- Clinical Medical Research Center, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Jun-Yi Zhang
- Department of Neural Surgery, People's Hospital of Dongsheng District of Erdos City, Erdos, Inner Mongolia, 017000, China
| | - Ying-Ying Wang
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Jun-Ting Cheng
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Wen-Qi Cai
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Zi-Wen Han
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Yang Zhou
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Shu-Zhong Cui
- State Key Laboratory of Respiratory Disease, Affiliated Cancer Hospital Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Xiao-Chun Peng
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Pathophysiology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Xian-Wang Wang
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Laboratory Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China
| | - Zhaowu Ma
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Ying Xiang
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Xiu-Lan Su
- Clinical Medical Research Center, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Hong-Wu Xin
- The First School of Clinical Medicine, Health Science Center, Yangtze University, Nanhuan Road, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
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7
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Flint Brodsly N, Bitman-Lotan E, Boico O, Shafat A, Monastirioti M, Gessler M, Delidakis C, Rincon-Arano H, Orian A. The transcription factor Hey and nuclear lamins specify and maintain cell identity. eLife 2019; 8:44745. [PMID: 31310235 PMCID: PMC6634966 DOI: 10.7554/elife.44745] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
The inability of differentiated cells to maintain their identity is a hallmark of age-related diseases. We found that the transcription factor Hey supervises the identity of differentiated enterocytes (ECs) in the adult Drosophila midgut. Lineage tracing established that Hey-deficient ECs are unable to maintain their unique nuclear organization and identity. To supervise cell identity, Hey determines the expression of nuclear lamins, switching from a stem-cell lamin configuration to a differentiated lamin configuration. Moreover, continued Hey expression is required to conserve large-scale nuclear organization. During aging, Hey levels decline, and EC identity and gut homeostasis are impaired, including pathological reprograming and compromised gut integrity. These phenotypes are highly similar to those observed upon acute targeting of Hey or perturbation of lamin expression in ECs in young adults. Indeed, aging phenotypes were suppressed by continued expression of Hey in ECs, suggesting that a Hey-lamin network safeguards nuclear organization and differentiated cell identity.
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Affiliation(s)
- Naama Flint Brodsly
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Olga Boico
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adi Shafat
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maria Monastirioti
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Manfred Gessler
- Biocenter of Developmental Biochemistry, University of Würzburg, Würzburg, Germany
| | - Christos Delidakis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Hector Rincon-Arano
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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8
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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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9
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Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV. Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster. Biophysics (Nagoya-shi) 2019; 63:43-51. [PMID: 30739944 DOI: 10.1134/s0006350918010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gene regulatory networks control the complex programs that drive development. Deciphering the connections between transcription factors (TFs) and target genes is challenging, in part because TFs bind to thousands of places in the genome but control expression through a subset of these binding events. We hypothesize that we can combine natural variation of expression levels and predictions of TF binding sites to identify TF targets. We gather RNA-seq data from 71 genetically distinct F1 Drosophila melanogaster embryos and calculate the correlations between TF and potential target genes' expression levels, which we call "regulatory strength." To separate direct and indirect TF targets, we hypothesize that direct TF targets will have a preponderance of binding sites in their upstream regions. Using 14 TFs active during embryogenesis, we find that 12 TFs showed a significant correlation between their binding strength and regulatory strength on downstream targets, and 10 TFs showed a significant correlation between the number of binding sites and the regulatory effect on target genes. The general roles, e.g. bicoid's role as an activator, and the particular interactions we observed between our TFs, e.g. twist's role as a repressor of sloppy paired and odd paired, generally coincide with the literature.
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Affiliation(s)
- Noha M Osman
- University of Southern California, Los Angeles, CA.,National Research Centre, Dokki, Giza, Egypt
| | | | - Srna Vlaho
- University of Southern California, Los Angeles, CA
| | | | - Sergey V Nuzhdin
- University of Southern California, Los Angeles, CA.,Saint Petersburg Polytechnical University, St Petersburg, Russia
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10
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Wang YY, Lyu YN, Xin HY, Cheng JT, Liu XQ, Wang XW, Peng XC, Xiang Y, Xin VW, Lu CB, Ren BX, Liang YF, Ji JF, Ma Z, Cui SZ, Xin HW. Identification of Putative UL54 (ICP27) Transcription Regulatory Sequences Binding to Oct-1, v-Myb, Pax-6 and Hairy in Herpes Simplex Viruses. J Cancer 2019; 10:430-440. [PMID: 30719137 PMCID: PMC6360293 DOI: 10.7150/jca.29787] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/23/2018] [Indexed: 02/03/2023] Open
Abstract
An oncolytic herpes simplex virus (oHSV) has proven amenable in oncolytic virotherapy and was approved to treat melanoma. The immediate-early (IE) protein ICP27 encoded by gene UL54 is essential for HSV infection. Post-transcriptional modification of UL54 would increase tumor targeting of oHSVs. However, UL54 gene transcription regulatory sequences and factors were not reported yet. Here we isolated a new strain LXMW of type 1 HSV (HSV-1-LXMW) in China and found it's closely related to HSV-1 strains Patton and H129 in the US by the first and next generation DNA sequencing viral DNA phylogenetic analysis. Using a weight matrix-based program Match, we found the UL54 transcription regulatory sequences binding to the transcription factors Oct-1, v-Myb and Pax-6 in HSV-1-LXMW, while the sequences binding to Oct-1 and Hairy in a HSV-2 strain. Further validation showed that HSV-1 and HSV-2 shared the common sequence binding to Oct-1, but had unique sequences to bind v-Myb and Pax-6, or Hairy, respectively, by DNA sequence alignment of total 11 HSV strains. The published results howed that the expression of transcription factors is consistent with the tissue tropism of HSV-1 and HSV-2. In the current article a new HSV-1 strain LXMW was isolated and its putative HSV UL54 transcription regulatory sequences and factors were identified for the first time. Our findings highlight the new understanding of the principles of transcriptional regulation in HSV biology and oncolytic virotherapy.
