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Molina-Gil S, Sotillos S, Espinosa-Vázquez JM, Almudi I, Hombría JCG. Interlocking of co-opted developmental gene networks in Drosophila and the evolution of pre-adaptive novelty. Nat Commun 2023; 14:5730. [PMID: 37714829 PMCID: PMC10504328 DOI: 10.1038/s41467-023-41414-3] [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: 12/29/2022] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
The re-use of genes in new organs forms the base of many evolutionary novelties. A well-characterised case is the recruitment of the posterior spiracle gene network to the Drosophila male genitalia. Here we find that this network has also been co-opted to the testis mesoderm where is required for sperm liberation, providing an example of sequentially repeated developmental co-options. Associated to this co-option event, an evolutionary expression novelty appeared, the activation of the posterior segment determinant Engrailed to the anterior A8 segment controlled by common testis and spiracle regulatory elements. Enhancer deletion shows that A8 anterior Engrailed activation is not required for spiracle development but only necessary in the testis. Our study presents an example of pre-adaptive developmental novelty: the activation of the Engrailed transcription factor in the anterior compartment of the A8 segment where, despite having no specific function, opens the possibility of this developmental factor acquiring one. We propose that recently co-opted networks become interlocked, so that any change to the network because of its function in one organ, will be mirrored by other organs even if it provides no selective advantage to them.
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Affiliation(s)
- Sara Molina-Gil
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-JA-UPO Ctra. de Utrera, km1, 41013, Seville, Spain
- Málaga Biomedical Research Institute and Andalusian Centre for Nanomedicine and Biotechnology Platform, Severo Ochoa, 35, 29590, Málaga, Spain
| | - Sol Sotillos
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-JA-UPO Ctra. de Utrera, km1, 41013, Seville, Spain
| | - José Manuel Espinosa-Vázquez
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-JA-UPO Ctra. de Utrera, km1, 41013, Seville, Spain
- Department of Food Biotechnology, Instituto de la Grasa. Campus de la Universidad Pablo de Olavide. Ctra. de Utrera, km. 1, 41013, Seville, Spain
| | - Isabel Almudi
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-JA-UPO Ctra. de Utrera, km1, 41013, Seville, Spain
- Department of Genetics, Microbiology and Statistics and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal, 643, 08028, Barcelona, Spain
| | - James C-G Hombría
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-JA-UPO Ctra. de Utrera, km1, 41013, Seville, Spain.
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2
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Carnesecchi J, Boumpas P, van Nierop Y Sanchez P, Domsch K, Pinto HD, Borges Pinto P, Lohmann I. The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II. Nucleic Acids Res 2021; 50:763-783. [PMID: 34931250 PMCID: PMC8789087 DOI: 10.1093/nar/gkab1250] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription factors (TFs) play a pivotal role in cell fate decision by coordinating gene expression programs. Although most TFs act at the DNA layer, few TFs bind RNA and modulate splicing. Yet, the mechanistic cues underlying TFs activity in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct outcomes in defined cellular contexts. Our results demonstrate a new RNA-binding ability of Ubx. We find that the N51 amino acid of the DNA-binding Homeodomain is non-essential for RNA interaction in vitro, but is required for RNA interaction in vivo and Ubx splicing activity. Moreover, mutation of the N51 amino acid weakens the interaction between Ubx and active RNA Polymerase II (Pol II). Our results reveal that Ubx regulates elongation-coupled splicing, which could be coordinated by a dynamic interplay with active Pol II on chromatin. Overall, our work uncovered a novel role of the Hox TFs at the mRNA regulatory layer. This could be an essential function for other classes of TFs to control cell diversity.
