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Newman SA. The Developmental Genetic Toolkit and the Molecular Homology—Analogy Paradox. ACTA ACUST UNITED AC 2015. [DOI: 10.1162/biot.2006.1.1.12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Janssen R, Eriksson BJ, Tait NN, Budd GE. Onychophoran Hox genes and the evolution of arthropod Hox gene expression. Front Zool 2014; 11:22. [PMID: 24594097 PMCID: PMC4015684 DOI: 10.1186/1742-9994-11-22] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/21/2014] [Indexed: 11/24/2022] Open
Abstract
Introduction Onychophora is a relatively small phylum within Ecdysozoa, and is considered to be the sister group to Arthropoda. Compared to the arthropods, that have radiated into countless divergent forms, the onychophoran body plan is overall comparably simple and does not display much in-phylum variation. An important component of arthropod morphological diversity consists of variation of tagmosis, i.e. the grouping of segments into functional units (tagmata), and this in turn is correlated with differences in expression patterns of the Hox genes. How these genes are expressed in the simpler onychophorans, the subject of this paper, would therefore be of interest in understanding their subsequent evolution in the arthropods, especially if an argument can be made for the onychophoran system broadly reflecting the ancestral state in the arthropods. Results The sequences and embryonic expression patterns of the complete set of ten Hox genes of an onychophoran (Euperipatoides kanangrensis) are described for the first time. We find that they are all expressed in characteristic patterns that suggest a function as classical Hox genes. The onychophoran Hox genes obey spatial colinearity, and with the exception of Ultrabithorax (Ubx), they all have different and distinct anterior expression borders. Notably, Ubx transcripts form a posterior to anterior gradient in the onychophoran trunk. Expression of all onychophoran Hox genes extends continuously from their anterior border to the rear end of the embryo. Conclusions The spatial expression pattern of the onychophoran Hox genes may contribute to a combinatorial Hox code that is involved in giving each segment its identity. This patterning of segments in the uniform trunk, however, apparently predates the evolution of distinct segmental differences in external morphology seen in arthropods. The gradient-like expression of Ubx may give posterior segments their specific identity, even though they otherwise express the same set of Hox genes. We suggest that the confined domains of Hox gene expression seen in arthropods evolved from an ancestral onychophoran-like Hox gene pattern. Reconstruction of the ancestral arthropod Hox pattern and comparison with the patterns in the different arthropod classes reveals phylogenetic support for Mandibulata and Tetraconata, but not Myriochelata and Atelocerata.
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Affiliation(s)
- Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236 Uppsala, Sweden.
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Merabet S, Dard A. Tracking context-specific transcription factors regulating hox activity. Dev Dyn 2013; 243:16-23. [PMID: 23794379 DOI: 10.1002/dvdy.24002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Hox proteins are key developmental regulators involved in almost every embryonic tissue for specifying cell fates along longitudinal axes or during organ formation. It is thought that the panoply of Hox activities relies on interactions with tissue-, stage-, and/or cell-specific transcription factors. High-throughput approaches in yeast or cell culture systems have shown that Hox proteins bind to various types of nuclear and cytoplasmic components, illustrating their remarkable potential to influence many different cell regulatory processes. However, these approaches failed to identify a relevant number of context-specific transcriptional partners, suggesting that these interactions are hard to uncover in non-physiological conditions. Here we discuss this problematic. RESULTS In this review, we present intrinsic Hox molecular signatures that are probably involved in multiple (yet specific) interactions with transcriptional partners. We also recapitulate the current knowledge on Hox cofactors, highlighting the difficulty to tracking context-specific cofactors through traditional large-scale approaches. CONCLUSION We propose experimental approaches that will allow a better characterisation of interaction networks underlying Hox contextual activities in the next future.