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Affiliation(s)
- Ying-Ying Wang
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Yan-Ning Lyu
- Institute for Infectious Diseases and Endemic Diseases Prevention and Control, Beijing Center for Diseases Prevention and Control, Beijing, 100013, China
| | - Hong-Yi Xin
- Animal Health Biotechnology, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
| | - Jun-Ting Cheng
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Xiao-Qin Liu
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Medical Imaging, School of Basic Medicine, Yangtze University, Jingzhou, Hubei 434023, China
| | - Xian-Wang Wang
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Laboratory Medicine, School of Basic Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China
| | - Xiao-Chun Peng
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Pathophysiology, School of Basic Medicine, Yangtze University, Jingzhou, Hubei 434023, China
| | - Ying Xiang
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Victoria W Xin
- Montgomery Blair High School Magnet Program Class of 2020, Silver Spring, MD 20901-2451, USA
| | - Cheng-Biao Lu
- Laboratory of Neuronal Network and Brain Diseases Modulation, School of Medicine, Yangtze University, Jingzhou, Hubei Province, China
| | - Bo-Xu Ren
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Pathophysiology, School of Basic Medicine, Yangtze University, Jingzhou, Hubei 434023, China
| | - Yan-Fang Liang
- Department of Radiology, Guangzhou Medical University Cancer Hospital, Guangzhou, China
| | - Jia-Fu Ji
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Zhaowu Ma
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Shu-Zhong Cui
- Department of Theromotherapy, Guangzhou Medical University Cancer Hospital, Guangzhou, China
| | - Hong-Wu Xin
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
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11
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CtBP represses Dpp-dependent Mad activation during Drosophila eye development. Dev Biol 2018; 442:188-198. [PMID: 30031756 DOI: 10.1016/j.ydbio.2018.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/05/2018] [Accepted: 07/18/2018] [Indexed: 12/13/2022]
Abstract
Complex networks of signaling pathways maintain the correct balance between positive and negative growth signals, ensuring that tissues achieve proper sizes and differentiation pattern during development. In Drosophila, Dpp, a member of the TGFβ family, plays two main roles during larval eye development. In the early eye primordium, Dpp promotes growth and cell survival, but later on, it switches its function to induce a developmentally-regulated cell cycle arrest in the G1 phase and neuronal photoreceptor differentiation. To advance in the identification and characterization of regulators and targets of Dpp signaling required for retinal development, we carried out an in vivo eye-targeted double-RNAi screen to identify punt (Type II TGFβ receptor) interactors. Using a set of 251 genes associated with eye development, we identified CtBP, Dad, Ago and Brk as punt genetic interactors. Here, we show that downregulation of Ago, or conditions causing increased tissue growth including overexpression of Myc or CyclinD-Cdk4 are sufficient to partially rescue punt-dependent growth and photoreceptor differentiation. Interestingly, we show a novel role for the transcriptional co-repressor CtBP in inhibiting Dpp-dependent Mad activation by phosphorylation, downstream or in parallel to Dad, the inhibitory Smad. Furthermore, CtBP downregulation activates JNK signaling pathway, implying a complex regulation of signaling pathways by CtBP during eye development.
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12
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The Biology of SUMO-Targeted Ubiquitin Ligases in Drosophila Development, Immunity, and Cancer. J Dev Biol 2018; 6:jdb6010002. [PMID: 29615551 PMCID: PMC5875560 DOI: 10.3390/jdb6010002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin and SUMO (small ubiquitin-like modifier) pathways modify proteins that in turn regulate diverse cellular processes, embryonic development, and adult tissue physiology. These pathways were originally discovered biochemically in vitro, leading to a long-standing challenge of elucidating both the molecular cross-talk between these pathways and their biological importance. Recent discoveries in Drosophila established that ubiquitin and SUMO pathways are interconnected via evolutionally conserved SUMO-targeted ubiquitin ligase (STUbL) proteins. STUbL are RING ubiquitin ligases that recognize SUMOylated substrates and catalyze their ubiquitination, and include Degringolade (Dgrn) in Drosophila and RNF4 and RNF111 in humans. STUbL are essential for early development of both the fly and mouse embryos. In the fly embryo, Dgrn regulates early cell cycle progression, sex determination, zygotic gene transcription, segmentation, and neurogenesis, among other processes. In the fly adult, Dgrn is required for systemic immune response to pathogens and intestinal stem cell regeneration upon infection. These functions of Dgrn are highly conserved in humans, where RNF4-dependent ubiquitination potentiates key oncoproteins, thereby accelerating tumorigenesis. Here, we review the lessons learned to date in Drosophila and highlight their relevance to cancer biology.
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13
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14
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Hunding A, Baumgartner S. Ancient role of ten-m/ odz in segmentation and the transition from sequential to syncytial segmentation. Hereditas 2017; 154:8. [PMID: 28461810 PMCID: PMC5408475 DOI: 10.1186/s41065-017-0029-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/11/2017] [Indexed: 02/07/2023] Open
Abstract
Background Until recently, mechanisms of segmentation established for Drosophila served as a paradigm for arthropod segmentation. However, with the discovery of gene expression waves in vertebrate segmentation, another paradigm based on oscillations linked to axial growth was established. The Notch pathway and hairy delay oscillator are basic components of this mechanism, as is the wnt pathway. With the establishment of oscillations during segmentation of the beetle Tribolium, a common segmentation mechanism may have been present in the last common ancestor of vertebrates and arthropods. However, the Notch pathway is not involved in segmentation of the initial Drosophila embryo. In arthropods, the engrailed, wingless pair has a much more conserved function in segmentation than most of the hierarchy established for Drosophila. Results Here, we work backwards from this conserved pair by discussing possible mechanisms which could have taken over the role of the Notch pathway. We propose a pivotal role for the large transmembrane protein Ten-m/Odz. Ten-m/Odz may have had an ancient role in cell-cell communication, parallel to the Notch and wnt pathways. The Ten-m protein binds to the membrane with properties which resemble other membrane-based biochemical oscillators. Conclusion We propose that such a simple transition could have formed the initial scaffold, on top of which the hierarchy, observed in the syncytium of dipterans, could have evolved.
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Affiliation(s)
- Axel Hunding
- Biophysical Chemistry, Department of Chemistry S01, H. C. 0rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Stefan Baumgartner
- Department of Experimental Medical Sciences, Lund University, BMC D10, 22184 Lund, Sweden
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15
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Wu F, Olson BG, Yao J. DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments. J Vis Exp 2016:e53620. [PMID: 26862720 DOI: 10.3791/53620] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The DNA adenine methyltransferase identification (DamID) assay is a powerful method to detect protein-DNA interactions both locally and genome-wide. It is an alternative approach to chromatin immunoprecipitation (ChIP). An expressed fusion protein consisting of the protein of interest and the E. coli DNA adenine methyltransferase can methylate the adenine base in GATC motifs near the sites of protein-DNA interactions. Adenine-methylated DNA fragments can then be specifically amplified and detected. The original DamID assay detects the genomic locations of methylated DNA fragments by hybridization to DNA microarrays, which is limited by the availability of microarrays and the density of predetermined probes. In this paper, we report the detailed protocol of integrating high throughput DNA sequencing into DamID (DamID-seq). The large number of short reads generated from DamID-seq enables detecting and localizing protein-DNA interactions genome-wide with high precision and sensitivity. We have used the DamID-seq assay to study genome-nuclear lamina (NL) interactions in mammalian cells, and have noticed that DamID-seq provides a high resolution and a wide dynamic range in detecting genome-NL interactions. The DamID-seq approach enables probing NL associations within gene structures and allows comparing genome-NL interaction maps with other functional genomic data, such as ChIP-seq and RNA-seq.
