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Masuda LHP, Sabino AU, Reinitz J, Ramos AF, Machado-Lima A, Andrioli LP. Global repression by tailless during segmentation. Dev Biol 2024; 505:11-23. [PMID: 37879494 PMCID: PMC10949167 DOI: 10.1016/j.ydbio.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
The orphan nuclear receptor Tailless (Tll) exhibits conserved roles in brain formation and maintenance that are shared, for example, with vertebrate orthologous forms (Tlx). However, the early expression of tll in two gap domains in the segmentation cascade of Drosophila is unusual even for most other insects. Here we investigate tll regulation on pair-rule stripes. With ectopic misexpression of tll we detected unexpected repression of almost all pair-rule stripes of hairy (h), even-skipped (eve), runt (run), and fushi-tarazu (ftz). Examining Tll embryonic ChIP-chip data with regions mapped as Cis-Regulatory Modules (CRMs) of pair-rule stripes we verified Tll interactions to these regions. With the ChIP-chip data we also verified Tll interactions to the CRMs of gap domains and in the misexpression assay, Tll-mediated repression on Kruppel (Kr), kni (kni) and giant (gt) according to their differential sensitivity to Tll. These results with gap genes confirmed previous data from the literature and argue against indirect repression roles of Tll in the striped pattern. Moreover, the prediction of Tll binding sites in the CRMs of eve stripes and the mathematical modeling of their removal using an experimentally validated theoretical framework shows effects on eve stripes compatible with the absence of a repressor binding to the CRMs. In addition, modeling increased tll levels in the embryo results in the differential repression of eve stripes, agreeing well with the results of the misexpression assay. In genetic assays we investigated eve 5, that is strongly repressed by the ectopic domain and representative of more central stripes not previously implied to be under direct regulation of tll. While this stripe is little affected in tll-, its posterior border is expanded in gt- but detected with even greater expansion in gt-;tll-. We end up by discussing tll with key roles in combinatorial repression mechanisms to contain the expression of medial patterns of the segmentation cascade in the extremities of the embryo.
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Affiliation(s)
| | - Alan Utsuni Sabino
- Departamento de Radiologia e Oncologia, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - John Reinitz
- Departments of Statistics, Ecology and Evolution, Molecular Genetics & Cell Biology, Institute of Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | | | - Ariane Machado-Lima
- Escola de Artes, Ciências e Humanidades da Universidade de São Paulo, São Paulo, Brazil
| | - Luiz Paulo Andrioli
- Escola de Artes, Ciências e Humanidades da Universidade de São Paulo, São Paulo, Brazil.
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2
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Bishop TR, Onal P, Xu Z, Zheng M, Gunasinghe H, Nien CY, Small S, Datta RR. Multi-level regulation of even-skipped stripes by the ubiquitous factor Zelda. Development 2023; 150:dev201860. [PMID: 37934130 PMCID: PMC10730019 DOI: 10.1242/dev.201860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
The zinc-finger protein Zelda (Zld) is a key activator of zygotic transcription in early Drosophila embryos. Here, we study Zld-dependent regulation of the seven-striped pattern of the pair-rule gene even-skipped (eve). Individual stripes are regulated by discrete enhancers that respond to broadly distributed activators; stripe boundaries are formed by localized repressors encoded by the gap genes. The strongest effects of Zld are on stripes 2, 3 and 7, which are regulated by two enhancers in a 3.8 kb genomic fragment that includes the eve basal promoter. We show that Zld facilitates binding of the activator Bicoid and the gap repressors to this fragment, consistent with its proposed role as a pioneer protein. To test whether the effects of Zld are direct, we mutated all canonical Zld sites in the 3.8 kb fragment, which reduced expression but failed to phenocopy the abolishment of stripes caused by removing Zld in trans. We show that Zld also indirectly regulates the eve stripes by establishing specific gap gene expression boundaries, which provides the embryonic spacing required for proper stripe activation.
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Affiliation(s)
- Timothy R. Bishop
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Pinar Onal
- Department of Molecular Biology and Genetics, Ihsan Dogramaci Bilkent University, Universiteler Mahallesi, 06800 Ankara, Turkey
| | - Zhe Xu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Michael Zheng
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Himari Gunasinghe
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Chung-Yi Nien
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Stephen Small
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Rhea R. Datta
- Department of Biology, Hamilton College, 198 College Hill Rd., Clinton, NY 13323, USA
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3
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Sugiyama M, Ozawa T, Ohta K, Okada K, Niimi T, Yamaguchi K, Shigenobu S, Okada Y. Transcriptomic and functional screening of weapon formation genes implies significance of cell adhesion molecules and female-biased genes in broad-horned flour beetle. PLoS Genet 2023; 19:e1011069. [PMID: 38051754 PMCID: PMC10723671 DOI: 10.1371/journal.pgen.1011069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/15/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
For understanding the evolutionary mechanism of sexually selected exaggerated traits, it is essential to uncover its molecular basis. By using broad-horned flour beetle that has male-specific exaggerated structures (mandibular horn, head horn and gena enlargement), we investigated the transcriptomic and functional characters of sex-biased genes. Comparative transcriptome of male vs. female prepupal heads elucidated 673 sex-biased genes. Counter-intuitively, majority of them were female-biased (584 genes), and GO enrichment analysis showed cell-adhesion molecules were frequently female-biased. This pattern motivated us to hypothesize that female-biased transcripts (i.e. the transcripts diminished in males) may play a role in outgrowth formation. Potentially, female-biased genes may act as suppressors of weapon structure. In order to test the functionality of female-biased genes, we performed RNAi-mediated functional screening for top 20 female-biased genes and 3 genes in the most enriched GO term (cell-cell adhesion, fat1/2/3, fat4 and dachsous). Knockdown of one transcription factor, zinc finger protein 608 (zfp608) resulted in the formation of male-like gena in females, supporting the outgrowth suppression function of this gene. Similarly, knockdown of fat4 induced rudimental, abnormal mandibular horn in female. fat1/2/3RNAi, fat4RNAi and dachsousRNAi males exhibited thick and/or short mandibular horns and legs. These cell adhesion molecules are known to regulate tissue growth direction and known to be involved in the weapon formation in Scarabaeoidea beetles. Functional evidence in phylogenetically distant broad-horned flour beetle suggest that cell adhesion genes are repeatedly deployed in the acquisition of outgrowth. In conclusion, this study clarified the overlooked functions of female-biased genes in weapon development.
