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Curt JR, Martín P, Foronda D, Hudry B, Kannan R, Shetty S, Merabet S, Saurin AJ, Graba Y, Sánchez- Herrero E. Ambivalent partnership of the Drosophila posterior class Hox protein Abdominal-B with Extradenticle and Homothorax. PLoS Genet 2025; 21:e1011355. [PMID: 39804927 PMCID: PMC11759358 DOI: 10.1371/journal.pgen.1011355] [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: 07/05/2024] [Revised: 01/24/2025] [Accepted: 12/09/2024] [Indexed: 01/16/2025] Open
Abstract
Hox proteins, a sub-group of the homeodomain (HD) transcription factor family, provide positional information for axial patterning in development and evolution. Hox protein functional specificity is reached, at least in part, through interactions with Pbc (Extradenticle (Exd) in Drosophila) and Meis/Prep (Homothorax (Hth) in Drosophila) proteins. Most of our current knowledge of Hox protein specificity stems from the study of anterior and central Hox proteins, identifying the molecular and structural bases for Hox/Pbc/Meis-Prep cooperative action. Posterior Hox class proteins, Abdominal-B (Abd-B) in Drosophila and Hox9-13 in vertebrates, have been comparatively less studied. They strongly diverge from anterior and central class Hox proteins, with a low degree of HD sequence conservation and the absence of a core canonical Pbc interaction motif. Here we explore how Abd-B function interface with that of Exd/Hth using several developmental contexts, studying mutual expression control, functional dependency and intrinsic protein requirements. Results identify cross-regulatory interactions setting relative expression and activity levels required for proper development. They also reveal organ-specific requirement and a binary functional interplay with Exd and Hth, either antagonistic, as previously reported, or synergistic. This highlights context specific use of Exd/Hth, and a similar context specific use of Abd-B intrinsic protein requirements.
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Affiliation(s)
- Jesús R. Curt
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Paloma Martín
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - David Foronda
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Departamento de Medicina, Facultad de Ciencias Biomédicas y de la Salud, Universidad Europea de Madrid, Madrid, Spain
| | - Bruno Hudry
- Aix-Marseille Univ., CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Parc Scientifique de Luminy, Marseille, France
- Institut de Biologie Valrose, Université Nice Sophia Antipolis, Faculté des Sciences Parc Valrose, Nice, France
| | - Ramakrishnan Kannan
- Molecular Genetics lab, Neurobiology Research Center (NRC), National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Srividya Shetty
- Molecular Genetics lab, Neurobiology Research Center (NRC), National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Samir Merabet
- Aix-Marseille Univ., CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Parc Scientifique de Luminy, Marseille, France
- Institut de Génétique Fonctionnelle, UMR 5242 CNRS/ENS Lyon, Lyon, France
| | - Andrew J. Saurin
- Aix-Marseille Univ., CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Parc Scientifique de Luminy, Marseille, France
| | - Yacine Graba
- Aix-Marseille Univ., CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Parc Scientifique de Luminy, Marseille, France
| | - Ernesto Sánchez- Herrero
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
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Boumpas P, Merabet S, Carnesecchi J. Integrating transcription and splicing into cell fate: Transcription factors on the block. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1752. [PMID: 35899407 DOI: 10.1002/wrna.1752] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022]
Abstract
Transcription factors (TFs) are present in all life forms and conserved across great evolutionary distances in eukaryotes. From yeast to complex multicellular organisms, they are pivotal players of cell fate decision by orchestrating gene expression at diverse molecular layers. Notably, TFs fine-tune gene expression by coordinating RNA fate at both the expression and splicing levels. They regulate alternative splicing, an essential mechanism for cell plasticity, allowing the production of many mRNA and protein isoforms in precise cell and tissue contexts. Despite this apparent role in splicing, how TFs integrate transcription and splicing to ultimately orchestrate diverse cell functions and cell fate decisions remains puzzling. We depict substantial studies in various model organisms underlining the key role of TFs in alternative splicing for promoting tissue-specific functions and cell fate. Furthermore, we emphasize recent advances describing the molecular link between the transcriptional and splicing activities of TFs. As TFs can bind both DNA and/or RNA to regulate transcription and splicing, we further discuss their flexibility and compatibility for DNA and RNA substrates. Finally, we propose several models integrating transcription and splicing activities of TFs in the coordination and diversification of cell and tissue identities. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Mechanisms.