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Affiliation(s)
- Feinan Wu
- Department of Cell Biology, Yale University School of Medicine
| | - Brennan G Olson
- Department of Cell Biology, Yale University School of Medicine
| | - Jie Yao
- Department of Cell Biology, Yale University School of Medicine;
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16
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Hairy and Groucho mediate the action of juvenile hormone receptor Methoprene-tolerant in gene repression. Proc Natl Acad Sci U S A 2016; 113:E735-43. [PMID: 26744312 DOI: 10.1073/pnas.1523838113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The arthropod-specific juvenile hormone (JH) controls numerous essential functions. Its involvement in gene activation is known to be mediated by the transcription factor Methoprene-tolerant (Met), which turns on JH-controlled genes by directly binding to E-box-like motifs in their regulatory regions. However, it remains unclear how JH represses genes. We used the Aedes aegypti female mosquito, in which JH is necessary for reproductive maturation, to show that a repressor, Hairy, is required for the gene-repressive action of JH and Met. The RNA interference (RNAi) screen for Met and Hairy in the Aedes female fat body revealed a large cohort of Met- and Hairy-corepressed genes. Analysis of selected genes from this cohort demonstrated that they are repressed by JH, but RNAi of either Met or Hairy renders JH ineffective in repressing these genes in an in vitro fat-body culture assay. Moreover, this JH action was prevented by the addition of the translational inhibitor cycloheximide (CHX) to the culture, indicating the existence of an indirect regulatory hierarchy. The lack of Hairy protein in the CHX-treated tissue was verified using immunoblot analysis, and the upstream regions of Met/Hairy-corepressed genes were shown to contain common binding motifs that interact with Hairy. Groucho (gro) RNAi silencing phenocopied the effect of Hairy RNAi knockdown, indicating that it is involved in the JH/Met/Hairy hierarchy. Finally, the requirement of Hairy and Gro for gene repression was confirmed in a cell transfection assay. Thus, our study has established that Hairy and its cofactor Gro mediate the repressive function of JH and Met.
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17
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Kok K, Ay A, Li LM, Arnosti DN. Genome-wide errant targeting by Hairy. eLife 2015; 4. [PMID: 26305409 PMCID: PMC4547095 DOI: 10.7554/elife.06394] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/24/2015] [Indexed: 01/08/2023] Open
Abstract
Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity on many loci that are uncoupled to changes in gene expression. Rather than representing inert binding sites, as suggested for many eukaryotic factors, many regions are targeted errantly by Hairy to modify the chromatin landscape. Our findings emphasize that identification of active cis-regulatory elements must extend beyond the survey of prototypical chromatin marks. We speculate that this errant activity may provide a path for creation of new regulatory elements, facilitating the evolution of novel transcriptional circuits.
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Affiliation(s)
- Kurtulus Kok
- Genetics Program, Michigan State University, East Lansing, United States
| | - Ahmet Ay
- Departments of Biology and Mathematics, Colgate University, Hamilton, United States
| | - Li M Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - David N Arnosti
- Genetics Program, Michigan State University, East Lansing, United States
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18
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McClure CD, Southall TD. Getting Down to Specifics: Profiling Gene Expression and Protein-DNA Interactions in a Cell Type-Specific Manner. ADVANCES IN GENETICS 2015; 91:103-151. [PMID: 26410031 PMCID: PMC4604662 DOI: 10.1016/bs.adgen.2015.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The majority of multicellular organisms are comprised of an extraordinary range of cell types, with different properties and gene expression profiles. Understanding what makes each cell type unique and how their individual characteristics are attributed are key questions for both developmental and neurobiologists alike. The brain is an excellent example of the cellular diversity expressed in the majority of eukaryotes. The mouse brain comprises of approximately 75 million neurons varying in morphology, electrophysiology, and preferences for synaptic partners. A powerful process in beginning to pick apart the mechanisms that specify individual characteristics of the cell, as well as their fate, is to profile gene expression patterns, chromatin states, and transcriptional networks in a cell type-specific manner, i.e., only profiling the cells of interest in a particular tissue. Depending on the organism, the questions being investigated, and the material available, certain cell type-specific profiling methods are more suitable than others. This chapter reviews the approaches presently available for selecting and isolating specific cell types and evaluates their key features.
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Affiliation(s)
- Colin D. McClure
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Tony D. Southall
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, United Kingdom
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19
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Artegiani B, de Jesus Domingues AM, Bragado Alonso S, Brandl E, Massalini S, Dahl A, Calegari F. Tox: a multifunctional transcription factor and novel regulator of mammalian corticogenesis. EMBO J 2014; 34:896-910. [PMID: 25527292 DOI: 10.15252/embj.201490061] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/03/2014] [Indexed: 01/17/2023] Open
Abstract
Major efforts are invested to characterize the factors controlling the proliferation of neural stem cells. During mammalian corticogenesis, our group has identified a small pool of genes that are transiently downregulated in the switch of neural stem cells to neurogenic division and reinduced in newborn neurons. Among these switch genes, we found Tox, a transcription factor with hitherto uncharacterized roles in the nervous system. Here, we investigated the role of Tox in corticogenesis by characterizing its expression at the tissue, cellular and temporal level. We found that Tox is regulated by calcineurin/Nfat signalling. Moreover, we combined DNA adenine methyltransferase identification (DamID) with deep sequencing to characterize the chromatin binding properties of Tox including its motif and downstream transcriptional targets including Sox2, Tbr2, Prox1 and other key factors. Finally, we manipulated Tox in the developing brain and validated its multiple roles in promoting neural stem cell proliferation and neurite outgrowth of newborn neurons. Our data provide a valuable resource to study the role of Tox in other tissues and highlight a novel key player in brain development.
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Affiliation(s)
- Benedetta Artegiani
- DFG-Research Center for Regenerative Therapies, Cluster of Excellence, TU-Dresden, Dresden, Germany
| | | | - Sara Bragado Alonso
- DFG-Research Center for Regenerative Therapies, Cluster of Excellence, TU-Dresden, Dresden, Germany
| | - Elisabeth Brandl
- DFG-Research Center for Regenerative Therapies, Cluster of Excellence, TU-Dresden, Dresden, Germany
| | - Simone Massalini
- DFG-Research Center for Regenerative Therapies, Cluster of Excellence, TU-Dresden, Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing Group-SFB655, Biotechnology Center, TU-Dresden, Dresden, Germany
| | - Federico Calegari
- DFG-Research Center for Regenerative Therapies, Cluster of Excellence, TU-Dresden, Dresden, Germany
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20
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Kaul A, Schuster E, Jennings BH. The Groucho co-repressor is primarily recruited to local target sites in active chromatin to attenuate transcription. PLoS Genet 2014; 10:e1004595. [PMID: 25165826 PMCID: PMC4148212 DOI: 10.1371/journal.pgen.1004595] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/03/2014] [Indexed: 12/25/2022] Open
Abstract
Gene expression is regulated by the complex interaction between transcriptional activators and repressors, which function in part by recruiting histone-modifying enzymes to control accessibility of DNA to RNA polymerase. The evolutionarily conserved family of Groucho/Transducin-Like Enhancer of split (Gro/TLE) proteins act as co-repressors for numerous transcription factors. Gro/TLE proteins act in several key pathways during development (including Notch and Wnt signaling), and are implicated in the pathogenesis of several human cancers. Gro/TLE proteins form oligomers and it has been proposed that their ability to exert long-range repression on target genes involves oligomerization over broad regions of chromatin. However, analysis of an endogenous gro mutation in Drosophila revealed that oligomerization of Gro is not always obligatory for repression in vivo. We have used chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) to profile Gro recruitment in two Drosophila cell lines. We find that Gro predominantly binds at discrete peaks (<1 kilobase). We also demonstrate that blocking Gro oligomerization does not reduce peak width as would be expected if Gro oligomerization induced spreading along the chromatin from the site of recruitment. Gro recruitment is enriched in “active” chromatin containing developmentally regulated genes. However, Gro binding is associated with local regions containing hypoacetylated histones H3 and H4, which is indicative of chromatin that is not fully open for efficient transcription. We also find that peaks of Gro binding frequently overlap the transcription start sites of expressed genes that exhibit strong RNA polymerase pausing and that depletion of Gro leads to release of polymerase pausing and increased transcription at a bona fide target gene. Our results demonstrate that Gro is recruited to local sites by transcription factors to attenuate rather than silence gene expression by promoting histone deacetylation and polymerase pausing. Repression by transcription factors plays a central role in gene regulation. The Groucho/Transducin-Like Enhancer of split (Gro/TLE) family of co-repressors interacts with many different transcription factors and has many essential roles during animal development. Groucho/TLE proteins form oligomers that are necessary for target gene repression in some contexts. We have profiled the genome-wide recruitment of the founding member of this family, Groucho (from Drosophila) to gain insight into how and where it binds with respect to target genes and to identify factors associated with its binding. We find that Groucho binds in discrete peaks, frequently at transcription start sites, and that blocking Groucho from forming oligomers does not significantly change the pattern of Groucho recruitment. Although Groucho acts as a repressor, Groucho binding is enriched in chromatin that is permissive for transcription, and we find that it acts to attenuate rather than completely silence target gene expression. Thus, Groucho does not act as an “on/off” switch on target gene expression, but rather as a “mute” button.