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Affiliation(s)
- Miyu Sugiyama
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Takane Ozawa
- Department of Life Sciences, The University of Tokyo, Komaba, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, The University of Tokyo, Komaba, Tokyo, Japan
| | - Kensuke Okada
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Tsushima-naka, Okayama, Japan
| | - Teruyuki Niimi
- National Institute for Basic Biology, Nishigonaka, Myodaiji, Okazaki, Japan
- Basic Biology Program, The Graduate University for Advanced Studies, SOKENDAI, Nishigonaka, Myodaiji, Okazaki, Japan
| | - Katsushi Yamaguchi
- National Institute for Basic Biology, Nishigonaka, Myodaiji, Okazaki, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Nishigonaka, Myodaiji, Okazaki, Japan
- Basic Biology Program, The Graduate University for Advanced Studies, SOKENDAI, Nishigonaka, Myodaiji, Okazaki, Japan
| | - Yasukazu Okada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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4
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Johnson SL, Tsou WL, Prifti MV, Harris AL, Todi SV. A survey of protein interactions and posttranslational modifications that influence the polyglutamine diseases. Front Mol Neurosci 2022; 15:974167. [PMID: 36187346 PMCID: PMC9515312 DOI: 10.3389/fnmol.2022.974167] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 01/20/2023] Open
Abstract
The presence and aggregation of misfolded proteins has deleterious effects in the nervous system. Among the various diseases caused by misfolded proteins is the family of the polyglutamine (polyQ) disorders. This family comprises nine members, all stemming from the same mutation—the abnormal elongation of a polyQ repeat in nine different proteins—which causes protein misfolding and aggregation, cellular dysfunction and disease. While it is the same type of mutation that causes them, each disease is distinct: it is influenced by regions and domains that surround the polyQ repeat; by proteins with which they interact; and by posttranslational modifications they receive. Here, we overview the role of non-polyQ regions that control the pathogenicity of the expanded polyQ repeat. We begin by introducing each polyQ disease, the genes affected, and the symptoms experienced by patients. Subsequently, we provide a survey of protein-protein interactions and posttranslational modifications that regulate polyQ toxicity. We conclude by discussing shared processes and pathways that bring some of the polyQ diseases together and may serve as common therapeutic entry points for this family of incurable disorders.
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Affiliation(s)
- Sean L. Johnson
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Matthew V. Prifti
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Autumn L. Harris
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
- Maximizing Access to Research Careers (MARC) Program, Wayne State University, Detroit, MI, United States
| | - Sokol V. Todi
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
- Maximizing Access to Research Careers (MARC) Program, Wayne State University, Detroit, MI, United States
- Department of Neurology, Wayne State University, Detroit, MI, United States
- *Correspondence: Sokol V. Todi,
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5
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Das P, Bhadra MP. Histone deacetylase (Rpd3) regulates Drosophila early brain development via regulation of Tailless. Open Biol 2020; 10:200029. [PMID: 32873153 PMCID: PMC7536075 DOI: 10.1098/rsob.200029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/29/2020] [Indexed: 11/29/2022] Open
Abstract
Tailless is a committed transcriptional repressor and principal regulator of the brain and eye development in Drosophila. Rpd3, the histone deacetylase, is an established repressor that interacts with co-repressors like Sin3a, Prospero, Brakeless and Atrophin. This study aims at deciphering the role of Rpd3 in embryonic segmentation and larval brain development in Drosophila. It delineates the mechanism of Tailless regulation by Rpd3, along with its interacting partners. There was a significant reduction in Tailless in Rpd3 heteroallelic mutant embryos, substantiating that Rpd3 is indispensable for the normal Tailless expression. The expression of the primary readout, Tailless was correlative to the expression of the neural cell adhesion molecule homologue, Fascilin2 (Fas2). Rpd3 also aids in the proper development of the mushroom body. Both Tailless and Fas2 expression are reported to be antagonistic to the epidermal growth factor receptor (EGFR) expression. The decrease in Tailless and Fas2 expression highlights that EGFR is upregulated in the larval mutants, hindering brain development. This study outlines the axis comprising Rpd3, dEGFR, Tailless and Fas2, which interact to fine-tune the early segmentation and larval brain development. Therefore, Rpd3 along with Tailless has immense significance in early embryogenesis and development of the larval brain.
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Affiliation(s)
- Paromita Das
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR) Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai 600 113, India
| | - Manika Pal Bhadra
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR) Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai 600 113, India
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6
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Pascini TV, Ramalho-Ortigão M, Ribeiro JM, Jacobs-Lorena M, Martins GF. Transcriptional profiling and physiological roles of Aedes aegypti spermathecal-related genes. BMC Genomics 2020; 21:143. [PMID: 32041546 PMCID: PMC7011475 DOI: 10.1186/s12864-020-6543-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Successful mating of female mosquitoes typically occurs once, with the male sperm being stored in the female spermatheca for every subsequent oviposition event. The female spermatheca is responsible for the maintenance, nourishment, and protection of the male sperm against damage during storage. Aedes aegypti is a major vector of arboviruses, including Yellow Fever, Dengue, Chikungunya, and Zika. Vector control is difficult due to this mosquito high reproductive capacity. RESULTS Following comparative RNA-seq analyses of spermathecae obtained from virgin and inseminated females, eight transcripts were selected based on their putative roles in sperm maintenance and survival, including energy metabolism, chitin components, transcriptional regulation, hormonal signaling, enzymatic activity, antimicrobial activity, and ionic homeostasis. In situ RNA hybridization confirmed tissue-specific expression of the eight transcripts. Following RNA interference (RNAi), observed outcomes varied between targeted transcripts, affecting mosquito survival, egg morphology, fecundity, and sperm motility within the spermathecae. CONCLUSIONS This study identified spermatheca-specific transcripts associated with sperm storage in Ae. aegypti. Using RNAi we characterized the role of eight spermathecal transcripts on various aspects of female fecundity and offspring survival. RNAi-induced knockdown of transcript AeSigP-66,427, coding for a Na+/Ca2+ protein exchanger, specifically interfered with egg production and reduced sperm motility. Our results bring new insights into the molecular basis of sperm storage and identify potential targets for Ae. aegypti control.