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Affiliation(s)
- Julie Carnesecchi
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Panagiotis Boumpas
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany
| | - Patrick van Nierop Y Sanchez
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany
| | - Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany.,Friedrich-Alexander-University Erlangen-Nürnberg, Department Biology, Division of Developmental Biology, Erlangen, Germany
| | - Hugo Daniel Pinto
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Pedro Borges Pinto
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany
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3
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Giraud G, Paul R, Duffraisse M, Khan S, Shashidhara LS, Merabet S. Developmental Robustness: The Haltere Case in Drosophila. Front Cell Dev Biol 2021; 9:713282. [PMID: 34368162 PMCID: PMC8343187 DOI: 10.3389/fcell.2021.713282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
Developmental processes have to be robust but also flexible enough to respond to genetic and environmental variations. Different mechanisms have been described to explain the apparent antagonistic nature of developmental robustness and plasticity. Here, we present a “self-sufficient” molecular model to explain the development of a particular flight organ that is under the control of the Hox gene Ultrabithorax (Ubx) in the fruit fly Drosophila melanogaster. Our model is based on a candidate RNAi screen and additional genetic analyses that all converge to an autonomous and cofactor-independent mode of action for Ubx. We postulate that this self-sufficient molecular mechanism is possible due to an unusually high expression level of the Hox protein. We propose that high dosage could constitute a so far poorly investigated molecular strategy for allowing Hox proteins to both innovate and stabilize new forms during evolution.
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Affiliation(s)
| | | | | | - Soumen Khan
- Indian Institute of Science Education and Research (IISER), Pune, India
| | - L S Shashidhara
- Indian Institute of Science Education and Research (IISER), Pune, India.,Ashoka University, Sonipat, India
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4
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Saurin AJ, Delfini MC, Maurel-Zaffran C, Graba Y. The Generic Facet of Hox Protein Function. Trends Genet 2018; 34:941-953. [PMID: 30241969 DOI: 10.1016/j.tig.2018.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/07/2018] [Accepted: 08/21/2018] [Indexed: 11/16/2022]
Abstract
Hox transcription factors are essential to promote morphological diversification of the animal body. A substantial number of studies have focused on how Hox proteins reach functional specificity, an issue that arises from the fact that these transcription factors control distinct developmental functions despite sharing similar molecular properties. In this review, we highlight that, besides specific functions, for which these transcription factors are renowned, Hox proteins also often have nonspecific functions. We next discuss some emerging principles of these generic functions and how they relate to specific functions and explore our current grasp of the underlying molecular mechanisms.
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Affiliation(s)
- Andrew J Saurin
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/.
| | - Marie Claire Delfini
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/
| | - Corinne Maurel-Zaffran
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/
| | - Yacine Graba
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/.
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5
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Abstract
Metazoans encode clusters of paralogous Hox genes that are critical for proper development of the body plan. However, there are a number of unresolved issues regarding how paralogous Hox factors achieve specificity to control distinct cell fates. First, how do Hox paralogs, which have very similar DNA binding preferences in vitro, drive different transcriptional programs in vivo? Second, the number of potential Hox binding sites within the genome is vast compared to the number of sites bound. Hence, what determines where in the genome Hox factors bind? Third, what determines whether a Hox factor will activate or repress a specific target gene? Here, we review the current evidence that is beginning to shed light onto these questions. In particular, we highlight how cooperative interactions with other transcription factors (especially PBC and HMP proteins) and the sequences of cis-regulatory modules provide a basis for the mechanisms of Hox specificity. We conclude by integrating a number of the concepts described throughout the review in a case study of a highly interrogated Drosophila cis-regulatory module named “The Distal-less Conserved Regulatory Element” (DCRE).