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Affiliation(s)
- Aamna Kaul
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Eugene Schuster
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Barbara H. Jennings
- UCL Cancer Institute, University College London, London, United Kingdom
- * E-mail:
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21
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Rosenberg MI, Brent AE, Payre F, Desplan C. Dual mode of embryonic development is highlighted by expression and function of Nasonia pair-rule genes. eLife 2014; 3:e01440. [PMID: 24599282 PMCID: PMC3941026 DOI: 10.7554/elife.01440] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Embryonic anterior-posterior patterning is well understood in Drosophila, which uses 'long germ' embryogenesis, in which all segments are patterned before cellularization. In contrast, most insects use 'short germ' embryogenesis, wherein only head and thorax are patterned in a syncytial environment while the remainder of the embryo is generated after cellularization. We use the wasp Nasonia (Nv) to address how the transition from short to long germ embryogenesis occurred. Maternal and gap gene expression in Nasonia suggest long germ embryogenesis. However, the Nasonia pair-rule genes even-skipped, odd-skipped, runt and hairy are all expressed as early blastoderm pair-rule stripes and late-forming posterior stripes. Knockdown of Nv eve, odd or h causes loss of alternate segments at the anterior and complete loss of abdominal segments. We propose that Nasonia uses a mixed mode of segmentation wherein pair-rule genes pattern the embryo in a manner resembling Drosophila at the anterior and ancestral Tribolium at the posterior. DOI: http://dx.doi.org/10.7554/eLife.01440.001.
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Affiliation(s)
- Miriam I Rosenberg
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
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22
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23
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Upadhyai P, Campbell G. Brinker possesses multiple mechanisms for repression because its primary co-repressor, Groucho, may be unavailable in some cell types. Development 2013; 140:4256-65. [PMID: 24086079 DOI: 10.1242/dev.099366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Transcriptional repressors function primarily by recruiting co-repressors, which are accessory proteins that antagonize transcription by modifying chromatin structure. Although a repressor could function by recruiting just a single co-repressor, many can recruit more than one, with Drosophila Brinker (Brk) recruiting the co-repressors CtBP and Groucho (Gro), in addition to possessing a third repression domain, 3R. Previous studies indicated that Gro is sufficient for Brk to repress targets in the wing, questioning why it should need to recruit CtBP, a short-range co-repressor, when Gro is known to be able to function over longer distances. To resolve this we have used genomic engineering to generate a series of brk mutants that are unable to recruit Gro, CtBP and/or have 3R deleted. These reveal that although the recruitment of Gro is necessary and can be sufficient for Brk to make an almost morphologically wild-type fly, it is insufficient during oogenesis, where Brk must utilize CtBP and 3R to pattern the egg shell appropriately. Gro insufficiency during oogenesis can be explained by its downregulation in Brk-expressing cells through phosphorylation downstream of EGFR signaling.
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Affiliation(s)
- Priyanka Upadhyai
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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24
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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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25
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Regulatory regions of the C elegans genome contain more low-affinity REF-1 transcription-factor binding sites than high-affinity sites. Genes Genomics 2012. [DOI: 10.1007/s13258-012-0213-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Rincon-Arano H, Halow J, Delrow JJ, Parkhurst SM, Groudine M. UpSET recruits HDAC complexes and restricts chromatin accessibility and acetylation at promoter regions. Cell 2012. [PMID: 23177352 DOI: 10.1016/j.cell.2012.11.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developmental gene expression results from the orchestrated interplay between genetic and epigenetic mechanisms. Here, we describe upSET, a transcriptional regulator encoding a SET domain-containing protein recruited to active and inducible genes in Drosophila. However, unlike other Drosophila SET proteins associated with gene transcription, UpSET is part of an Rpd3/Sin3-containing complex that restricts chromatin accessibility and histone acetylation to promoter regions. In the absence of UpSET, active chromatin marks and chromatin accessibility increase and spread to genic and flanking regions due to destabilization of the histone deacetylase complex. Consistent with this, transcriptional noise increases, as manifest by activation of repetitive elements and off-target genes. Interestingly, upSET mutant flies are female sterile due to upregulation of key components of Notch signaling during oogenesis. Thus UpSET defines a class of metazoan transcriptional regulators required to fine tune transcription by preventing the spread of active chromatin.
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Affiliation(s)
- Hector Rincon-Arano
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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27
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Cerf A, Tian HC, Craighead HG. Ordered arrays of native chromatin molecules for high-resolution imaging and analysis. ACS NANO 2012; 6:7928-34. [PMID: 22816516 PMCID: PMC3703913 DOI: 10.1021/nn3023624] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Individual chromatin molecules contain valuable genetic and epigenetic information. To date, there have not been reliable techniques available for the controlled stretching and manipulation of individual chromatin fragments for high-resolution imaging and analysis of these molecules. We report the controlled stretching of single chromatin fragments extracted from two different cancerous cell types (M091 and HeLa) characterized through fluorescence microscopy and atomic force microscopy (AFM). Our method combines soft lithography with molecular stretching to form ordered arrays of more than 250,000 individual chromatin fragments immobilized into a beads-on-a-string structure on a solid transparent support. Using fluorescence microscopy and AFM, we verified the presence of histone proteins after the stretching and transfer process.