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Affiliation(s)
- Panagiotis Boumpas
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Julie Carnesecchi
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
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Duffraisse M, Paul R, Carnesecchi J, Hudry B, Banreti A, Reboulet J, Ajuria L, Lohmann I, Merabet S. Role of a versatile peptide motif controlling Hox nuclear export and autophagy in the Drosophila fat body. J Cell Sci 2020; 133:jcs241943. [PMID: 32878938 DOI: 10.1242/jcs.241943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
Hox proteins are major regulators of embryonic development, acting in the nucleus to regulate the expression of their numerous downstream target genes. By analyzing deletion forms of the Drosophila Hox protein Ultrabithorax (Ubx), we identified the presence of an unconventional nuclear export signal (NES) that overlaps with a highly conserved motif originally described as mediating the interaction with the PBC proteins, a generic and crucial class of Hox transcriptional cofactors that act in development and cancer. We show that this unconventional NES is involved in the interaction with the major exportin protein CRM1 (also known as Embargoed in flies) in vivo and in vitro We find that this interaction is tightly regulated in the Drosophila fat body to control the autophagy-repressive activity of Ubx during larval development. The role of the PBC interaction motif as part of an unconventional NES was also uncovered in other Drosophila and human Hox proteins, highlighting the evolutionary conservation of this novel function. Together, our results reveal the extreme molecular versatility of a unique short peptide motif for controlling the context-dependent activity of Hox proteins both at transcriptional and non-transcriptional levels.
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Affiliation(s)
- Marilyne Duffraisse
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
| | - Rachel Paul
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
| | - Julie Carnesecchi
- Centre for Organismal Studies, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Bruno Hudry
- Institut de Biologie Valrose, Parc Valrose, 06108 Nice, France
| | - Agnes Banreti
- Institut de Biologie Valrose, Parc Valrose, 06108 Nice, France
| | - Jonathan Reboulet
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
| | - Leiore Ajuria
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
| | - Ingrid Lohmann
- Centre for Organismal Studies, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
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Baëza M, Viala S, Heim M, Dard A, Hudry B, Duffraisse M, Rogulja-Ortmann A, Brun C, Merabet S. Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo. eLife 2015; 4. [PMID: 25869471 PMCID: PMC4392834 DOI: 10.7554/elife.06034] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/16/2015] [Indexed: 12/30/2022] Open
Abstract
Hox proteins are well-established developmental regulators that coordinate cell fate and morphogenesis throughout embryogenesis. In contrast, our knowledge of their specific molecular modes of action is limited to the interaction with few cofactors. Here, we show that Hox proteins are able to interact with a wide range of transcription factors in the live Drosophila embryo. In this context, specificity relies on a versatile usage of conserved short linear motifs (SLiMs), which, surprisingly, often restrains the interaction potential of Hox proteins. This novel buffering activity of SLiMs was observed in different tissues and found in Hox proteins from cnidarian to mouse species. Although these interactions remain to be analysed in the context of endogenous Hox regulatory activities, our observations challenge the traditional role assigned to SLiMs and provide an alternative concept to explain how Hox interactome specificity could be achieved during the embryonic development. DOI:http://dx.doi.org/10.7554/eLife.06034.001 In all animals, it is important that cells are correctly organised into tissues and organs. This organisation starts in the embryo, and cells are instructed to perform different roles depending on their position within the body. A family of proteins called the Hox proteins coordinates the organisation of the cells in the animal embryo by binding to and controlling the expression of specific genes. To properly control their target genes, Hox proteins need to interact with other proteins called transcription factors that can also bind to the genes. However, only a few of these transcription factors have been identified so far, and it is not clear how Hox proteins are able to interact with them. Here, Baëza, Viala, Heim et al. identified several more transcription factors that can bind to the Hox proteins in fruit fly embryos. The experiments show that Hox proteins are able to bind to many transcription factors that are very different from each other. Baëza, Viala, Heim et al. also show that two short sections within the Hox proteins known as short linear motifs are important for controlling these interactions. A fly Hox protein that was missing these motifs was able to interact with new transcription factors. This inhibitory role was found in Hox proteins from mice and sea anemones, suggesting that these motifs may play the same role in all animals. Baëza, Viala, Heim et al.'s findings challenge the traditional view of the role of the short linear motifs in interactions between proteins. Also, the findings provide an alternative explanation for how the Hox proteins are only able to interact with particular transcription factors in animal embryos. The next step will be to find out whether the inhibitory role of short linear motifs could more generally apply to many other protein families. DOI:http://dx.doi.org/10.7554/eLife.06034.002