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Affiliation(s)
- Tales Vicari Pascini
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900 Brazil
| | - Marcelo Ramalho-Ortigão
- Division of Tropical Public Health, Department of Preventive Medicine and Biostatistics, Uniformed Services University, 4301 Jones Bridge Road, Rm A-3083, Bethesda, MD 20814 USA
| | - José Marcos Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway, Rm 2E32D, Rockville, MD 20852 USA
| | - Marcelo Jacobs-Lorena
- Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
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7
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Yeung K, Boija A, Karlsson E, Holmqvist PH, Tsatskis Y, Nisoli I, Yap D, Lorzadeh A, Moksa M, Hirst M, Aparicio S, Fanto M, Stenberg P, Mannervik M, McNeill H. Atrophin controls developmental signaling pathways via interactions with Trithorax-like. eLife 2017; 6:e23084. [PMID: 28327288 PMCID: PMC5409829 DOI: 10.7554/elife.23084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/15/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atro's critical role in development and disease, relatively little is known about Atro's binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. ChIP-seq identified 1300 potential direct targets of Atro including engrailed, and components of the Dpp and Notch signaling pathways. We show that Atro regulates Dpp and Notch signaling in larval imaginal discs, at least partially via regulation of thickveins and fringe. In addition, bioinformatics analyses, sequential ChIP and coimmunoprecipitation experiments reveal that Atro interacts with the Drosophila GAGA Factor, Trithorax-like (Trl), and they bind to the same loci simultaneously. Phenotypic analyses of Trl and Atro clones suggest that Atro is required to modulate the transcription activation by Trl in larval imaginal discs. Taken together, these data indicate that Atro is a major Trl cofactor that functions to moderate developmental gene transcription.
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Affiliation(s)
- Kelvin Yeung
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ann Boija
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Edvin Karlsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden
| | - Per-Henrik Holmqvist
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Yonit Tsatskis
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ilaria Nisoli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Damian Yap
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Alireza Lorzadeh
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Manolis Fanto
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Helen McNeill
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
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8
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van den Berg DLC, Azzarelli R, Oishi K, Martynoga B, Urbán N, Dekkers DHW, Demmers JA, Guillemot F. Nipbl Interacts with Zfp609 and the Integrator Complex to Regulate Cortical Neuron Migration. Neuron 2017; 93:348-361. [PMID: 28041881 PMCID: PMC5263256 DOI: 10.1016/j.neuron.2016.11.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 10/10/2016] [Accepted: 11/17/2016] [Indexed: 12/18/2022]
Abstract
Mutations in NIPBL are the most frequent cause of Cornelia de Lange syndrome (CdLS), a developmental disorder encompassing several neurological defects, including intellectual disability and seizures. How NIPBL mutations affect brain development is not understood. Here we identify Nipbl as a functional interaction partner of the neural transcription factor Zfp609 in brain development. Depletion of Zfp609 or Nipbl from cortical neural progenitors in vivo is detrimental to neuronal migration. Zfp609 and Nipbl overlap at genomic binding sites independently of cohesin and regulate genes that control cortical neuron migration. We find that Zfp609 and Nipbl interact with the Integrator complex, which functions in RNA polymerase 2 pause release. Indeed, Zfp609 and Nipbl co-localize at gene promoters containing paused RNA polymerase 2, and Integrator similarly regulates neuronal migration. Our data provide a rationale and mechanistic insights for the role of Nipbl in the neurological defects associated with CdLS.
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Affiliation(s)
| | - Roberta Azzarelli
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Koji Oishi
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Ben Martynoga
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Noelia Urbán
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Dick H W Dekkers
- Center for Proteomics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Jeroen A Demmers
- Center for Proteomics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - François Guillemot
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK.
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9
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The Function and Evolution of Nuclear Receptors in Insect Embryonic Development. Curr Top Dev Biol 2017; 125:39-70. [DOI: 10.1016/bs.ctdb.2017.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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10
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Andrioli LP, Dos Santos WS, Aguiar FDS, Digiampietri LA. Repression activity of Tailless on h 1 and eve 1 pair-rule stripes. Mech Dev 2016; 144:156-162. [PMID: 27773632 DOI: 10.1016/j.mod.2016.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 10/18/2016] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
We investigated the hypothesis that several transcriptional repressors are necessary to set the boundaries of anterior pair-rule stripes in Drosophila. Specifically, we tested whether Tailless (Tll) is part of a repression mechanism that correctly sets the anterior boundaries of hairy 1 (h 1) and even-skipped 1 (eve 1) stripes. Single mutant tll embryos displayed subtle deviations from the normal positions of h 1 and eve 1 stripes. Moreover, we observed stronger stripe deviations in embryos lacking both Tll and Sloppy-paired 1 (Slp 1), a common repressor for anterior pair-rule stripes. Using h 1 and eve 1 reporter constructs in the genetic assays, we provided further evidence that interference with normal mechanisms of stripe expression is mediated by Tll repression. Indeed, Tll represses both h 1 and eve 1 reporter stripes when misexpressed. Investigating the expression of other anterior gap genes in different genetic backgrounds and in the misexpression assays strengthened Tll direct repression in the regulation of h 1 and eve 1. Our results are consistent with tll being a newly-identified component of a combinatorial network of repressor genes that control pair-rule stripe formation in the anterior blastoderm of Drosophila.