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Affiliation(s)
- Aline Cerf
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Harvey C. Tian
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Harold G. Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
- To whom correspondence should be addressed. ; Fax: (607) 255-7658
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Luo SD, Shi GW, Baker BS. Direct targets of the D. melanogaster DSXF protein and the evolution of sexual development. Development 2011; 138:2761-71. [PMID: 21652649 DOI: 10.1242/dev.065227] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Uncovering the direct regulatory targets of doublesex (dsx) and fruitless (fru) is crucial for an understanding of how they regulate sexual development, morphogenesis, differentiation and adult functions (including behavior) in Drosophila melanogaster. Using a modified DamID approach, we identified 650 DSX-binding regions in the genome from which we then extracted an optimal palindromic 13 bp DSX-binding sequence. This sequence is functional in vivo, and the base identity at each position is important for DSX binding in vitro. In addition, this sequence is enriched in the genomes of D. melanogaster (58 copies versus approximately the three expected from random) and in the 11 other sequenced Drosophila species, as well as in some other Dipterans. Twenty-three genes are associated with both an in vivo peak in DSX binding and an optimal DSX-binding sequence, and thus are almost certainly direct DSX targets. The association of these 23 genes with optimum DSX binding sites was used to examine the evolutionary changes occurring in DSX and its targets in insects.
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Affiliation(s)
- Shengzhan D Luo
- Biology Department, Stanford University, Stanford, CA 94305, USA
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29
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Spasskaya DS, Karpov DS, Karpov VL. Escherichia coli Dam-methylase as a molecular tool for mapping binding sites of the yeast transcription factor Rpn4. Mol Biol 2011. [DOI: 10.1134/s0026893311030186] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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30
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Xiao R, Moore DD. DamIP: using mutant DNA adenine methyltransferase to study DNA-protein interactions in vivo. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2011; Chapter 21:Unit21.21. [PMID: 21472695 DOI: 10.1002/0471142727.mb2121s94] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
DamIP is a new method for studying DNA-protein interaction in vivo. A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N(6)-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched by immunopreciptation with an antibody that recognizes N(6)-methyladenine, and can then be used for further analysis, e.g., real-time PCR, microarray, or high-throughput sequencing. This method is simple and does not require protein-DNA crosslinking or a specific antibody to the protein of interest. This unit describes the application of this method for identification of DNA binding sites in vivo.
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Affiliation(s)
- Rui Xiao
- Baylor College of Medicine, Houston, Texas, USA
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31
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Barry KC, Abed M, Kenyagin D, Werwie TR, Boico O, Orian A, Parkhurst SM. The Drosophila STUbL protein Degringolade limits HES functions during embryogenesis. Development 2011; 138:1759-69. [PMID: 21486924 DOI: 10.1242/dev.058420] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Degringolade (Dgrn) encodes a Drosophila SUMO-targeted ubiquitin ligase (STUbL) protein similar to that of mammalian RNF4. Dgrn facilitates the ubiquitylation of the HES protein Hairy, which disrupts the repressive activity of Hairy by inhibiting the recruitment of its cofactor Groucho. We show that Hey and all HES family members, except Her, interact with Dgrn and are substrates for its E3 ubiquitin ligase activity. Dgrn displays dynamic subcellular localization, accumulates in the nucleus at times when HES family members are active and limits Hey and HES family activity during sex determination, segmentation and neurogenesis. We show that Dgrn interacts with the Notch signaling pathway by it antagonizing the activity of E(spl)-C proteins. dgrn null mutants are female sterile, producing embryos that arrest development after two or three nuclear divisions. These mutant embryos exhibit fragmented or decondensed nuclei and accumulate higher levels of SUMO-conjugated proteins, suggesting a role for Dgrn in genome stability.
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Affiliation(s)
- Kevin C Barry
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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32
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Phosphorylation of Groucho Mediates RTK Feedback Inhibition and Prolonged Pathway Target Gene Expression. Curr Biol 2011; 21:1102-10. [DOI: 10.1016/j.cub.2011.05.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2010] [Revised: 04/05/2011] [Accepted: 05/24/2011] [Indexed: 12/31/2022]
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33
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Abed M, Barry KC, Kenyagin D, Koltun B, Phippen TM, Delrow JJ, Parkhurst SM, Orian A. Degringolade, a SUMO-targeted ubiquitin ligase, inhibits Hairy/Groucho-mediated repression. EMBO J 2011; 30:1289-301. [PMID: 21343912 PMCID: PMC3094120 DOI: 10.1038/emboj.2011.42] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 01/26/2011] [Indexed: 11/09/2022] Open
Abstract
Transcriptional cofactors are essential for proper embryonic development. One such cofactor in Drosophila, Degringolade (Dgrn), encodes a RING finger/E3 ubiquitin ligase. Dgrn and its mammalian ortholog RNF4 are SUMO-targeted ubiquitin ligases (STUbLs). STUbLs bind to SUMOylated proteins via their SUMO interaction motif (SIM) domains and facilitate substrate ubiquitylation. In this study, we show that Dgrn is a negative regulator of the repressor Hairy and its corepressor Groucho (Gro/transducin-like enhancer (TLE)) during embryonic segmentation and neurogenesis, as dgrn heterozygosity suppresses Hairy mutant phenotypes and embryonic lethality. Mechanistically Dgrn functions as a molecular selector: it targets Hairy for SUMO-independent ubiquitylation that inhibits the recruitment of its corepressor Gro, without affecting the recruitment of its other cofactors or the stability of Hairy. Concomitantly, Dgrn specifically targets SUMOylated Gro for sequestration and antagonizes Gro functions in vivo. Our findings suggest that by targeting SUMOylated Gro, Dgrn serves as a molecular switch that regulates cofactor recruitment and function during development. As Gro/TLE proteins are conserved universal corepressors, this may be a general paradigm used to regulate the Gro/TLE corepressors in other developmental processes.
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Affiliation(s)
- Mona Abed
- Cancer and Vascular Biology Research Center, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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34
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Hoang CQ, Burnett ME, Curtiss J. Drosophila CtBP regulates proliferation and differentiation of eye precursors and complexes with Eyeless, Dachshund, Dan, and Danr during eye and antennal development. Dev Dyn 2011; 239:2367-85. [PMID: 20730908 DOI: 10.1002/dvdy.22380] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Specification factors regulate cell fate in part by interacting with transcriptional co-regulators like CtBP to regulate gene expression. Here, we demonstrate that CtBP forms a complex or complexes with the Drosophila melanogaster Pax6 homolog Eyeless (Ey), and with Distal antenna (Dan), Distal antenna related (Danr), and Dachshund to promote eye and antennal specification. Phenotypic analysis together with molecular data indicate that CtBP interacts with Ey to prevent overproliferation of eye precursors. In contrast, CtBP,dan,danr triple mutant adult eyes have significantly fewer ommatidia than CtBP single or dan,danr double mutants, suggesting that the CtBP/Dan/Danr complex functions to recruit ommatidia from the eye precursor pool. Furthermore, CtBP single and to a greater extent CtBP,dan,danr triple mutants affect the establishment and maintenance of the R8 precursor, which is the founding ommatidial cell. Thus, CtBP interacts with different eye specification factors to regulate gene expression appropriate for proliferative vs. differentiative stages of eye development.