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Affiliation(s)
- Arya Zandvakili
- Molecular and Developmental Biology Graduate Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Correspondence: ; Tel.: +1-513-636-3366
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6
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Uhl JD, Zandvakili A, Gebelein B. A Hox Transcription Factor Collective Binds a Highly Conserved Distal-less cis-Regulatory Module to Generate Robust Transcriptional Outcomes. PLoS Genet 2016; 12:e1005981. [PMID: 27058369 PMCID: PMC4825978 DOI: 10.1371/journal.pgen.1005981] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/16/2016] [Indexed: 12/19/2022] Open
Abstract
cis-regulatory modules (CRMs) generate precise expression patterns by integrating numerous transcription factors (TFs). Surprisingly, CRMs that control essential gene patterns can differ greatly in conservation, suggesting distinct constraints on TF binding sites. Here, we show that a highly conserved Distal-less regulatory element (DCRE) that controls gene expression in leg precursor cells recruits multiple Hox, Extradenticle (Exd) and Homothorax (Hth) complexes to mediate dual outputs: thoracic activation and abdominal repression. Using reporter assays, we found that abdominal repression is particularly robust, as neither individual binding site mutations nor a DNA binding deficient Hth protein abolished cooperative DNA binding and in vivo repression. Moreover, a re-engineered DCRE containing a distinct configuration of Hox, Exd, and Hth sites also mediated abdominal Hox repression. However, the re-engineered DCRE failed to perform additional segment-specific functions such as thoracic activation. These findings are consistent with two emerging concepts in gene regulation: First, the abdominal Hox/Exd/Hth factors utilize protein-protein and protein-DNA interactions to form repression complexes on flexible combinations of sites, consistent with the TF collective model of CRM organization. Second, the conserved DCRE mediates multiple cell-type specific outputs, consistent with recent findings that pleiotropic CRMs are associated with conserved TF binding and added evolutionary constraints. Enhancers are regulatory elements that interact with transcription factor proteins to control cell-specific gene expression during development. Surprisingly, only a subset of enhancers are highly conserved at the sequence level, even though the expression patterns they control are often conserved and essential for proper development. Why some enhancer sequences are highly conserved whereas others are not is not well understood. In this study, we characterize a highly conserved enhancer that regulates gene expression in leg precursor cells. We find that this enhancer has dual regulatory activities that include gene activation in thoracic segments and gene repression in abdominal segments. Surprisingly, we show that the conserved enhancer can tolerate numerous sequence changes yet mediate robust transcription factor binding and abdominal repression. These findings are consistent with abdominal transcription factors binding numerous different configurations of binding sites. So, why is this enhancer highly conserved? We found that overlapping sequences within the enhancer also contribute to thoracic activation, suggesting the enhancer sequences are under added functional constraints. Altogether, our results provide new insights into why some enhancers are highly conserved at the sequence level while others can tolerate sequence changes.
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Affiliation(s)
- Juli D Uhl
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, Ohio, United States of America.,Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Arya Zandvakili
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, Ohio, United States of America.,Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, Ohio, United States of America
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7
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Merabet S, Mann RS. To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins. Trends Genet 2016; 32:334-347. [PMID: 27066866 DOI: 10.1016/j.tig.2016.03.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Hox proteins are key regulatory transcription factors that act in different tissues of the embryo to provide specific spatial and temporal coordinates to each cell. These patterning functions often depend on the presence of the TALE-homeodomain class cofactors, which form cooperative DNA-binding complexes with all Hox proteins. How this family of cofactors contributes to the highly diverse and specific functions of Hox proteins in vivo remains an important unsolved question. We review here the most recent advances in understanding the molecular mechanisms underlying Hox-TALE function. In particular, we discuss the role of DNA shape, DNA-binding affinity, and protein-protein interaction flexibility in dictating Hox-TALE specificity. We propose several models to explain how these mechanisms are integrated with each other in the context of the many distinct functions that Hox and TALE factors carry out in vivo.
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Affiliation(s)
- Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, Centre National de Recherche Scientifique, Ecole Normale Supérieure de Lyon, France.
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8
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Rezsohazy R, Saurin AJ, Maurel-Zaffran C, Graba Y. Cellular and molecular insights into Hox protein action. Development 2016; 142:1212-27. [PMID: 25804734 DOI: 10.1242/dev.109785] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hox genes encode homeodomain transcription factors that control morphogenesis and have established functions in development and evolution. Hox proteins have remained enigmatic with regard to the molecular mechanisms that endow them with specific and diverse functions, and to the cellular functions that they control. Here, we review recent examples of Hox-controlled cellular functions that highlight their versatile and highly context-dependent activity. This provides the setting to discuss how Hox proteins control morphogenesis and organogenesis. We then summarise the molecular modalities underlying Hox protein function, in particular in light of current models of transcription factor function. Finally, we discuss how functional divergence between Hox proteins might be achieved to give rise to the many facets of their action.
