Publications by authors named "Yacine Graba"

41 Publications

HOXB8 Counteracts MAPK/ERK Oncogenic Signaling in a Chicken Embryo Model of Neoplasia.

Int J Mol Sci 2021 Aug 18;22(16). Epub 2021 Aug 18.

Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM-UMR 7288), 13288 Marseille, France.

HOX transcription factors are members of an evolutionarily conserved family of proteins required for the establishment of the anteroposterior body axis during bilaterian development. Although they are often deregulated in cancers, the molecular mechanisms by which they act as oncogenes or tumor suppressor genes are only partially understood. Since the MAPK/ERK signaling pathway is deregulated in most cancers, we aimed at apprehending if and how the Hox proteins interact with ERK oncogenicity. Using an in vivo neoplasia model in the chicken embryo consisting in the overactivation of the ERK1/2 kinases in the trunk neural tube, we analyzed the consequences of the HOXB8 gain of function at the morphological and transcriptional levels. We found that HOXB8 acts as a tumor suppressor, counteracting ERK-induced neoplasia. The HOXB8 tumor suppressor function relies on a large reversion of the oncogenic transcriptome induced by ERK. In addition to showing that the HOXB8 protein controls the transcriptional responsiveness to ERK oncogenic signaling, our study identified new downstream targets of ERK oncogenic activation in an in vivo context that could provide clues for therapeutic strategies.
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http://dx.doi.org/10.3390/ijms22168911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8396257PMC
August 2021

HoxB genes regulate neuronal delamination in the trunk neural tube by controlling the expression of .

Development 2021 02 18;148(4). Epub 2021 Feb 18.

Aix Marseille University, CNRS, IBDM, 13288 Marseille, France

Differential Hox gene expression is central for specification of axial neuronal diversity in the spinal cord. Here, we uncover an additional function of Hox proteins in the developing spinal cord, restricted to B cluster Hox genes. We found that members of the HoxB cluster are expressed in the trunk neural tube of chicken embryo earlier than Hox from the other clusters, with poor antero-posterior axial specificity and with overlapping expression in the intermediate zone (IZ). Gain-of-function experiments of HoxB4, HoxB8 and HoxB9, respectively, representative of anterior, central and posterior HoxB genes, resulted in ectopic progenitor cells in the mantle zone. The search for HoxB8 downstream targets in the early neural tube identified the leucine zipper tumor suppressor 1 gene (), the expression of which is also activated by HoxB4 and HoxB9. Gain- and loss-of-function experiments showed that Lzts1, which is expressed endogenously in the IZ, controls neuronal delamination. These data collectively indicate that HoxB genes have a generic function in the developing spinal cord, controlling the expression of and neuronal delamination.
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http://dx.doi.org/10.1242/dev.195404DOI Listing
February 2021

Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation.

Sci Rep 2020 06 15;10(1):9653. Epub 2020 Jun 15.

Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, 13288, Cedex 09, France.

Autophagy is an essential cellular process that maintains homeostasis by recycling damaged organelles and nutrients during development and cellular stress. ZKSCAN3 is the sole identified master transcriptional repressor of autophagy in human cell lines. How ZKSCAN3 achieves autophagy repression at the mechanistic or organismal level however still remains to be elucidated. Furthermore, Zkscan3 knockout mice display no discernable autophagy-related phenotypes, suggesting that there may be substantial differences in the regulation of autophagy between normal tissues and tumor cell lines. Here, we demonstrate that vertebrate ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy repression. Expression of ZKSCAN3 in Drosophila prevents premature autophagy onset due to loss of M1BP function and conversely, M1BP expression in human cells can prevent starvation-induced autophagy due to loss of nuclear ZKSCAN3 function. In Drosophila ZKSCAN3 binds genome-wide to sequences targeted by M1BP and transcriptionally regulates the majority of M1BP-controlled genes, demonstrating the evolutionary conservation of the transcriptional repression of autophagy. This study thus  allows the potential for transitioning the mechanisms, gene targets and plethora metabolic processes controlled by M1BP onto ZKSCAN3 and opens up Drosophila as a tool in studying the function of ZKSCAN3 in autophagy and tumourigenesis.
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http://dx.doi.org/10.1038/s41598-020-66377-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296029PMC
June 2020

Cooperation of axial and sex specific information controls Drosophila female genitalia growth by regulating the Decapentaplegic pathway.

Dev Biol 2019 10 25;454(2):145-155. Epub 2019 Jun 25.