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Affiliation(s)
- Luiz Paulo Andrioli
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, R. Arlindo Béttio 1000, Ermelino Matarazzo, 03828-000 São Paulo, SP, Brazil.
| | - Wesley Silva Dos Santos
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, R. Arlindo Béttio 1000, Ermelino Matarazzo, 03828-000 São Paulo, SP, Brazil
| | - Francisco Dos Santos Aguiar
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, R. Arlindo Béttio 1000, Ermelino Matarazzo, 03828-000 São Paulo, SP, Brazil
| | - Luciano Antonio Digiampietri
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, R. Arlindo Béttio 1000, Ermelino Matarazzo, 03828-000 São Paulo, SP, Brazil
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11
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Davis SM, Thomas AL, Nomie KJ, Huang L, Dierick HA. Tailless and Atrophin control Drosophila aggression by regulating neuropeptide signalling in the pars intercerebralis. Nat Commun 2016; 5:3177. [PMID: 24495972 DOI: 10.1038/ncomms4177] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/23/2013] [Indexed: 01/21/2023] Open
Abstract
Aggressive behaviour is widespread throughout the animal kingdom. However, its mechanisms are poorly understood, and the degree of molecular conservation between distantly related species is unknown. Here we show that knockdown of tailless (tll) increases aggression in Drosophila, similar to the effect of its mouse orthologue Nr2e1. Tll localizes to the adult pars intercerebralis (PI), which shows similarity to the mammalian hypothalamus. Knockdown of tll in the PI is sufficient to increase aggression and is rescued by co-expressing human NR2E1. Knockdown of Atrophin, a Tll co-repressor, also increases aggression, and both proteins physically interact in the PI. tll knockdown-induced aggression is fully suppressed by blocking neuropeptide processing or release from the PI. In addition, genetically activating PI neurons increases aggression, mimicking the aggression-inducing effect of hypothalamic stimulation. Together, our results suggest that a transcriptional control module regulates neuropeptide signalling from the neurosecretory cells of the brain to control aggressive behaviour.
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Affiliation(s)
- Shaun M Davis
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA [2]
| | - Amanda L Thomas
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA [2]
| | - Krystle J Nomie
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA [2]
| | - Longwen Huang
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Herman A Dierick
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA [3] Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA [4] Program in Developmental Biology, Houston, Texas 77030, USA
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12
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TLX-Its Emerging Role for Neurogenesis in Health and Disease. Mol Neurobiol 2016; 54:272-280. [PMID: 26738856 PMCID: PMC5219886 DOI: 10.1007/s12035-015-9608-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/03/2015] [Indexed: 02/07/2023]
Abstract
The orphan nuclear receptor TLX, also called NR2E1, is a factor important in the regulation of neural stem cell (NSC) self-renewal, neurogenesis, and maintenance. As a transcription factor, TLX is vital for the expression of genes implicated in neurogenesis, such as DNA replication, cell cycle, adhesion and migration. It acts by way of repressing or activating target genes, as well as controlling protein-protein interactions. Growing evidence suggests that dysregulated TLX acts in the initiation and progression of human disorders of the nervous system. This review describes recent knowledge about TLX expression, structure, targets, and biological functions, relevant to maintaining adult neural stem cells related to both neuropsychiatric conditions and certain nervous system tumours.
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Crona F, Holmqvist PH, Tang M, Singla B, Vakifahmetoglu-Norberg H, Fantur K, Mannervik M. The Brakeless co-regulator can directly activate and repress transcription in early Drosophila embryos. Dev Biol 2015; 407:173-81. [PMID: 26260775 DOI: 10.1016/j.ydbio.2015.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/22/2015] [Accepted: 08/06/2015] [Indexed: 11/25/2022]
Abstract
The Brakeless protein performs many important functions during Drosophila development, but how it controls gene expression is poorly understood. We previously showed that Brakeless can function as a transcriptional co-repressor. In this work, we perform transcriptional profiling of brakeless mutant embryos. Unexpectedly, the majority of affected genes are down-regulated in brakeless mutants. We demonstrate that genomic regions in close proximity to some of these genes are occupied by Brakeless, that over-expression of Brakeless causes a reciprocal effect on expression of these genes, and that Brakeless remains an activator of the genes upon fusion to an activation domain. Together, our results show that Brakeless can both repress and activate gene expression. A yeast two-hybrid screen identified the Mediator complex subunit Med19 as interacting with an evolutionarily conserved part of Brakeless. Both down- and up-regulated Brakeless target genes are also affected in Med19-depleted embryos, but only down-regulated targets are influenced in embryos depleted of both Brakeless and Med19. Our data provide support for a Brakeless activator function that regulates transcription by interacting with Med19. We conclude that the transcriptional co-regulator Brakeless can either activate or repress transcription depending on context.
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Affiliation(s)
- Filip Crona
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Per-Henrik Holmqvist
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Min Tang
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Bhumica Singla
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Helin Vakifahmetoglu-Norberg
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Katrin Fantur
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden
| | - Mattias Mannervik
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, Arrheniuslaboratories E3, Stockholm, Sweden.
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Crona F, Singla B, Mannervik M. Gene expression profiling of brakeless mutant Drosophila embryos. Data Brief 2015; 5:134-7. [PMID: 26509186 PMCID: PMC4579289 DOI: 10.1016/j.dib.2015.08.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 12/04/2022] Open
Abstract
The transcriptional co-regulator Brakeless performs many important functions during Drosophila development, but few target genes have been identified. Here we use Affymetrix microarrays to identify Brakeless-regulated genes in 2–4 h old Drosophila embryos. Robust multi-array analysis (RMA) and statistical tests revealed 240 genes that changed their expression more than 1.5 fold. We find that up- and down-regulated genes fall into distinct gene ontology categories. In our associated study [2] we demonstrate that both up- and down-regulated genes can be direct Brakeless targets. Our results indicate that the co-repressor and co-activator activities of Brakeless may result in distinct biological responses. The microarray data complies with MIAME guidelines and is deposited in GEO under accession number GSE60048.