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Busser BW, Gisselbrecht SS, Shokri L, Tansey TR, Gamble CE, Bulyk ML, Michelson AM. Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs. PLoS One 2013; 8:e69385. [PMID: 23922708 PMCID: PMC3724861 DOI: 10.1371/journal.pone.0069385] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/26/2013] [Indexed: 11/18/2022] Open
Abstract
Homeodomain (HD) proteins are a large family of evolutionarily conserved transcription factors (TFs) having diverse developmental functions, often acting within the same cell types, yet many members of this family paradoxically recognize similar DNA sequences. Thus, with multiple family members having the potential to recognize the same DNA sequences in cis-regulatory elements, it is difficult to ascertain the role of an individual HD or a subclass of HDs in mediating a particular developmental function. To investigate this problem, we focused our studies on the Drosophila embryonic mesoderm where HD TFs are required to establish not only segmental identities (such as the Hox TFs), but also tissue and cell fate specification and differentiation (such as the NK-2 HDs, Six HDs and identity HDs (I-HDs)). Here we utilized the complete spectrum of DNA binding specificities determined by protein binding microarrays (PBMs) for a diverse collection of HDs to modify the nucleotide sequences of numerous mesodermal enhancers to be recognized by either no or a single subclass of HDs, and subsequently assayed the consequences of these changes on enhancer function in transgenic reporter assays. These studies show that individual mesodermal enhancers receive separate transcriptional input from both I-HD and Hox subclasses of HDs. In addition, we demonstrate that enhancers regulating upstream components of the mesodermal regulatory network are targeted by the Six class of HDs. Finally, we establish the necessity of NK-2 HD binding sequences to activate gene expression in multiple mesodermal tissues, supporting a potential role for the NK-2 HD TF Tinman (Tin) as a pioneer factor that cooperates with other factors to regulate cell-specific gene expression programs. Collectively, these results underscore the critical role played by HDs of multiple subclasses in inducing the unique genetic programs of individual mesodermal cells, and in coordinating the gene regulatory networks directing mesoderm development.
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Affiliation(s)
- Brian W. Busser
- Laboratory of Developmental Systems Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen S. Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Leila Shokri
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Terese R. Tansey
- Laboratory of Developmental Systems Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Caitlin E. Gamble
- Laboratory of Developmental Systems Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alan M. Michelson
- Laboratory of Developmental Systems Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Busser BW, Taher L, Kim Y, Tansey T, Bloom MJ, Ovcharenko I, Michelson AM. A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PLoS Genet 2012; 8:e1002531. [PMID: 22412381 PMCID: PMC3297574 DOI: 10.1371/journal.pgen.1002531] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 12/23/2011] [Indexed: 12/22/2022] Open
Abstract
Transcriptional enhancers integrate the contributions of multiple classes of transcription factors (TFs) to orchestrate the myriad spatio-temporal gene expression programs that occur during development. A molecular understanding of enhancers with similar activities requires the identification of both their unique and their shared sequence features. To address this problem, we combined phylogenetic profiling with a DNA-based enhancer sequence classifier that analyzes the TF binding sites (TFBSs) governing the transcription of a co-expressed gene set. We first assembled a small number of enhancers that are active in Drosophila melanogaster muscle founder cells (FCs) and other mesodermal cell types. Using phylogenetic profiling, we increased the number of enhancers by incorporating orthologous but divergent sequences from other Drosophila species. Functional assays revealed that the diverged enhancer orthologs were active in largely similar patterns as their D. melanogaster counterparts, although there was extensive evolutionary shuffling of known TFBSs. We then built and trained a classifier using this enhancer set and identified additional related enhancers based on the presence or absence of known and putative TFBSs. Predicted FC enhancers were over-represented in proximity to known FC genes; and many of the TFBSs learned by the classifier were found to be critical for enhancer activity, including POU homeodomain, Myb, Ets, Forkhead, and T-box motifs. Empirical testing also revealed that the T-box TF encoded by org-1 is a previously uncharacterized regulator of muscle cell identity. Finally, we found extensive diversity in the composition of TFBSs within known FC enhancers, suggesting that motif combinatorics plays an essential role in the cellular specificity exhibited by such enhancers. In summary, machine learning combined with evolutionary sequence analysis is useful for recognizing novel TFBSs and for facilitating the identification of cognate TFs that coordinate cell type-specific developmental gene expression patterns.