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Affiliation(s)
- Manon Baëza
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | - Séverine Viala
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | - Marjorie Heim
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | - Amélie Dard
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | - Bruno Hudry
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Marilyne Duffraisse
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | | | - Christine Brun
- Technological Advances for Genomics and clinics, Institut national de la santé et de la recherche médicale, University Aix-Marseille, Parc Scientifique de Luminy, Marseille, France
| | - Samir Merabet
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
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Sivanantharajah L, Percival-Smith A. Differential pleiotropy and HOX functional organization. Dev Biol 2014; 398:1-10. [PMID: 25448696 DOI: 10.1016/j.ydbio.2014.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/31/2014] [Accepted: 11/01/2014] [Indexed: 12/14/2022]
Abstract
Key studies led to the idea that transcription factors are composed of defined modular protein motifs or domains, each with separable, unique function. During evolution, the recombination of these modular domains could give rise to transcription factors with new properties, as has been shown using recombinant molecules. This archetypic, modular view of transcription factor organization is based on the analyses of a few transcription factors such as GAL4, which may represent extreme exemplars rather than an archetype or the norm. Recent work with a set of Homeotic selector (HOX) proteins has revealed differential pleiotropy: the observation that highly-conserved HOX protein motifs and domains make small, additive, tissue specific contributions to HOX activity. Many of these differentially pleiotropic HOX motifs may represent plastic sequence elements called short linear motifs (SLiMs). The coupling of differential pleiotropy with SLiMs, suggests that protein sequence changes in HOX transcription factors may have had a greater impact on morphological diversity during evolution than previously believed. Furthermore, differential pleiotropy may be the genetic consequence of an ensemble nature of HOX transcription factor allostery, where HOX proteins exist as an ensemble of states with the capacity to integrate an extensive array of developmental information. Given a new structural model for HOX functional domain organization, the properties of the archetypic TF may require reassessment.
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Affiliation(s)
- Lovesha Sivanantharajah
- Department of Biology, The University of Western Ontario, BGS231, London, Ontario, Canada N6A 5B7.
| | - Anthony Percival-Smith
- Department of Biology, The University of Western Ontario, BGS231, London, Ontario, Canada N6A 5B7
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Hueber SD. Revisiting the context dependence of cofactor-recruiting motifs. Bioessays 2013; 35:585. [DOI: 10.1002/bies.201300039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Stefanie Diana Hueber
- Applied Bioinformatics; Department of Biology; University of Konstanz; Konstanz; Germany
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7
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Huang S. The molecular and mathematical basis of Waddington's epigenetic landscape: a framework for post-Darwinian biology? Bioessays 2011; 34:149-57. [PMID: 22102361 DOI: 10.1002/bies.201100031] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Neo-Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo-Darwinism. It needs to incorporate the non-linear, stochastic dynamics of gene networks. A first step is to consider the mathematical correspondence between gene regulatory networks and Waddington's metaphoric 'epigenetic landscape', which actually represents the quasi-potential function of global network dynamics. It explains the coexistence of multiple stable phenotypes within one genotype. The landscape's topography with its attractors is shaped by evolution through mutational re-wiring of regulatory interactions - offering a link between genetic mutation and sudden, broad evolutionary changes.
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Affiliation(s)
- Sui Huang
- Institute for Systems Biology, Seattle, WA, USA.
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8
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Heffer A, Löhr U, Pick L. ftz Evolution: Findings, hypotheses and speculations (response to DOI 10.1002/bies.201100019). Bioessays 2011; 33:910-8. [DOI: 10.1002/bies.201100112] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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