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Affiliation(s)
- Filip Crona
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Bhumica Singla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Zhi X, Zhou XE, He Y, Searose-Xu K, Zhang CL, Tsai CC, Melcher K, Xu HE. Structural basis for corepressor assembly by the orphan nuclear receptor TLX. Genes Dev 2015; 29:440-50. [PMID: 25691470 PMCID: PMC4335298 DOI: 10.1101/gad.254904.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The orphan nuclear receptor TLX regulates neural stem cell self-renewal in the adult brain and functions primarily as a transcription repressor through recruitment of Atrophin corepressors, which bind to TLX via a conserved peptide motif termed the Atro box. Zhi et al. report crystal structures of the human and insect TLX ligand-binding domain in complex with Atro box peptides. Mutations that weaken the TLX–Atrophin interaction compromise the repressive activity of TLX. In addition, mutations of corresponding residues in other members of this class of receptors diminish their repressor activities. The orphan nuclear receptor TLX regulates neural stem cell self-renewal in the adult brain and functions primarily as a transcription repressor through recruitment of Atrophin corepressors, which bind to TLX via a conserved peptide motif termed the Atro box. Here we report crystal structures of the human and insect TLX ligand-binding domain in complex with Atro box peptides. In these structures, TLX adopts an autorepressed conformation in which its helix H12 occupies the coactivator-binding groove. Unexpectedly, H12 in this autorepressed conformation forms a novel binding pocket with residues from helix H3 that accommodates a short helix formed by the conserved ALXXLXXY motif of the Atro box. Mutations that weaken the TLX–Atrophin interaction compromise the repressive activity of TLX, demonstrating that this interaction is required for Atrophin to confer repressor activity to TLX. Moreover, the autorepressed conformation is conserved in the repressor class of orphan nuclear receptors, and mutations of corresponding residues in other members of this class of receptors diminish their repressor activities. Together, our results establish the functional conservation of the autorepressed conformation and define a key sequence motif in the Atro box that is essential for TLX-mediated repression.
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Affiliation(s)
- Xiaoyong Zhi
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA; Autophagy Research Center,
| | - X Edward Zhou
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Yuanzheng He
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Kelvin Searose-Xu
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Chun-Li Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Texas 75390, USA
| | - Chih-Cheng Tsai
- Department of Cell Biology and Neuroscience, University of California at Riverside, Riverside, California 92521, USA
| | - Karsten Melcher
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - H Eric Xu
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA; Van Andel Research Institute-Shanghai Institute of Materia Medica (VARI/SIMM) Center, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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Zhang Z, Feng J, Pan C, Lv X, Wu W, Zhou Z, Liu F, Zhang L, Zhao Y. Atrophin-Rpd3 complex represses Hedgehog signaling by acting as a corepressor of CiR. ACTA ACUST UNITED AC 2014; 203:575-83. [PMID: 24385484 PMCID: PMC3840934 DOI: 10.1083/jcb.201306012] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The evolutionarily conserved Hedgehog (Hh) signaling pathway is transduced by the Cubitus interruptus (Ci)/Gli family of transcription factors that exist in two distinct repressor (Ci(R)/Gli(R)) and activator (Ci(A)/Gli(A)) forms. Aberrant activation of Hh signaling is associated with various human cancers, but the mechanism through which Ci(R)/Gli(R) properly represses target gene expression is poorly understood. Here, we used Drosophila melanogaster and zebrafish models to define a repressor function of Atrophin (Atro) in Hh signaling. Atro directly bound to Ci through its C terminus. The N terminus of Atro interacted with a histone deacetylase, Rpd3, to recruit it to a Ci-binding site at the decapentaplegic (dpp) locus and reduce dpp transcription through histone acetylation regulation. The repressor function of Atro in Hh signaling was dependent on Ci. Furthermore, Rerea, a homologue of Atro in zebrafish, repressed the expression of Hh-responsive genes. We propose that the Atro-Rpd3 complex plays a conserved role to function as a Ci(R) corepressor.
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Affiliation(s)
- Zhao Zhang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Alkhori L, Öst A, Alenius M. The corepressor Atrophin specifies odorant receptor expression in Drosophila. FASEB J 2013; 28:1355-64. [PMID: 24334704 DOI: 10.1096/fj.13-240325] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In both insects and vertebrates, each olfactory sensory neuron (OSN) expresses one odorant receptor (OR) from a large genomic repertoire. How a receptor is specified is a tantalizing question addressing fundamental aspects of cell differentiation. Here, we demonstrate that the corepressor Atrophin (Atro) segregates OR gene expression between OSN classes in Drosophila. We show that the knockdown of Atro result in either loss or gain of a broad set of ORs. Each OR phenotypic group correlated with one of two opposing Notch fates, Notch responding, Nba (N(on)), and nonresponding, Nab (N(off)) OSNs. Our data show that Atro segregates ORs expressed in the Nba OSN classes and helps establish the Nab fate during OSN development. Consistent with a role in recruiting histone deacetylates, immunohistochemistry revealed that Atro regulates global histone 3 acetylation (H3ac) in OSNs and requires Hdac3 to segregate OR gene expression. We further found that Nba OSN classes exhibit variable but higher H3ac levels than the Nab OSNs. Together, these data suggest that Atro determines the level of H3ac, which ensures correct OR gene expression within the Nba OSNs. We propose a mechanism by which a single corepressor can specify a large number of neuron classes.
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Affiliation(s)
- Liza Alkhori
- 1Department of Clinical and Experimental Medicine, Linköping University, S-581 83 Linköping, Sweden.