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Affiliation(s)
- Brian W. Busser
- Laboratory of Developmental Systems Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Leila Taher
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yongsok Kim
- Laboratory of Developmental Systems Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Terese Tansey
- Laboratory of Developmental Systems Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Molly J. Bloom
- Laboratory of Developmental Systems Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (IO); (AMM)
| | - Alan M. Michelson
- Laboratory of Developmental Systems Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (IO); (AMM)
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Busser BW, Shokri L, Jaeger SA, Gisselbrecht SS, Singhania A, Berger MF, Zhou B, Bulyk ML, Michelson AM. Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Development 2012; 139:1164-74. [PMID: 22296846 PMCID: PMC3283125 DOI: 10.1242/dev.077362] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A subfamily of Drosophila homeodomain (HD) transcription factors (TFs) controls the identities of individual muscle founder cells (FCs). However, the molecular mechanisms by which these TFs generate unique FC genetic programs remain unknown. To investigate this problem, we first applied genome-wide mRNA expression profiling to identify genes that are activated or repressed by the muscle HD TFs Slouch (Slou) and Muscle segment homeobox (Msh). Next, we used protein-binding microarrays to define the sequences that are bound by Slou, Msh and other HD TFs that have mesodermal expression. These studies revealed that a large class of HDs, including Slou and Msh, predominantly recognize TAAT core sequences but that each HD also binds to unique sites that deviate from this canonical motif. To understand better the regulatory specificity of an individual FC identity HD, we evaluated the functions of atypical binding sites that are preferentially bound by Slou relative to other HDs within muscle enhancers that are either activated or repressed by this TF. These studies showed that Slou regulates the activities of particular myoblast enhancers through Slou-preferred sequences, whereas swapping these sequences for sites that are capable of binding to multiple HD family members does not support the normal regulatory functions of Slou. Moreover, atypical Slou-binding sites are overrepresented in putative enhancers associated with additional Slou-responsive FC genes. Collectively, these studies provide new insights into the roles of individual HD TFs in determining cellular identity, and suggest that the diversity of HD binding preferences can confer regulatory specificity.
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Affiliation(s)
- Brian W Busser
- Laboratory of Developmental Systems Biology, Genetics and Developmental Biology Center, Division of Intramural Research, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
Despite decades of research, morphogenesis along the various body axes remains one of the major mysteries in developmental biology. A milestone in the field was the realisation that a set of closely related regulators, called Hox genes, specifies the identity of body segments along the anterior-posterior (AP) axis in most animals. Hox genes have been highly conserved throughout metazoan evolution and code for homeodomain-containing transcription factors. Thus, they exert their function mainly through activation or repression of downstream genes. However, while much is known about Hox gene structure and molecular function, only a few target genes have been identified and studied in detail. Our knowledge of Hox downstream genes is therefore far from complete and consequently Hox-controlled morphogenesis is still poorly understood. Genome-wide approaches have facilitated the identification of large numbers of Hox downstream genes both in Drosophila and vertebrates, and represent a crucial step towards a comprehensive understanding of how Hox proteins drive morphological diversification. In this review, we focus on the role of Hox genes in shaping segmental morphologies along the AP axis in Drosophila, discuss some of the conclusions drawn from analyses of large target gene sets and highlight methods that could be used to gain a more thorough understanding of Hox molecular function. In addition, the mechanisms of Hox target gene regulation are considered with special emphasis on recent findings and their implications for Hox protein specificity in the context of the whole organism.