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Affiliation(s)
- René Rezsohazy
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve B-1348, Belgium
| | - Andrew J Saurin
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille 13288, Cedex 09, France
| | | | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille 13288, Cedex 09, France
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9
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Martin A, Serano JM, Jarvis E, Bruce HS, Wang J, Ray S, Barker CA, O'Connell LC, Patel NH. CRISPR/Cas9 Mutagenesis Reveals Versatile Roles of Hox Genes in Crustacean Limb Specification and Evolution. Curr Biol 2015; 26:14-26. [PMID: 26687626 DOI: 10.1016/j.cub.2015.11.021] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 12/11/2022]
Abstract
Crustaceans possess a diverse array of specialized limbs. Although shifts in Hox gene expression domains have been postulated to play a role in generating this limb diversity, little functional data have been provided to understand the precise roles of Hox genes during crustacean development. We used a combination of CRISPR/Cas9-targeted mutagenesis and RNAi knockdown to decipher the function of the six Hox genes expressed in the developing mouth and trunk of the amphipod Parhyale hawaiensis. These experimentally manipulated animals display specific and striking homeotic transformations. We found that abdominal-A (abd-A) and Abdominal-B (Abd-B) are required for proper posterior patterning, with knockout of Abd-B resulting in an animal with thoracic type legs along what would have been an abdomen, and abd-A disruption generating a simplified body plan characterized by a loss of specialization in both abdominal and thoracic appendages. In the thorax, Ubx is necessary for gill development and for repression of gnathal fate, and Antp dictates claw morphology. In the mouth, Scr and Antp confer the part-gnathal, part-thoracic hybrid identity of the maxilliped, and Scr and Dfd prevent antennal identity in posterior head segments. Our results allow us to define the role Hox genes play in specifying each appendage type in Parhyale, including the modular nature by which some appendages are patterned by Hox gene inputs. In addition, we define how changes in Hox gene expression have generated morphological differences between crustacean species. Finally, we also highlight the utility of CRISPR/Cas9-based somatic mutagenesis in emerging model organisms.
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Affiliation(s)
- Arnaud Martin
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200 USA
| | - Julia M Serano
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200 USA
| | - Erin Jarvis
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140 USA
| | - Heather S Bruce
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200 USA
| | - Jennifer Wang
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140 USA
| | - Shagnik Ray
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200 USA
| | - Carryn A Barker
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200 USA
| | - Liam C O'Connell
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140 USA
| | - Nipam H Patel
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200 USA; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140 USA.
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10
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Foos N, Maurel-Zaffran C, Maté MJ, Vincentelli R, Hainaut M, Berenger H, Pradel J, Saurin AJ, Ortiz-Lombardía M, Graba Y. A flexible extension of the Drosophila ultrabithorax homeodomain defines a novel Hox/PBC interaction mode. Structure 2015; 23:270-9. [PMID: 25651060 DOI: 10.1016/j.str.2014.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/05/2014] [Accepted: 12/06/2014] [Indexed: 11/17/2022]
Abstract
The patterning function of Hox proteins relies on assembling protein complexes with PBC proteins, which often involves a protein motif found in most Hox proteins, the so-called Hexapeptide (HX). Hox/PBC complexes likely gained functional diversity by acquiring additional modes of interaction. Here, we structurally characterize the first HX alternative interaction mode based on the paralogue-specific UbdA motif and further functionally validate structure-based predictions. The UbdA motif folds as a flexible extension of the homeodomain recognition helix and defines Hox/PBC contacts that occur, compared with those mediated by the HX motif, on the opposing side of the DNA double helix. This provides a new molecular facet to Hox/PBC complex assembly and suggests possible mechanisms for the diversification of Hox protein function.
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Affiliation(s)
- Nicolas Foos
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Corinne Maurel-Zaffran
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - María Jesús Maté
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Renaud Vincentelli
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Matthieu Hainaut
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - Hélène Berenger
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - Jacques Pradel
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - Andrew J Saurin
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - Miguel Ortiz-Lombardía
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France.
| | - Yacine Graba
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France.