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18
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Mannervik M. Control of Drosophila embryo patterning by transcriptional co-regulators. Exp Cell Res 2013; 321:47-57. [PMID: 24157250 DOI: 10.1016/j.yexcr.2013.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 12/29/2022]
Abstract
A combination of broadly expressed transcriptional activators and spatially restricted repressors are used to pattern embryos into cells of different fate. Transcriptional co-regulators are essential mediators of transcription factor function, and contribute to selective transcriptional responses in embryo development. A two step mechanism of transcriptional regulation is discussed, where remodeling of chromatin is initially required, followed by stimulation of recruitment or release of RNA polymerase from the promoter. Transcriptional co-regulators are essential for both of these steps. In particular, most co-activators are associated with histone acetylation and co-repressors with histone deacetylation. In the early Drosophila embryo, genome-wide studies have shown that the CBP co-activator has a preference for associating with some transcription factors and regulatory regions. The Groucho, CtBP, Ebi, Atrophin and Brakeless co-repressors are selectively used to limit zygotic gene expression. New findings are summarized which show that different co-repressors are often utilized by a single repressor, that the context in which a co-repressor is recruited to DNA can affect its activity, and that co-regulators may switch from co-repressors to co-activators and vice versa. The possibility that co-regulator activity is regulated and plays an instructive role in development is discussed as well. This review highlights how findings in Drosophila embryos have contributed to the understanding of transcriptional regulation in eukaryotes as well as to mechanisms of animal embryo patterning.
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Affiliation(s)
- Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Arrheniuslaboratories E3, SE-106 91 Stockholm, Sweden.
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19
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Wang Y, Liu HK, Schütz G. Role of the nuclear receptor Tailless in adult neural stem cells. Mech Dev 2013; 130:388-90. [DOI: 10.1016/j.mod.2013.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/25/2012] [Accepted: 02/01/2013] [Indexed: 10/27/2022]
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20
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Williams MJ, Almén MS, Fredriksson R, Schiöth HB. What model organisms and interactomics can reveal about the genetics of human obesity. Cell Mol Life Sci 2012; 69:3819-34. [PMID: 22618246 PMCID: PMC11114734 DOI: 10.1007/s00018-012-1022-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/22/2012] [Accepted: 05/02/2012] [Indexed: 01/05/2023]
Abstract
Genome-wide association studies have identified a number of genes associated with human body weight. While some of these genes are large fields within obesity research, such as MC4R, POMC, FTO and BDNF, the majority do not have a clearly defined functional role explaining why they may affect body weight. Here, we searched biological databases and discovered 33 additional genes associated with human obesity (CADM2, GIPR, GPCR5B, LRP1B, NEGR1, NRXN3, SH2B1, FANCL, GNPDA2, HMGCR, MAP2K5, NUDT3, PRKD1, QPCTL, TNNI3K, MTCH2, DNAJC27, SLC39A8, MTIF3, RPL27A, SEC16B, ETV5, HMGA1, TFAP2B, TUB, ZNF608, FAIM2, KCTD15, LINGO2, POC5, PTBP2, TMEM18, TMEM160). We find that the majority have orthologues in distant species, such as D. melanogaster and C. elegans, suggesting that they are important for the biology of most bilateral species. Intriguingly, signalling cascade genes and transcription factors are enriched among these obesity genes, and several of the genes show properties that could be useful for potential drug discovery. In this review, we demonstrate how information from several distant model species, interactomics and signalling pathway analysis represents an important way to better understand the functional diversity of the surprisingly high number of molecules that seem to be important for human obesity.
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Affiliation(s)
- Michael J. Williams
- Department of Neuroscience, Functional Pharmacology, Biomedical Center, Uppsala University, Box 593, 75 124 Uppsala, Sweden
| | - Markus S. Almén
- Department of Neuroscience, Functional Pharmacology, Biomedical Center, Uppsala University, Box 593, 75 124 Uppsala, Sweden
| | - Robert Fredriksson
- Department of Neuroscience, Functional Pharmacology, Biomedical Center, Uppsala University, Box 593, 75 124 Uppsala, Sweden
| | - Helgi B. Schiöth
- Department of Neuroscience, Functional Pharmacology, Biomedical Center, Uppsala University, Box 593, 75 124 Uppsala, Sweden
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21
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Reed NP, Henderson MA, Oltz EM, Aune TM. Reciprocal regulation of Rag expression in thymocytes by the zinc-finger proteins, Zfp608 and Zfp609. Genes Immun 2012; 14:7-12. [PMID: 23076336 DOI: 10.1038/gene.2012.47] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recombination-activating gene 1 (Rag1) and Rag2 enzymes are required for T cell receptor assembly and thymocyte development. The mechanisms underlying the transcriptional activation and repression of Rag1 and Rag2 are incompletely understood. The zinc-finger protein, Zfp608, represses Rag1 and Rag2 expression when expressed in thymocytes blocking T-cell maturation. Here we show that the related zinc-finger protein, Zfp609, is necessary for Rag1 and Rag2 expression in developing thymocytes. Zfp608 represses Rag1 and Rag2 expression indirectly by repressing the expression of Zfp609. Thus, the balance of Zfp608 and Zfp609 plays a critical role in regulating Rag1 and Rag2 expression, which may manifest itself not only during development of immature thymocytes into mature T cells but also in generation of the T-cell arm of the adaptive immune system, which does not fully develop until after birth.
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Affiliation(s)
- N P Reed
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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22
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Struffi P, Corado M, Kaplan L, Yu D, Rushlow C, Small S. Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer. Development 2011; 138:4291-9. [PMID: 21865322 DOI: 10.1242/dev.065987] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Despite years of study, the precise mechanisms that control position-specific gene expression during development are not understood. Here, we analyze an enhancer element from the even skipped (eve) gene, which activates and positions two stripes of expression (stripes 3 and 7) in blastoderm stage Drosophila embryos. Previous genetic studies showed that the JAK-STAT pathway is required for full activation of the enhancer, whereas the gap genes hunchback (hb) and knirps (kni) are required for placement of the boundaries of both stripes. We show that the maternal zinc-finger protein Zelda (Zld) is absolutely required for activation, and present evidence that Zld binds to multiple non-canonical sites. We also use a combination of in vitro binding experiments and bioinformatics analysis to redefine the Kni-binding motif, and mutational analysis and in vivo tests to show that Kni and Hb are dedicated repressors that function by direct DNA binding. These experiments significantly extend our understanding of how the eve enhancer integrates positive and negative transcriptional activities to generate sharp boundaries in the early embryo.