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Affiliation(s)
- Stefanie D Hueber
- Department of Molecular Biology, AG I. Lohmann, MPI for Developmental Biology, Tübingen, Germany
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Cross-regulatory protein-protein interactions between Hox and Pax transcription factors. Proc Natl Acad Sci U S A 2008; 105:13439-44. [PMID: 18755899 DOI: 10.1073/pnas.0806106105] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Homeotic Hox selector genes encode highly conserved transcriptional regulators involved in the differentiation of multicellular organisms. Ectopic expression of the Antennapedia (ANTP) homeodomain protein in Drosophila imaginal discs induces distinct phenotypes, including an antenna-to-leg transformation and eye reduction. We have proposed that the eye loss phenotype is a consequence of a negative posttranslational control mechanism because of direct protein-protein interactions between ANTP and Eyeless (EY). In the present work, we analyzed the effect of various ANTP homeodomain mutations for their interaction with EY and for head development. Contrasting with the eye loss phenotype, we provide evidence that the antenna-to-leg transformation involves ANTP DNA-binding activity. In a complementary genetic screen performed in yeast, we isolated mutations located in the N terminus of the ANTP homeodomain that inhibit direct interactions with EY without abolishing DNA binding in vitro and in vivo. In a bimolecular fluorescence complementation assay, we detected the ANTP-EY interaction in vivo, these interactions occurring through the paired domain and/or the homeodomain of EY. These results demonstrate that the homeodomain supports multiple molecular regulatory functions in addition to protein-DNA and protein-RNA interactions; it is also involved in protein-protein interactions.
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Onorati M, Cremisi F, Liu Y, He RQ, Barsacchi G, Vignali R. A specific box switches the cell fate determining activity of XOTX2 and XOTX5b in the Xenopus retina. Neural Dev 2007; 2:12. [PMID: 17597530 PMCID: PMC1929070 DOI: 10.1186/1749-8104-2-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2006] [Accepted: 06/27/2007] [Indexed: 11/27/2022] Open
Abstract
Background Otx genes, orthologues of the Drosophila orthodenticle gene (otd), play crucial roles in vertebrate brain development. In the Xenopus eye, Xotx2 and Xotx5b promote bipolar and photoreceptor cell fates, respectively. The molecular basis of their differential action is not completely understood, though the carboxyl termini of the two proteins seem to be crucial. To define the molecular domains that make the action of these proteins so different, and to determine whether their retinal abilities are shared by Drosophila OTD, we performed an in vivo molecular dissection of their activity by transfecting retinal progenitors with several wild-type, deletion and chimeric constructs of Xotx2, Xotx5b and otd. Results We identified a small 8–10 amino acid divergent region, directly downstream of the homeodomain, that is crucial for the respective activities of XOTX2 and XOTX5b. In lipofection experiments, the exchange of this 'specificity box' completely switches the retinal activity of XOTX5b into that of XOTX2 and vice versa. Moreover, the insertion of this box into Drosophila OTD, which has no effect on retinal cell fate, endows it with the specific activity of either XOTX protein. Significantly, in cell transfection experiments, the diverse ability of XOTX2 and XOTX5b to synergize with NRL, a cofactor essential for vertebrate rod development, to transactivate the rhodopsin promoter is also switched depending on the box. We also show by GST-pull down that XOTX2 and XOTX5b differentially interact with NRL, though this property is not strictly dependent on the box. Conclusion Our data provide molecular evidence on how closely related homeodomain gene products can differentiate their functions to regulate distinct cell fates. A small 'specificity box' is both necessary and sufficient to confer on XOTX2 and XOTX5b their distinct activities in the developing frog retina and to convert the neutral orthologous OTD protein of Drosophila into a positive and specific XOTX-like retinal regulator. Relatively little is known of what gives developmental specificity to homeodomain regulators. We propose that this box is a major domain of XOTX proteins that provides them with the appropriate developmental specificity in retinal histogenesis.