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11
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Papadopoulos DK, Krmpot AJ, Nikolić SN, Krautz R, Terenius L, Tomancak P, Rigler R, Gehring WJ, Vukojević V. Probing the kinetic landscape of Hox transcription factor-DNA binding in live cells by massively parallel Fluorescence Correlation Spectroscopy. Mech Dev 2015; 138 Pt 2:218-225. [PMID: 26428533 DOI: 10.1016/j.mod.2015.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 11/25/2022]
Abstract
Hox genes encode transcription factors that control the formation of body structures, segment-specifically along the anterior-posterior axis of metazoans. Hox transcription factors bind nuclear DNA pervasively and regulate a plethora of target genes, deploying various molecular mechanisms that depend on the developmental and cellular context. To analyze quantitatively the dynamics of their DNA-binding behavior we have used confocal laser scanning microscopy (CLSM), single-point fluorescence correlation spectroscopy (FCS), fluorescence cross-correlation spectroscopy (FCCS) and bimolecular fluorescence complementation (BiFC). We show that the Hox transcription factor Sex combs reduced (Scr) forms dimers that strongly associate with its specific fork head binding site (fkh250) in live salivary gland cell nuclei. In contrast, dimers of a constitutively inactive, phospho-mimicking variant of Scr show weak, non-specific DNA-binding. Our studies reveal that nuclear dynamics of Scr is complex, exhibiting a changing landscape of interactions that is difficult to characterize by probing one point at a time. Therefore, we also provide mechanistic evidence using massively parallel FCS (mpFCS). We found that Scr dimers are predominantly formed on the DNA and are equally abundant at the chromosomes and an introduced multimeric fkh250 binding-site, indicating different mobilities, presumably reflecting transient binding with different affinities on the DNA. Our proof-of-principle results emphasize the advantages of mpFCS for quantitative characterization of fast dynamic processes in live cells.
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Affiliation(s)
| | - Aleksandar J Krmpot
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden; Institute of Physics, University of Belgrade, 11080 Belgrade, Serbia
| | - Stanko N Nikolić
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden; Institute of Physics, University of Belgrade, 11080 Belgrade, Serbia
| | - Robert Krautz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Lars Terenius
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
| | - Pavel Tomancak
- Max-Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Rudolf Rigler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Laboratory of Biomedical Optics, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Walter J Gehring
- Department of Cell Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Vladana Vukojević
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.
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12
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Moris-Sanz M, Estacio-Gómez A, Sánchez-Herrero E, Díaz-Benjumea FJ. The study of the Bithorax-complex genes in patterning CCAP neurons reveals a temporal control of neuronal differentiation by Abd-B. Biol Open 2015; 4:1132-42. [PMID: 26276099 PMCID: PMC4582124 DOI: 10.1242/bio.012872] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
During development, HOX genes play critical roles in the establishment of segmental differences. In the Drosophila central nervous system, these differences are manifested in the number and type of neurons generated by each neuroblast in each segment. HOX genes can act either in neuroblasts or in postmitotic cells, and either early or late in a lineage. Additionally, they can be continuously required during development or just at a specific stage. Moreover, these features are generally segment-specific. Lately, it has been shown that contrary to what happens in other tissues, where HOX genes define domains of expression, these genes are expressed in individual cells as part of the combinatorial codes involved in cell type specification. In this report we analyse the role of the Bithorax-complex genes - Ultrabithorax, abdominal-A and Abdominal-B - in sculpting the pattern of crustacean cardioactive peptide (CCAP)-expressing neurons. These neurons are widespread in invertebrates, express CCAP, Bursicon and MIP neuropeptides and play major roles in controlling ecdysis. There are two types of CCAP neuron: interneurons and efferent neurons. Our results indicate that Ultrabithorax and Abdominal-A are not necessary for specification of the CCAP-interneurons, but are absolutely required to prevent the death by apoptosis of the CCAP-efferent neurons. Furthermore, Abdominal-B controls by repression the temporal onset of neuropeptide expression in a subset of CCAP-efferent neurons, and a peak of ecdysone hormone at the end of larval life counteracts this repression. Thus, Bithorax complex genes control the developmental appearance of these neuropeptides both temporally and spatially.