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Affiliation(s)
- Paolo Struffi
- Department of Biology, New York University, New York, NY 10003, USA
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23
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A cis-regulatory map of the Drosophila genome. Nature 2011; 471:527-31. [PMID: 21430782 DOI: 10.1038/nature09990] [Citation(s) in RCA: 397] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 02/02/2011] [Indexed: 01/01/2023]
Abstract
Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships.
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Napoletano F, Occhi S, Calamita P, Volpi V, Blanc E, Charroux B, Royet J, Fanto M. Polyglutamine Atrophin provokes neurodegeneration in Drosophila by repressing fat. EMBO J 2011; 30:945-58. [PMID: 21278706 DOI: 10.1038/emboj.2011.1] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 12/22/2010] [Indexed: 01/13/2023] Open
Abstract
Large alterations in transcription accompany neurodegeneration in polyglutamine (polyQ) diseases. These pathologies manifest both general polyQ toxicity and mutant protein-specific effects. In this study, we report that the fat tumour suppressor gene mediates neurodegeneration induced by the polyQ protein Atrophin. We have monitored early transcriptional alterations in a Drosophila model of Dentatorubral-pallidoluysian Atrophy and found that polyQ Atrophins downregulate fat. Fat protects from neurodegeneration and Atrophin toxicity through the Hippo kinase cascade. Fat/Hippo signalling does not provoke neurodegeneration by stimulating overgrowth; rather, it alters the autophagic flux in photoreceptor neurons, thereby affecting cell homeostasis. Our data thus provide a crucial insight into the specific mechanism of a polyQ disease and reveal an unexpected neuroprotective role of the Fat/Hippo pathway.
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Affiliation(s)
- Francesco Napoletano
- Dulbecco Telethon Institute and Division of Neuroscience, DIBIT-San Raffaele Scientific Institute, Milan, Italy
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25
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Abstract
Gap genes are involved in segment determination during the early development of the fruit fly Drosophila melanogaster as well as in other insects. This review attempts to synthesize the current knowledge of the gap gene network through a comprehensive survey of the experimental literature. I focus on genetic and molecular evidence, which provides us with an almost-complete picture of the regulatory interactions responsible for trunk gap gene expression. I discuss the regulatory mechanisms involved, and highlight the remaining ambiguities and gaps in the evidence. This is followed by a brief discussion of molecular regulatory mechanisms for transcriptional regulation, as well as precision and size-regulation provided by the system. Finally, I discuss evidence on the evolution of gap gene expression from species other than Drosophila. My survey concludes that studies of the gap gene system continue to reveal interesting and important new insights into the role of gene regulatory networks in development and evolution.
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Affiliation(s)
- Johannes Jaeger
- Centre de Regulació Genòmica, Universtitat Pompeu Fabra, Barcelona, Spain.
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Astigarraga S, Hofmeyer K, Treisman JE. Missed connections: photoreceptor axon seeks target neuron for synaptogenesis. Curr Opin Genet Dev 2010; 20:400-7. [PMID: 20434326 DOI: 10.1016/j.gde.2010.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Revised: 03/31/2010] [Accepted: 04/02/2010] [Indexed: 02/06/2023]
Abstract
Extending axons must choose the appropriate synaptic target cells in order to assemble functional neural circuitry. The axons of the Drosophila color-sensitive photoreceptors R7 and R8 project as a single fascicle from each ommatidium, but their terminals are segregated into distinct layers within their target region. Recent studies have begun to reveal the molecular mechanisms that establish this projection pattern. Both homophilic adhesion molecules and specific ligand-receptor interactions make important contributions to stabilizing R7 and R8 terminals in the appropriate target layers. These cell recognition molecules are regulated by the same transcription factors that control R7 and R8 cell fates. Autocrine and repulsive signaling mechanisms prevent photoreceptor terminals from encroaching on their neighbors, preserving the spatial resolution of visual information.
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Affiliation(s)
- Sergio Astigarraga
- Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
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27
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Tailless patterning functions are conserved in the honeybee even in the absence of Torso signaling. Dev Biol 2009; 335:276-87. [DOI: 10.1016/j.ydbio.2009.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 08/21/2009] [Accepted: 09/01/2009] [Indexed: 02/07/2023]
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28
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Wang L, Tsai CC. Atrophin proteins: an overview of a new class of nuclear receptor corepressors. NUCLEAR RECEPTOR SIGNALING 2008; 6:e009. [PMID: 19043594 PMCID: PMC2586093 DOI: 10.1621/nrs.06009] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 09/22/2008] [Indexed: 12/12/2022]
Abstract
The normal development and physiological functions of multicellular organisms are regulated by complex gene transcriptional networks that include myriad transcription factors, their associating coregulators, and multiple chromatin-modifying factors. Aberrant gene transcriptional regulation resulting from mutations among these elements often leads to developmental defects and diseases. This review article concentrates on the Atrophin family proteins, including vertebrate Atrophin-1 (ATN1), vertebrate arginine-glutamic acid dipeptide repeats protein (RERE), and Drosophila Atrophin (Atro), which we recently identified as nuclear receptor corepressors. Disruption of Atrophin-mediated pathways causes multiple developmental defects in mouse, zebrafish, and Drosophila, while an aberrant form of ATN1 and altered expression levels of RERE are associated with neurodegenerative disease and cancer in humans, respectively. We here provide an overview of current knowledge about these Atrophin proteins. We hope that this information on Atrophin proteins may help stimulate fresh ideas about how this newly identified class of nuclear receptor corepressors aids specific nuclear receptors and other transcriptional factors in regulating gene transcription, manifesting physiological effects, and causing diseases.