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Affiliation(s)
- Marco Onorati
- Dipartimento di Biologia, Unità di Biologia Cellulare e dello Sviluppo, Università di Pisa, Via G. Carducci 13, 56010 Ghezzano (Pisa), Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56100 Pisa, Italy
| | - Federico Cremisi
- Dipartimento di Biologia, Unità di Biologia Cellulare e dello Sviluppo, Università di Pisa, Via G. Carducci 13, 56010 Ghezzano (Pisa), Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56100 Pisa, Italy
| | - Yang Liu
- State Key Lab of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Da Tun Road, Chao Yang District, Beijing 100101, China RP
- Dana-Farber Cancer Institute, Jimmy Fund Way, Boston, MA 02115, USA
| | - Rong-Qiao He
- State Key Lab of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Da Tun Road, Chao Yang District, Beijing 100101, China RP
| | - Giuseppina Barsacchi
- Dipartimento di Biologia, Unità di Biologia Cellulare e dello Sviluppo, Università di Pisa, Via G. Carducci 13, 56010 Ghezzano (Pisa), Italy
- AMBISEN Center, High Technology Center for the Study of the Environmental Damage of the Endocrine and Nervous System, Università di Pisa, Pisa, Italy
| | - Robert Vignali
- Dipartimento di Biologia, Unità di Biologia Cellulare e dello Sviluppo, Università di Pisa, Via G. Carducci 13, 56010 Ghezzano (Pisa), Italy
- AMBISEN Center, High Technology Center for the Study of the Environmental Damage of the Endocrine and Nervous System, Università di Pisa, Pisa, Italy
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Patel M, Farzana L, Robertson LK, Hutchinson J, Grubbs N, Shepherd MN, Mahaffey JW. The appendage role of insect disco genes and possible implications on the evolution of the maggot larval form. Dev Biol 2007; 309:56-69. [PMID: 17643406 DOI: 10.1016/j.ydbio.2007.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 06/08/2007] [Accepted: 06/21/2007] [Indexed: 11/19/2022]
Abstract
Though initially identified as necessary for neural migration, Disconnected and its partially redundant paralog, Disco-related, are required for proper head segment identity during Drosophila embryogenesis. Here, we present evidence that these genes are also required for proper ventral appendage development during development of the adult fly, where they specify medial to distal appendage development. Cells lacking the disco genes cannot contribute to the medial and distal portions of ventral appendages. Further, ectopic disco transforms dorsal appendages toward ventral fates; in wing discs, the medial and distal leg development pathways are activated. Interestingly, this appendage role is conserved in the red flour beetle, Tribolium (where legs develop during embryogenesis), yet in the beetle we found no evidence for a head segmentation role. The lack of an embryonic head specification role in Tribolium could be interpreted as a loss of the head segmentation function in Tribolium or gain of this function during evolution of flies. However, we suggest an alternative explanation. We propose that the disco genes always function as appendage factors, but their appendage nature is masked during Drosophila embryogenesis due to the reduction of limb fields in the maggot style Drosophila larva.
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Affiliation(s)
- Mukund Patel
- Department of Genetics, Campus Box 7614, North Carolina State University, Raleigh, NC 27695-7614, USA
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Laurent A, Bihan R, Deschamps S, Guerrier D, Dupé V, Omilli F, Burel A, Pellerin I. Identification of a new type of PBX1 partner that contains zinc finger motifs and inhibits the binding of HOXA9-PBX1 to DNA. Mech Dev 2007; 124:364-76. [PMID: 17353115 DOI: 10.1016/j.mod.2007.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 01/30/2007] [Accepted: 01/31/2007] [Indexed: 10/23/2022]
Abstract
PBX1 belongs to the TALE-class of homeodomain protein and has a wide functional diversity during development. Indeed, PBX1 is required for haematopoiesis as well as for multiple developmental processes such as skeletal patterning and organogenesis. It has furthermore been shown that PBX1 functions as a HOX cofactor during development. More recent data suggest that PBX1 may act even more broadly by modulating the activity of non-homeodomain transcription factors. To better understand molecular mechanisms triggered by PBX1 during female genital tract development, we searched for additional PBX1 partners that might be involved in this process. Using a two hybrid screen, we identified a new PBX1 interacting protein containing several zinc finger motifs that we called ZFPIP for Zinc Finger PBX1 Interacting Protein. We demonstrated that ZFPIP is expressed in embryonic female genital tract but also in other PBX1 expression domains such as the developing head and the limb buds. We further showed that ZFPIP is able to bind physically and in vivo to PBX1 and moreover, that it prevents the binding of HOXA9/PBX complexes to their consensus DNA site. We suggest that ZFPIP is a new type of PBX1 partner that could participate in PBX1 function during several developmental pathways.