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Affiliation(s)
- M Moris-Sanz
- Centro de Biología Molecular-Severo Ochoa (CSIC-UAM), c./Nicolás Cabrera 1, Universidad Autónoma, Madrid 28049, Spain
| | - A Estacio-Gómez
- Centro de Biología Molecular-Severo Ochoa (CSIC-UAM), c./Nicolás Cabrera 1, Universidad Autónoma, Madrid 28049, Spain
| | - E Sánchez-Herrero
- Centro de Biología Molecular-Severo Ochoa (CSIC-UAM), c./Nicolás Cabrera 1, Universidad Autónoma, Madrid 28049, Spain
| | - F J Díaz-Benjumea
- Centro de Biología Molecular-Severo Ochoa (CSIC-UAM), c./Nicolás Cabrera 1, Universidad Autónoma, Madrid 28049, Spain
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13
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Saadaoui M, Litim-Mecheri I, Macchi M, Graba Y, Maurel-Zaffran C. A survey of conservation of sea spider and Drosophila Hox protein activities. Mech Dev 2015; 138 Pt 2:73-86. [PMID: 26238019 DOI: 10.1016/j.mod.2015.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 01/29/2023]
Abstract
Hox proteins have well-established functions in development and evolution, controlling the final morphology of bilaterian animals. The common phylogenetic origin of Hox proteins and the associated evolutionary diversification of protein sequences provide a unique framework to explore the relationship between changes in protein sequence and function. In this study, we aimed at questioning how sequence variation within arthropod Hox proteins influences function. This was achieved by exploring the functional impact of sequence conservation/divergence of the Hox genes, labial, Sex comb reduced, Deformed, Ultrabithorax and abdominalA from two distant arthropods, the sea spider and the well-studied Drosophila. Results highlight a correlation between sequence conservation within the homeodomain and the degree of functional conservation, and identify a novel functional domain in the Labial protein.
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Affiliation(s)
- Mehdi Saadaoui
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France; Institut de Biologie de l'ENS, 46, rue d'Ulm, 75005 Paris, France
| | - Isma Litim-Mecheri
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France; IGBMC, INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Meiggie Macchi
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
| | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
| | - Corinne Maurel-Zaffran
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
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14
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Role of HOXA9 in leukemia: dysregulation, cofactors and essential targets. Oncogene 2015; 35:1090-8. [PMID: 26028034 DOI: 10.1038/onc.2015.174] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/24/2015] [Accepted: 04/14/2015] [Indexed: 02/08/2023]
Abstract
HOXA9 is a homeodomain-containing transcription factor that has an important role in hematopoietic stem cell expansion and is commonly deregulated in acute leukemias. A variety of upstream genetic alterations in acute myeloid leukemia lead to overexpression of HOXA9, which is a strong predictor of poor prognosis. In many cases, HOXA9 has been shown to be necessary for maintaining leukemic transformation; however, the molecular mechanisms through which it promotes leukemogenesis remain elusive. Recent work has established that HOXA9 regulates downstream gene expression through binding at promoter distal enhancers along with a subset of cell-specific cofactor and collaborator proteins. Increasing efforts are being made to identify both the critical cofactors and target genes required for maintaining transformation in HOXA9-overexpressing leukemias. With continued advances in understanding HOXA9-mediated transformation, there is a wealth of opportunity for developing novel therapeutics that would be applicable for greater than 50% of AML with overexpression of HOXA9.
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15
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Smith FW, Jockusch EL. Hox genes require homothorax and extradenticle for body wall identity specification but not for appendage identity specification during metamorphosis of Tribolium castaneum. Dev Biol 2014; 395:182-97. [DOI: 10.1016/j.ydbio.2014.08.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 08/17/2014] [Accepted: 08/18/2014] [Indexed: 11/29/2022]
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16
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Sambrani N, Pradel J, Graba Y. Distinct genetic requirements for BX-C-mediated specification of abdominal denticles. Dev Dyn 2014; 243:192-200. [DOI: 10.1002/dvdy.24081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 10/09/2013] [Accepted: 10/09/2013] [Indexed: 11/07/2022] Open
Affiliation(s)
| | | | - Yacine Graba
- CNRS; Aix Marseille Université; Marseille France
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17
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Longobardi E, Penkov D, Mateos D, De Florian G, Torres M, Blasi F. Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates. Dev Dyn 2014; 243:59-75. [PMID: 23873833 PMCID: PMC4232920 DOI: 10.1002/dvdy.24016] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 06/19/2013] [Accepted: 07/05/2013] [Indexed: 12/22/2022] Open
Abstract
TALE (three amino acids loop extension) homeodomain transcription factors are required in various steps of embryo development, in many adult physiological functions, and are involved in important pathologies. This review focuses on the PREP, MEIS, and PBX sub-families of TALE factors and aims at giving information on their biochemical properties, i.e., structure, interactors, and interaction surfaces. Members of the three sets of protein form dimers in which the common partner is PBX but they can also directly interact with other proteins forming higher-order complexes, in particular HOX. Finally, recent advances in determining the genome-wide DNA-binding sites of PREP1, MEIS1, and PBX1, and their partial correspondence with the binding sites of some HOX proteins, are reviewed. These studies have generated a few general rules that can be applied to all members of the three gene families. PREP and MEIS recognize slightly different consensus sequences: PREP prefers to bind to promoters and to have PBX as a DNA-binding partner; MEIS prefers HOX as partner, and both PREP and MEIS drive PBX to their own binding sites. This outlines the clear individuality of the PREP and MEIS proteins, the former mostly devoted to basic cellular functions, the latter more to developmental functions.