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Affiliation(s)
- Chinh Q Hoang
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
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35
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Germann S, Gaudin V. Mapping in vivo protein-DNA interactions in plants by DamID, a DNA adenine methylation-based method. Methods Mol Biol 2011; 754:307-21. [PMID: 21720961 DOI: 10.1007/978-1-61779-154-3_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DamID (DNA adenine methylation identification) is an adenine methylation-based tagging method designed to map protein-DNA interactions in vivo. DamID, an alternative method to chromatin immunoprecipitation (ChIP), is based on the covalent linking of a "fingerprint" in the vicinity of the DNA-binding sites of the protein of interest. The fingerprints can be further mapped by simple molecular approaches. First developed by van Steensel's group in Drosophila melanogaster, DamID was successfully adapted to Arabidopsis thaliana, and its feasibility demonstrated by using the well-known yeast GAL4 transcription factor. The method was further used to establish a genome-wide map of the target sites of LHP1, a regulatory chromatin protein in A. thaliana.
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Affiliation(s)
- Sophie Germann
- Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Léon Bérard, Lyon Cedex, France.
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36
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Sartorelli V, Juan AH. Sculpting chromatin beyond the double helix: epigenetic control of skeletal myogenesis. Curr Top Dev Biol 2011; 96:57-83. [PMID: 21621067 DOI: 10.1016/b978-0-12-385940-2.00003-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Satellite cells (SCs) are the main source of adult skeletal muscle stem cells responsible for muscle growth and regeneration. By interpreting extracellular cues, developmental regulators control quiescence, proliferation, and differentiation of SCs by influencing coordinate gene expression. The scope of this review is limited to the description and discussion of protein complexes that introduce and decode heritable histone and chromatin modifications and how these modifications are relevant for SC biology.
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Affiliation(s)
- Vittorio Sartorelli
- Laboratory of Muscle Stem Cell and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
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37
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Woolcock KJ, Gaidatzis D, Punga T, Bühler M. Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe. Nat Struct Mol Biol 2010; 18:94-9. [PMID: 21151114 DOI: 10.1038/nsmb.1935] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 09/20/2010] [Indexed: 01/06/2023]
Abstract
In the fission yeast S. pombe, the RNA interference (RNAi) pathway is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic silencing of centromeric repeats. Here, we demonstrate that RNAi also functions to repress genomic elements other than constitutive heterochromatin. Using DNA adenine methyltransferase identification (DamID), we show that the RNAi proteins Dcr1 and Rdp1 physically associate with some euchromatic genes, noncoding RNA genes and retrotransposon long terminal repeats, and that this association is independent of the Clr4 histone methyltransferase. Physical association of RNAi with chromatin is sufficient to trigger a silencing response but not to assemble heterochromatin. The mode of silencing at the newly identified RNAi targets is consistent with a co-transcriptional gene silencing model, as proposed earlier, and functions with trace amounts of siRNAs. We anticipate that similar mechanisms could also be operational in other eukaryotes.
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Affiliation(s)
- Katrina J Woolcock
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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38
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Conserved catalytic and C-terminal regulatory domains of the C-terminal binding protein corepressor fine-tune the transcriptional response in development. Mol Cell Biol 2010; 31:375-84. [PMID: 21078873 DOI: 10.1128/mcb.00772-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Transcriptional corepressors play complex roles in developmental gene regulation. These proteins control transcription by recruiting diverse chromatin-modifying enzymes, but it is not known whether corepressor activities are finely regulated in different developmental settings or whether their basic activities are identical in most contexts. The evolutionarily conserved C-terminal binding protein (CtBP) is recruited by a variety of transcription factors that play crucial roles in development and disease. CtBP contains a central NAD(H) binding core domain that is homologous to D2 hydroxy acid dehydrogenase enzymes, as well as an unstructured C-terminal domain. NAD(H) binding is important for CtBP function, but the significance of its intrinsic dehydrogenase activity, as well as that of the unstructured C terminus, is poorly understood. To clarify the biological relevance of these features, we established genetic rescue assays to determine how different forms of CtBP function in the context of Drosophila melanogaster development. The mutant phenotypes and specific gene regulatory effects indicate that both the catalytic site of CtBP and the C-terminal extension play important, if nonessential roles in development. Our results indicate that the structural and enzymatic features of CtBP, previously thought to be dispensable for overall transcriptional control, are critical for modulating this protein's activity in diverse developmental settings.
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39
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Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 2010; 143:212-24. [PMID: 20888037 DOI: 10.1016/j.cell.2010.09.009] [Citation(s) in RCA: 683] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 08/02/2010] [Accepted: 08/27/2010] [Indexed: 01/03/2023]
Abstract
Chromatin is important for the regulation of transcription and other functions, yet the diversity of chromatin composition and the distribution along chromosomes are still poorly characterized. By integrative analysis of genome-wide binding maps of 53 broadly selected chromatin components in Drosophila cells, we show that the genome is segmented into five principal chromatin types that are defined by unique yet overlapping combinations of proteins and form domains that can extend over > 100 kb. We identify a repressive chromatin type that covers about half of the genome and lacks classic heterochromatin markers. Furthermore, transcriptionally active euchromatin consists of two types that differ in molecular organization and H3K36 methylation and regulate distinct classes of genes. Finally, we provide evidence that the different chromatin types help to target DNA-binding factors to specific genomic regions. These results provide a global view of chromatin diversity and domain organization in a metazoan cell.
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40
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Xiao R, Roman-Sanchez R, Moore DD. DamIP: a novel method to identify DNA binding sites in vivo. NUCLEAR RECEPTOR SIGNALING 2010; 8:e003. [PMID: 20419059 PMCID: PMC2858267 DOI: 10.1621/nrs.08003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 03/09/2010] [Indexed: 11/20/2022]
Abstract
Identifying binding sites and target genes of transcription factors is a major biologic problem. The most commonly used current technique, chromatin immunoprecipitation (ChIP), is dependent on a high quality antibody for each protein of interest, which is not always available, and is also cumbersome, involving sequential cross-linking and reversal of cross-linking. We have developed a novel strategy to study protein DNA binding sites in vivo, which we term DamIP. By tethering a mutant form of E. coli DNA adenine methyltransferase to the target protein, the fusion protein introduces N-6-adenosine methylation to sequences proximal to the protein binding sites. DNA fragments with this modification, which is absent in eukaryotes, are detected using an antibody directed against methylated adenosine. For an initial test of the method we used human estrogen receptor α (hERα), one of the best studied transcription factors. We found that expression of Dam-hERα fusion proteins in MCF-7 cells introduces adenosine methylation near a series of known direct hERα binding sites. Specific methylation tags are also found at indirect hERα binding sites, including both primary binding sites for the ER interactors AP-1 and SP1, and promoters that are activated by upstream ER bound enhancers. DamIP provides a new tool for the study of DNA interacting protein function in vivo.