Centro de Biología Molecular Severo Ochoa (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain. Electronic address:

The specification and morphogenesis of an organ requires the coordinate deployment and integration of regulatory information, including sex specific information when the organ is sex specific. Only a few gene networks controlling size and pattern development have been deciphered, which limits the emergence of principles, general or not, underlying the organ-specifying gene networks. Here we elucidate the genetic and molecular network determining the control of size in the Drosophila abdominal A9 primordium, contributing to the female genitalia. This network requires axial regulatory information provided by the Hox protein Abdominal-BR (Abd-BR), the Hox cofactors Extradenticle (Exd) and Homothorax (Hth), and the sex specific transcription factor Doublesex Female (DsxF). These factors synergize to control size in the female A9 by the coordinate regulation of the Decapentaplegic (Dpp) growth pathway. Molecular dissection of the dpp regulatory region and in vivo protein interaction experiments suggest that Abd-BR, Exd, Hth and DsxF coordinately regulate a short dpp enhancer to repress dpp expression and restrict female A9 size. The same regulators can also suppress dpp expression in the A8, but this requires the absence of the Abd-BM isoform, which specifies A8. These results delineate the network controlling female A9 growth in Drosophila.
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http://dx.doi.org/10.1016/j.ydbio.2019.06.014DOI Listing
October 2019

Fattening the perspective of Hox protein specificity through SLiMming.

Int J Dev Biol 2018 ;62(11-12):755-766

Aix Marseille Univ, CNRS, IBDM, Marseille, France.

The functional identification and dissection of protein domains has been a successful approach towards the understanding of Hox protein specificity. However, only a few functional protein domains have been identified; this has been a major limitation in deciphering the molecular modalities of Hox protein action. We explore here, by in silico survey of short linear motifs (SLiMs) in Hox proteins, the contribution of SLiMs to Hox proteins, focusing on the mouse, chick and Drosophila Hox complement. Our findings reveal a widespread and uniform distribution of SLiMs along Hox protein sequences and identify the most apparent features of Hox associated SLiMs. While few motifs have been associated with Hox proteins so far, this work suggests that many more contribute to Hox protein functions. The potential and difficulties to apprehend the full contribution of SLiMs in controlling Hox protein functions are discussed.
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http://dx.doi.org/10.1387/ijdb.180306ygDOI Listing
May 2019

Post-translational modifications of HOX proteins, an underestimated issue.

Int J Dev Biol 2018 ;62(11-12):733-744

Animal Molecular and Cellular Biology, Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain, Louvain-la-Neuve, Belgium.

Post-translational modifications (PTMs) are important determinants which contribute to modulating the turn-over, intracellular localisation, molecular interactions and activity of most eukaryotic proteins. Such modifications and their consequences have been extensively examined for some proteins or classes of proteins. This is not the case for the HOX transcription factors which are crucial regulators of animal development. In this review, we provide a survey of the literature and data repositories pertaining to HOX-associated PTMs. This highlights that HOX proteins are also likely widely post-translationally modified, and defines HOX PTMs as an under-valued facet of their biology.
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http://dx.doi.org/10.1387/ijdb.180178rrDOI Listing
May 2019

The Generic Facet of Hox Protein Function.

Trends Genet 2018 12 18;34(12):941-953. Epub 2018 Sep 18.

Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/. Electronic address:

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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http://dx.doi.org/10.1016/j.tig.2018.08.006DOI Listing
December 2018

The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription.

EMBO J 2017 10 4;36(19):2887-2906. Epub 2017 Sep 4.

Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France

In metazoans, the pausing of RNA polymerase II at the promoter (paused Pol II) has emerged as a widespread and conserved mechanism in the regulation of gene transcription. While critical in recruiting Pol II to the promoter, the role transcription factors play in transitioning paused Pol II into productive Pol II is, however, little known. By studying how Hox transcription factors control transcription, we uncovered a molecular mechanism that increases productive transcription. We found that the Hox proteins AbdA and Ubx target gene promoters previously bound by the transcription pausing factor M1BP, containing paused Pol II and enriched with promoter-proximal Polycomb Group (PcG) proteins, yet lacking the classical H3K27me3 PcG signature. We found that AbdA binding to M1BP-regulated genes results in reduction in PcG binding, the release of paused Pol II, increases in promoter H3K4me3 histone marks and increased gene transcription. Linking transcription factors, PcG proteins and paused Pol II states, these data identify a two-step mechanism of Hox-driven transcription, with M1BP binding leading to Pol II recruitment followed by AbdA targeting, which results in a change in the chromatin landscape and enhanced transcription.
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http://dx.doi.org/10.15252/embj.201695751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5623858PMC
October 2017

Hox functional diversity: Novel insights from flexible motif folding and plastic protein interaction.