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Affiliation(s)
- Audrey Laurent
- UMR CNRS 6061, Génétique et Développement, IFR 140, Faculté de Médecine, Université de Rennes 1, Campus Villejean, 2 avenue du Professeur Léon Bernard, CS34317, F-35043 Rennes Cedex, France
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Hueber SD, Bezdan D, Henz SR, Blank M, Wu H, Lohmann I. Comparative analysis of Hox downstream genes in Drosophila. Development 2006; 134:381-92. [PMID: 17166915 DOI: 10.1242/dev.02746] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Functional diversification of body parts is dependent on the formation of specialized structures along the various body axes. In animals, region-specific morphogenesis along the anteroposterior axis is controlled by a group of conserved transcription factors encoded by the Hox genes. Although it has long been assumed that Hox proteins carry out their function by regulating distinct sets of downstream genes, only a small number of such genes have been found, with very few having direct roles in controlling cellular behavior. We have quantitatively identified hundreds of Hox downstream genes in Drosophila by microarray analysis, and validated many of them by in situ hybridizations on loss- and gain-of-function mutants. One important finding is that Hox proteins, despite their similar DNA-binding properties in vitro, have highly specific effects on the transcriptome in vivo, because expression of many downstream genes respond primarily to a single Hox protein. In addition, a large fraction of downstream genes encodes realizator functions, which directly affect morphogenetic processes, such as orientation and rate of cell divisions, cell-cell adhesion and communication, cell shape and migration, or cell death. Focusing on these realizators, we provide a framework for the morphogenesis of the maxillary segment. As the genomic organization of Hox genes and the interaction of Hox proteins with specific co-factors are conserved in vertebrates and invertebrates, and similar classes of downstream genes are regulated by Hox proteins across the metazoan phylogeny, our findings represent a first step toward a mechanistic understanding of morphological diversification within a species as well as between species.
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Affiliation(s)
- Stefanie D Hueber
- Max Planck Institute for Developmental Biology, Spemanstrasse 37-39, D-72076 Tübingen, Germany
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Jeong S, Rokas A, Carroll SB. Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution. Cell 2006; 125:1387-99. [PMID: 16814723 DOI: 10.1016/j.cell.2006.04.043] [Citation(s) in RCA: 173] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 03/24/2006] [Accepted: 04/25/2006] [Indexed: 11/18/2022]
Abstract
Hox genes have been implicated in the evolution of many animal body patterns, but the molecular events underlying trait modification have not been elucidated. Pigmentation of the posterior male abdomen is a recently acquired trait in the Drosophila melanogaster lineage. Here, we show that the Abdominal-B (ABD-B) Hox protein directly activates expression of the yellow pigmentation gene in posterior segments. ABD-B regulation of pigmentation evolved through the gain of ABD-B binding sites in a specific cis-regulatory element of the yellow gene of a common ancestor of sexually dimorphic species. Within the melanogaster species group, male-specific pigmentation has subsequently been lost by at least three different mechanisms, including the mutational inactivation of a key ABD-B binding site in one lineage. These results demonstrate how Hox regulation of traits and target genes is gained and lost at the species level and have general implications for the evolution of body form at higher taxonomic levels.