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Affiliation(s)
- Rui Xiao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
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41
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Kong EC, Allouche L, Chapot PA, Vranizan K, Moore MS, Heberlein U, Wolf FW. Ethanol-regulated genes that contribute to ethanol sensitivity and rapid tolerance in Drosophila. Alcohol Clin Exp Res 2010; 34:302-16. [PMID: 19951294 PMCID: PMC2903447 DOI: 10.1111/j.1530-0277.2009.01093.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Increased ethanol intake, a major predictor for the development of alcohol use disorders, is facilitated by the development of tolerance to both the aversive and pleasurable effects of the drug. The molecular mechanisms underlying ethanol tolerance development are complex and are not yet well understood. METHODS To identify genetic mechanisms that contribute to ethanol tolerance, we examined the time course of gene expression changes elicited by a single sedating dose of ethanol in Drosophila, and completed a behavioral survey of strains harboring mutations in ethanol-regulated genes. RESULTS Enrichment for genes in metabolism, nucleic acid binding, olfaction, regulation of signal transduction, and stress suggests that these biological processes are coordinately affected by ethanol exposure. We also detected a coordinate up-regulation of genes in the Toll and Imd innate immunity signal transduction pathways. A multi-study comparison revealed a small set of genes showing similar regulation, including increased expression of 3 genes for serine biosynthesis. A survey of Drosophila strains harboring mutations in ethanol-regulated genes for ethanol sensitivity and tolerance phenotypes revealed roles for serine biosynthesis, olfaction, transcriptional regulation, immunity, and metabolism. Flies harboring deletions of the genes encoding the olfactory co-receptor Or83b or the sirtuin Sir2 showed marked changes in the development of ethanol tolerance. CONCLUSIONS Our findings implicate novel roles for these genes in regulating ethanol behavioral responses.
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Affiliation(s)
- Eric C Kong
- Ernest Gallo Clinic and Research Center, Emeryville, California, USA
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42
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Neural stem cell transcriptional networks highlight genes essential for nervous system development. EMBO J 2010; 28:3799-807. [PMID: 19851284 PMCID: PMC2770102 DOI: 10.1038/emboj.2009.309] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 09/14/2009] [Indexed: 11/30/2022] Open
Abstract
Neural stem cells must strike a balance between self-renewal and multipotency, and differentiation. Identification of the transcriptional networks regulating stem cell division is an essential step in understanding how this balance is achieved. We have shown that the homeodomain transcription factor, Prospero, acts to repress self-renewal and promote differentiation. Among its targets are three neural stem cell transcription factors, Asense, Deadpan and Snail, of which Asense and Deadpan are repressed by Prospero. Here, we identify the targets of these three factors throughout the genome. We find a large overlap in their target genes, and indeed with the targets of Prospero, with 245 genomic loci bound by all factors. Many of the genes have been implicated in vertebrate stem cell self-renewal, suggesting that this core set of genes is crucial in the switch between self-renewal and differentiation. We also show that multiply bound loci are enriched for genes previously linked to nervous system phenotypes, thereby providing a shortcut to identifying genes important for nervous system development.
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Abstract
The proteolytic cleavages elicited by activation of the Notch receptor release an intracellular fragment, Notch intracellular domain, which enters the nucleus to activate the transcription of targets. Changes in transcription are therefore a major output of this pathway. However, the Notch outputs clearly differ from cell type to cell type. In this review we discuss current understanding of Notch targets, the mechanisms involved in their transcriptional regulation, and what might underlie the activation of different sets of targets in different cell types.
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Affiliation(s)
- Sarah Bray
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
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44
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van Steensel B, Braunschweig U, Filion GJ, Chen M, van Bemmel JG, Ideker T. Bayesian network analysis of targeting interactions in chromatin. Genome Res 2009; 20:190-200. [PMID: 20007327 DOI: 10.1101/gr.098822.109] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In eukaryotes, many chromatin proteins together regulate gene expression. Chromatin proteins often direct the genomic binding pattern of other chromatin proteins, for example, by recruitment or competition mechanisms. The network of such targeting interactions in chromatin is complex and still poorly understood. Based on genome-wide binding maps, we constructed a Bayesian network model of the targeting interactions among a broad set of 43 chromatin components in Drosophila cells. This model predicts many novel functional relationships. For example, we found that the homologous proteins HP1 and HP1C each target the heterochromatin protein HP3 to distinct sets of genes in a competitive manner. We also discovered a central role for the remodeling factor Brahma in the targeting of several DNA-binding factors, including GAGA factor, JRA, and SU(VAR)3-7. Our network model provides a global view of the targeting interplay among dozens of chromatin components.
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Affiliation(s)
- Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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45
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Azad P, Zhou D, Russo E, Haddad GG. Distinct mechanisms underlying tolerance to intermittent and constant hypoxia in Drosophila melanogaster. PLoS One 2009; 4:e5371. [PMID: 19401761 PMCID: PMC2670512 DOI: 10.1371/journal.pone.0005371] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Accepted: 04/02/2009] [Indexed: 01/26/2023] Open
Abstract
Background Constant hypoxia (CH) and intermittent hypoxia (IH) occur during several pathological conditions such as asthma and obstructive sleep apnea. Our research is focused on understanding the molecular mechanisms that lead to injury or adaptation to hypoxic stress using Drosophila as a model system. Our current genome-wide study is designed to investigate gene expression changes and identify protective mechanism(s) in D. melanogaster after exposure to severe (1% O2) intermittent or constant hypoxia. Methodology/Principal Findings Our microarray analysis has identified multiple gene families that are up- or down-regulated in response to acute CH or IH. We observed distinct responses to IH and CH in gene expression that varied in the number of genes and type of gene families. We then studied the role of candidate genes (up-or down-regulated) in hypoxia tolerance (adult survival) for longer periods (CH-7 days, IH-10 days) under severe CH or IH. Heat shock proteins up-regulation (specifically Hsp23 and Hsp70) led to a significant increase in adult survival (as compared to controls) of P-element lines during CH. In contrast, during IH treatment the up-regulation of Mdr49 and l(2)08717 genes (P-element lines) provided survival advantage over controls. This suggests that the increased transcript levels following treatment with either paradigm play an important role in tolerance to severe hypoxia. Furthermore, by over-expressing Hsp70 in specific tissues, we found that up-regulation of Hsp70 in heart and brain play critical role in tolerance to CH in flies. Conclusions/Significance We observed that the gene expression response to IH or CH is specific and paradigm-dependent. We have identified several genes Hsp23, Hsp70, CG1600, l(2)08717 and Mdr49 that play an important role in hypoxia tolerance whether it is in CH or IH. These data provide further clues about the mechanisms by which IH or CH lead to cell injury and morbidity or adaptation and survival.