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Affiliation(s)
- Lei Wang
- Department of Physiology and Biophysics, UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
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29
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Benn CL, Fox H, Bates GP. Optimisation of region-specific reference gene selection and relative gene expression analysis methods for pre-clinical trials of Huntington's disease. Mol Neurodegener 2008; 3:17. [PMID: 18954449 PMCID: PMC2584034 DOI: 10.1186/1750-1326-3-17] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 10/27/2008] [Indexed: 12/01/2022] Open
Abstract
Background Transcriptional dysregulation is an early, key pathogenic mechanism in Huntington's disease (HD). Therefore, gene expression analyses have biomarker potential for measuring therapeutic efficacy in pre-clinical trials, particularly those aimed at correcting gene expression abnormalities. Housekeeping genes are commonly used as endogenous references in gene expression studies. However, a systematic study comparing the suitability of candidate reference genes for use in HD mouse models has not been performed. To remedy this situation, 12 housekeeping genes were examined to identify suitable reference genes for use in expression assays. Results We found that commonly used reference genes are dysregulated at later time points in the R6/2 mouse model of HD. Therefore, in order to reliably measure gene expression changes for use as pre-clinical trial biomarkers, we set out to identify suitable reference genes for use in R6/2 mice. The expression of potential reference genes was examined in striatum, cortex and cerebellum from 15 week old R6/2 and matched wild-type littermates. Expression levels of candidate reference genes varied according to genotype and brain region. GeNorm software was used to identify the three most stably expressed genes for each brain region. Relative quantification methods using the geometric mean of three reference genes for normalisation enables accurate determination of gene expression levels in wild-type and R6/2 mouse brain regions. Conclusion Our study has identified a reproducible, reliable method by which we able to accurately determine the relative expression level of target genes in specific brain regions, thus increasing the potential of gene expression analysis as a biomarker in HD pre-clinical trials.
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Affiliation(s)
- Caroline L Benn
- Medical and Molecular Genetics, King's College London School of Medicine, 8th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
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Stielow B, Sapetschnig A, Krüger I, Kunert N, Brehm A, Boutros M, Suske G. Identification of SUMO-Dependent Chromatin-Associated Transcriptional Repression Components by a Genome-wide RNAi Screen. Mol Cell 2008; 29:742-54. [PMID: 18374648 DOI: 10.1016/j.molcel.2007.12.032] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2007] [Revised: 10/26/2007] [Accepted: 12/24/2007] [Indexed: 11/18/2022]
Affiliation(s)
- Bastian Stielow
- Institute of Molecular Biology and Tumor Research, Philipps-University of Marburg, Emil-Mannkopff-Strasse 2, D-35032 Marburg, Germany
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Drosophila Ebi mediates Snail-dependent transcriptional repression through HDAC3-induced histone deacetylation. EMBO J 2008; 27:898-909. [PMID: 18309295 DOI: 10.1038/emboj.2008.26] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 02/07/2008] [Indexed: 01/14/2023] Open
Abstract
The Drosophila Snail protein is a transcriptional repressor that is necessary for mesoderm formation. Here, we identify the Ebi protein as an essential Snail co-repressor. In ebi mutant embryos, Snail target genes are derepressed in the presumptive mesoderm. Ebi and Snail interact both genetically and physically. We identify a Snail domain that is sufficient for Ebi binding, and which functions independently of another Snail co-repressor, Drosophila CtBP. This Ebi interaction domain is conserved among all insect Snail-related proteins, is a potent repression domain and is required for Snail function in transgenic embryos. In mammalian cells, the Ebi homologue TBL1 is part of the NCoR/SMRT-HDAC3 (histone deacetylase 3) co-repressor complex. We found that Ebi interacts with Drosophila HDAC3, and that HDAC3 knockdown or addition of a HDAC inhibitor impairs Snail-mediated repression in cells. In the early embryo, Ebi is recruited to a Snail target gene in a Snail-dependent manner, which coincides with histone hypoacetylation. Our results demonstrate that Snail requires the combined activities of Ebi and CtBP, and indicate that histone deacetylation is a repression mechanism in early Drosophila development.
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Pauli A, Althoff F, Oliveira RA, Heidmann S, Schuldiner O, Lehner CF, Dickson BJ, Nasmyth K. Cell-type-specific TEV protease cleavage reveals cohesin functions in Drosophila neurons. Dev Cell 2008; 14:239-51. [PMID: 18267092 PMCID: PMC2258333 DOI: 10.1016/j.devcel.2007.12.009] [Citation(s) in RCA: 220] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 12/07/2007] [Accepted: 12/12/2007] [Indexed: 12/22/2022]
Abstract
Cohesin is a highly conserved multisubunit complex that holds sister chromatids together in mitotic cells. At the metaphase to anaphase transition, proteolytic cleavage of the alpha kleisin subunit (Rad21) by separase causes cohesin's dissociation from chromosomes and triggers sister-chromatid disjunction. To investigate cohesin's function in postmitotic cells, where it is widely expressed, we have created fruit flies whose Rad21 can be cleaved by TEV protease. Cleavage causes precocious separation of sister chromatids and massive chromosome missegregation in proliferating cells, but not disaggregation of polytene chromosomes in salivary glands. Crucially, cleavage in postmitotic neurons is lethal. In mushroom-body neurons, it causes defects in axon pruning, whereas in cholinergic neurons it causes highly abnormal larval locomotion. These data demonstrate essential roles for cohesin in nondividing cells and also introduce a powerful tool by which to investigate protein function in metazoa.
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Affiliation(s)
- Andrea Pauli
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | | | - Stefan Heidmann
- Department of Genetics, University of Bayreuth, 95440 Bayreuth, Germany
| | - Oren Schuldiner
- Stanford University, Department of Biological Sciences, Stanford, CA 94305, USA
| | | | | | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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