Bioessays 2017 04 16;39(4). Epub 2017 Jan 16.

Aix-Marseille-Université, CNRS UMR 7288, case 907, IBDM, Marseille, France.

How the formidable diversity of forms emerges from developmental and evolutionary processes is one of the most fascinating questions in biology. The homeodomain-containing Hox proteins were recognized early on as major actors in diversifying animal body plans. The molecular mechanisms underlying how this transcription factor family controls a large array of context- and cell-specific biological functions is, however, still poorly understood. Clues to functional diversity have emerged from studies exploring how Hox protein activity is controlled through interactions with PBC class proteins, also evolutionary conserved HD-containing proteins. Recent structural data and molecular dynamic simulations add further mechanistic insights into Hox protein mode of action, suggesting that flexible folding of protein motifs allows for plastic protein interaction. As we discuss in this review, these findings define a novel type of Hox-PBC interaction, weak and dynamic instead of strong and static, hence providing novel clues to understanding Hox transcriptional specificity and diversity.
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http://dx.doi.org/10.1002/bies.201600246DOI Listing
April 2017

Hox Service Warranty Extends to Adult Bone Repair.

Dev Cell 2016 12;39(6):627-629

Aix-Marseille Université, CNRS, IBDM, UMR7288, case 907, 13288 Marseille Cedex 09, France. Electronic address:

Hox genes are key developmental regulators. In this issue of Developmental Cell, Rux et al. (2016) uncover an adult role for Hox11 genes in regionalized bone repair. This function relies on Hox activity in bone marrow multipotent mesenchymal stem progenitor cells, which promotes skeletal cell differentiation.
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http://dx.doi.org/10.1016/j.devcel.2016.12.007DOI Listing
December 2016

Autophagy : Moving Benchside Promises to Patient Bedsides.

Curr Cancer Drug Targets 2015 ;15(8):684-702

Institute of Research on Cancer and Ageing of Nice (IRCAN); Université de Nice-Sophia Antipolis; Centre Antoine Lacassagne, Avenue de Valombrose; 06107 Nice Cedex 02, France.

Survival rates of patients with metastatic or recurrent cancers have remained virtually unchanged during the past 30 years. This fact makes the need for new therapeutic options even more urgent. An attractive option would be to target autophagy, an essential quality control process that degrades toxic aggregates, damaged organelles, and signaling proteins, and acts as a tumor suppressor pathway of tumor initiation. Conversely, other fascinating observations suggest that autophagy supports cancer progression, relapse, metastasis, dormancy and resistance to therapy. This review provides an overview of the contradictory roles that autophagy plays in cancer initiation and progression and discusses the promises and challenges of current strategies that target autophagy for cancer therapy.
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http://dx.doi.org/10.2174/156800961508151001102452DOI Listing
July 2016

A survey of conservation of sea spider and Drosophila Hox protein activities.

Mech Dev 2015 Nov 1;138 Pt 2:73-86. Epub 2015 Aug 1.

Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France.

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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http://dx.doi.org/10.1016/j.mod.2015.07.010DOI Listing
November 2015

Cellular and molecular insights into Hox protein action.

Development 2015 Apr;142(7):1212-27

Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille 13288, Cedex 09, France

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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http://dx.doi.org/10.1242/dev.109785DOI Listing
April 2015

A flexible extension of the Drosophila ultrabithorax homeodomain defines a novel Hox/PBC interaction mode.

Structure 2015 Feb;23(2):270-9

Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France. Electronic address:

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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http://dx.doi.org/10.1016/j.str.2014.12.011DOI Listing
February 2015

Drosophila melanogaster Hox transcription factors access the RNA polymerase II machinery through direct homeodomain binding to a conserved motif of mediator subunit Med19.

PLoS Genet 2014 May 1;10(5):e1004303. Epub 2014 May 1.

Centre de Biologie du Développement, CBD, UMR5547 CNRS/UPS, Université de Toulouse, Toulouse, France.