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Affiliation(s)
- Priti Azad
- Department of Pediatrics, Section of Respiratory Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Dan Zhou
- Department of Pediatrics, Section of Respiratory Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Erilynn Russo
- Department of Pediatrics, Section of Respiratory Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Gabriel G. Haddad
- Department of Pediatrics, Section of Respiratory Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Neuroscience, University of California San Diego, La Jolla, California, United States of America
- The Rady Children's Hospital, San Diego, California, United States of America
- * E-mail:
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Gauhar Z, Sun LV, Hua S, Mason CE, Fuchs F, Li TR, Boutros M, White KP. Genomic mapping of binding regions for the Ecdysone receptor protein complex. Genome Res 2009; 19:1006-13. [PMID: 19237466 DOI: 10.1101/gr.081349.108] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We determined the physical locations of the heterodimeric Ecdysone receptor/Ultraspiracle (ECR/USP) nuclear hormone receptor complex throughout the entire nonrepetitive genome of Drosophila melanogaster using a cell line (Kc167) that differentiates in response to 20-hydroxyecdysone (20-HE). 20-HE, the natural ligand of this complex, controls major aspects of insect development, including molting, metamorphosis, and reproduction. Direct gene targets of 20-HE signaling were identified by combining this physical binding-site profiling with gene expression profiling after treatment with 20-HE. We found 502 significant regions of ECR/USP binding throughout the genome. Only 42% of these regions are nearby genes that are 20-HE responsive in these cells. However, at least three quarters of the remaining ECR/USP regions are near 20-HE-regulated genes in other tissue and cell types during metamorphosis, suggesting that binding at many regulatory elements in the genome is largely noncell-type specific. The majority (21/26) of the early targets of 20-HE encode transcriptional regulatory factors. To determine whether any of these targets are required for the morphological differentiation of these cells, we used RNAi to reduce the expression of each of the 26 early genes. Accordingly, we found that three direct targets of ECR/USP--hairy, vrille, and Hr4--are required for cellular differentiation in response to the hormone. Initial mutational analysis of vrille in vivo reveals that it is required for metamorphosis.
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Affiliation(s)
- Zareen Gauhar
- Institute for Genomics and Systems Biology, Departments of Human Genetics and Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA
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47
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Orian A, Abed M, Kenyagin-Karsenti D, Boico O. DamID: a methylation-based chromatin profiling approach. Methods Mol Biol 2009; 567:155-69. [PMID: 19588092 DOI: 10.1007/978-1-60327-414-2_11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Gene expression is a dynamic process and is tightly connected to changes in chromatin structure and nuclear organization (Schneider, R. and Grosschedl, R., 2007, Genes Dev. 21, 3027-3043; Kosak, S. T. and Groudine, M., 2004, Genes Dev. 18, 1371-1384). Our ability to understand the intimate interactions between proteins and the rapidly changing chromatin environment requires methods that will be able to provide accurate, sensitive, and unbiased mapping of these interactions in vivo (van Steensel, B., 2005, Nat. Genet. 37 Suppl, S18-24). One such tool is DamID chromatin profiling, a methylation-based tagging method used to identify the direct genomic loci bound by sequence-specific transcription factors, co-factors as well as chromatin- and nuclear-associated proteins genome wide (van Steensel, B. and Henikoff, S., 2000, Nat. Biotechnol. 18, 424-428; van Steensel, Delrow, and Henikoff, 2001, Nat. Genet. 27, 304-308). Combined with other functional genomic methods and bioinformatics analysis (such as expression profiles and 5C analysis), DamID emerges as a powerful tool for analysis of chromatin structure and function in eukaryotes. DamID allows the detection of the direct genomic targets of any given factor independent of antibodies and without the need for DNA cross-linking. It is highly valuable for mapping proteins that associate with the genome indirectly or loosely (e.g., co-factors). DamID is based on the ability to fuse a bacterial Dam-methylase to a protein of interest and subsequently mark the factor's genomic binding site by adenine methylation. This marking is simple, highly specific, sensitive, inert, and can be done in both cell culture and living organisms. Below is a short description of the method, followed by a step-by-step protocol for performing DamID in Drosophila cells and embryos. Due to space limitations, the reader is referred to recent reviews that compare the method with other profiling techniques such as ChIP-chip as well as protocols for performing DamID in mammalian cells (NSouthall, T. D. and Brand, A. H., 2007, Nat. Struct. Mol. Biol. 14, 869-871; Orian, A., 2006, Curr. Opin. Genet. Dev. 16, 157-164; Vogel, M. J., Peric-Hupkes, D. and van Steensel, B. 2007, Nat. Protoc. 2, 1467-1478).
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Affiliation(s)
- Amir Orian
- Center for Vascular and Cancer Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
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A role of Pygopus as an anti-repressor in facilitating Wnt-dependent transcription. Proc Natl Acad Sci U S A 2008; 105:19324-9. [PMID: 19036929 DOI: 10.1073/pnas.0806098105] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Wnt/beta-catenin signaling controls animal development and tissue homeostasis, and is also an important cancer pathway. Pygopus (Pygo) is a conserved nuclear Wnt signaling component that is essential for Wingless-induced transcription throughout Drosophila development. It associates with Armadillo/beta-catenin and T cell factor (TCF) through the Legless/BCL9 adaptor, but its molecular function in TCF-mediated transcription is unknown. Here, we use a groucho-null allele to show that Groucho represses Wingless target genes during Drosophila development. Interestingly, groucho pygo double-mutants revealed that Pygo is not obligatory for transcriptional and phenotypic Wingless signaling outputs if the interaction between Groucho and Drosophila TCF is compromised genetically. Pygo function is also non-essential for Wingless outputs in the absence of other transcriptional antagonists of Wingless signaling. This indicates an anti-repressor function of Pygo: we propose that Pygo predisposes Drosophila TCF target genes for rapid Wingless-induced transcription, or that it protects them against premature shut-down.
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Maternal Groucho and bHLH repressors amplify the dose-sensitive X chromosome signal in Drosophila sex determination. Dev Biol 2008; 323:248-60. [PMID: 18773886 DOI: 10.1016/j.ydbio.2008.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 07/07/2008] [Accepted: 08/09/2008] [Indexed: 10/21/2022]
Abstract
In Drosophila, XX embryos are fated to develop as females, and XY embryos as males, because the diplo-X dose of four X-linked signal element genes, XSEs, activates the Sex-lethal establishment promoter, SxlPe, whereas the haplo-X XSE dose leaves SxlPe off. The threshold response of SxlPe to XSE concentrations depends in part on the bHLH repressor, Deadpan, present in equal amounts in XX and XY embryos. We identified canonical and non-canonical DNA-binding sites for Dpn at SxlPe and found that cis-acting mutations in the Dpn-binding sites caused stronger and earlier Sxl expression than did deletion of dpn implicating other bHLH repressors in Sxl regulation. Maternal Hey encodes one such bHLH regulator but the E(spl) locus does not. Elimination of the maternal corepressor Groucho also caused strong ectopic Sxl expression in XY, and premature Sxl activation in XX embryos, but Sxl was still expressed differently in the sexes. Our findings suggest that Groucho and associated maternal and zygotic bHLH repressors define the threshold XSE concentrations needed to activate SxlPe and that they participate directly in sex signal amplification. We present a model in which the XSE signal is amplified by a feedback mechanism that interferes with Gro-mediated repression in XX, but not XY embryos.
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Furman DP, Bukharina TA. Genetic control of macrochaetae development in Drosophila melanogaster. Russ J Dev Biol 2008. [DOI: 10.1134/s1062360408040012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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