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Affiliation(s)
- Sangyun Jeong
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, 1525 Linden Drive, Madison, WI 53706, USA
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Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, Weiss RL, Borkovich KA, Dunlap JC. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A 2006; 103:10352-10357. [PMID: 16801547 PMCID: PMC1482798 DOI: 10.1073/pnas.0601456103] [Citation(s) in RCA: 889] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The low rate of homologous recombination exhibited by wild-type strains of filamentous fungi has hindered development of high-throughput gene knockout procedures for this group of organisms. In this study, we describe a method for rapidly creating knockout mutants in which we make use of yeast recombinational cloning, Neurospora mutant strains deficient in nonhomologous end-joining DNA repair, custom-written software tools, and robotics. To illustrate our approach, we have created strains bearing deletions of 103 Neurospora genes encoding transcription factors. Characterization of strains during growth and both asexual and sexual development revealed phenotypes for 43% of the deletion mutants, with more than half of these strains possessing multiple defects. Overall, the methodology, which achieves high-throughput gene disruption at an efficiency >90% in this filamentous fungus, promises to be applicable to other eukaryotic organisms that have a low frequency of homologous recombination.
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Affiliation(s)
- Hildur V Colot
- *Department of Genetics, Dartmouth Medical School, HB7400, Hanover, NH 03755
| | - Gyungsoon Park
- Department of Plant Pathology, University of California, Riverside, CA 92521; and
| | - Gloria E Turner
- Department of Chemistry and Biochemistry, 405 Hilgard Avenue, University of California, Los Angeles, CA 90095
| | - Carol Ringelberg
- *Department of Genetics, Dartmouth Medical School, HB7400, Hanover, NH 03755
| | - Christopher M Crew
- Department of Plant Pathology, University of California, Riverside, CA 92521; and
| | - Liubov Litvinkova
- Department of Plant Pathology, University of California, Riverside, CA 92521; and
| | - Richard L Weiss
- Department of Chemistry and Biochemistry, 405 Hilgard Avenue, University of California, Los Angeles, CA 90095
| | | | - Jay C Dunlap
- *Department of Genetics, Dartmouth Medical School, HB7400, Hanover, NH 03755;
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Monier B, Astier M, Sémériva M, Perrin L. Steroid-dependent modification of Hox function drives myocyte reprogramming in the Drosophila heart. Development 2005; 132:5283-93. [PMID: 16284119 DOI: 10.1242/dev.02091] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the Drosophila larval cardiac tube, aorta and heart differentiation are controlled by the Hox genes Ultrabithorax(Ubx) and abdominal A (abdA), respectively. There is evidence that the cardiac tube undergoes extensive morphological and functional changes during metamorphosis to form the adult organ, but both the origin of adult cardiac tube myocytes and the underlying genetic control have not been established. Using in vivo time-lapse analysis, we show that the adult fruit fly cardiac tube is formed during metamorphosis by the reprogramming of differentiated and already functional larval cardiomyocytes,without cell proliferation. We characterise the genetic control of the process, which is cell autonomously ensured by the modulation of Ubxexpression and AbdA activity. Larval aorta myocytes are remodelled to differentiate into the functional adult heart, in a process that requires the regulation of Ubx expression. Conversely, the shape, polarity,function and molecular characteristics of the surviving larval contractile heart myocytes are profoundly transformed as these cells are reprogrammed to form the adult terminal chamber. This process is mediated by the regulation of AbdA protein function, which is successively required within these persisting myocytes for the acquisition of both larval and adult differentiated states. Importantly, AbdA specificity is switched at metamorphosis to induce a novel genetic program that leads to differentiation of the terminal chamber. Finally, the steroid hormone ecdysone controls cardiac tube remodelling by impinging on both the regulation of Ubx expression and the modification of AbdA function. Our results shed light on the genetic control of one in vivo occurring remodelling process, which involves a steroid-dependent modification of Hox expression and function.
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Affiliation(s)
- Bruno Monier
- Laboratoire de Génétique et Physiologie du Développement, UMR 6545 CNRS-Université, Campus de Luminy, Case 907, 13288 Marseille Cedex 09, France
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