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Affiliation(s)
- E Longobardi
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milano, Italy
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18
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Sánchez-Herrero E. Hox targets and cellular functions. SCIENTIFICA 2013; 2013:738257. [PMID: 24490109 PMCID: PMC3892749 DOI: 10.1155/2013/738257] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/20/2013] [Indexed: 06/03/2023]
Abstract
Hox genes are a group of genes that specify structures along the anteroposterior axis in bilaterians. Although in many cases they do so by modifying a homologous structure with a different (or no) Hox input, there are also examples of Hox genes constructing new organs with no homology in other regions of the body. Hox genes determine structures though the regulation of targets implementing cellular functions and by coordinating cell behavior. The genetic organization to construct or modify a certain organ involves both a genetic cascade through intermediate transcription factors and a direct regulation of targets carrying out cellular functions. In this review I discuss new data from genome-wide techniques, as well as previous genetic and developmental information, to describe some examples of Hox regulation of different cell functions. I also discuss the organization of genetic cascades leading to the development of new organs, mainly using Drosophila melanogaster as the model to analyze Hox function.
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Affiliation(s)
- Ernesto Sánchez-Herrero
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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19
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Rivas ML, Espinosa-Vázquez JM, Sambrani N, Greig S, Merabet S, Graba Y, Castelli-Gair Hombría J. Antagonism versus cooperativity with TALE cofactors at the base of the functional diversification of Hox protein function. PLoS Genet 2013; 9:e1003252. [PMID: 23408901 PMCID: PMC3567137 DOI: 10.1371/journal.pgen.1003252] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/03/2012] [Indexed: 11/18/2022] Open
Abstract
Extradenticle (Exd) and Homothorax (Hth) function as positive transcriptional cofactors of Hox proteins, helping them to bind specifically their direct targets. The posterior Hox protein Abdominal-B (Abd-B) does not require Exd/Hth to bind DNA; and, during embryogenesis, Abd-B represses hth and exd transcription. Here we show that this repression is necessary for Abd-B function, as maintained Exd/Hth expression results in transformations similar to those observed in loss-of-function Abd-B mutants. We characterize the cis regulatory module directly regulated by Abd-B in the empty spiracles gene and show that the Exd/Hth complex interferes with Abd-B binding to this enhancer. Our results suggest that this novel Exd/Hth function does not require the complex to bind DNA and may be mediated by direct Exd/Hth binding to the Abd-B homeodomain. Thus, in some instances, the main positive cofactor complex for anterior Hox proteins can act as a negative factor for the posterior Hox protein Abd-B. This antagonistic interaction uncovers an alternative way in which MEIS and PBC cofactors can modulate Abd-B like posterior Hox genes during development.
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Affiliation(s)
| | | | - Nagraj Sambrani
- IBDML, CNRS/Université de la Méditerranée, Marseille, France
| | - Stephen Greig
- Akam Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Samir Merabet
- IBDML, CNRS/Université de la Méditerranée, Marseille, France
| | - Yacine Graba
- IBDML, CNRS/Université de la Méditerranée, Marseille, France
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