Hox genes in species across the metazoa encode transcription factors (TFs) containing highly-conserved homeodomains that bind target DNA sequences to regulate batteries of developmental target genes. DNA-bound Hox proteins, together with other TF partners, induce an appropriate transcriptional response by RNA Polymerase II (PolII) and its associated general transcription factors. How the evolutionarily conserved Hox TFs interface with this general machinery to generate finely regulated transcriptional responses remains obscure. One major component of the PolII machinery, the Mediator (MED) transcription complex, is composed of roughly 30 protein subunits organized in modules that bridge the PolII enzyme to DNA-bound TFs. Here, we investigate the physical and functional interplay between Drosophila melanogaster Hox developmental TFs and MED complex proteins. We find that the Med19 subunit directly binds Hox homeodomains, in vitro and in vivo. Loss-of-function Med19 mutations act as dose-sensitive genetic modifiers that synergistically modulate Hox-directed developmental outcomes. Using clonal analysis, we identify a role for Med19 in Hox-dependent target gene activation. We identify a conserved, animal-specific motif that is required for Med19 homeodomain binding, and for activation of a specific Ultrabithorax target. These results provide the first direct molecular link between Hox homeodomain proteins and the general PolII machinery. They support a role for Med19 as a PolII holoenzyme-embedded "co-factor" that acts together with Hox proteins through their homeodomains in regulated developmental transcription.
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http://dx.doi.org/10.1371/journal.pgen.1004303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006704PMC
May 2014

Hox proteins mediate developmental and environmental control of autophagy.

Dev Cell 2014 Jan 2;28(1):56-69. Epub 2014 Jan 2.

CNRS, Aix Marseille Université, IBDML, UMR 7288, Campus de Luminy, Marseille, cedex 09, 13288, France. Electronic address:

Hox genes encode evolutionarily conserved transcription factors, providing positional information used for differential morphogenesis along the anteroposterior axis. Here, we show that Drosophila Hox proteins are potent repressors of the autophagic process. In inhibiting autophagy, Hox proteins display no apparent paralog specificity and do not provide positional information. Instead, they impose temporality on developmental autophagy and act as effectors of environmental signals in starvation-induced autophagy. Further characterization establishes that temporality is controlled by Pontin, a facultative component of the Brahma chromatin remodeling complex, and that Hox proteins impact on autophagy by repressing the expression of core components of the autophagy machinery. Finally, the potential of central and posterior mouse Hox proteins to inhibit autophagy in Drosophila and in vertebrate COS-7 cells indicates that regulation of autophagy is an evolutionary conserved feature of Hox proteins.
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http://dx.doi.org/10.1016/j.devcel.2013.11.024DOI Listing
January 2014

Distinct genetic requirements for BX-C-mediated specification of abdominal denticles.

Dev Dyn 2014 Jan 28;243(1):192-200. Epub 2013 Nov 28.

CNRS, Aix Marseille Université, Marseille, France.

Background: Hox genes encode transcription factors playing important role in segment specific morphogenesis along the anterior posterior axis. Most work in the Hox field aimed at understanding the basis for specialised Hox functions, while little attention was given to Hox common function. In Drosophila, genes of the Bithorax complex [Ultrabithorax (Ubx), abdominalA (abdA), and AbdominalB (AbdB)] all promote abdominal identity. While Ubx and AbdA share extensive sequence conservation, AbdB is highly divergent, questioning how it can perform similar functions as Ubx and AbdA.

Results: In this study, we investigate the genetic requirement for the specification of abdominal-type denticles by Ubx, AbdA, and AbdB. The impact of ectopic expression of Hox proteins in embryos mutant for Exd as well as of Wingless or Hedgehog signaling involved in intrasegmental patterning was analyzed. Results indicated that Ubx and AbdA do not require Exd, Wg, and Hh activity for specifying abdominal-type denticles, while AbdB does.

Conclusions: Our results support that distinct regulatory mechanisms underlie Ubx/AbdA- and AbdB-mediated specification of abdominal-type denticles, highlighting distinct strategies for achieving a similar biological output. This suggests that common function performed by distinct paralogue Hox proteins may also rely on newly acquired property, instead of conserved/ancestral properties.
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http://dx.doi.org/10.1002/dvdy.24081DOI Listing
January 2014

Distinct molecular strategies for Hox-mediated limb suppression in Drosophila: from cooperativity to dispensability/antagonism in TALE partnership.

PLoS Genet 2013 7;9(3):e1003307. Epub 2013 Mar 7.

Centre National de la Recherche Scientifique, Aix Marseille Université, Institut de Biologie du Développement de Marseille Luminy, UMR 7288, Parc Scientifique de Luminy, Marseille, France.

The emergence following gene duplication of a large repertoire of Hox paralogue proteins underlies the importance taken by Hox proteins in controlling animal body plans in development and evolution. Sequence divergence of paralogous proteins accounts for functional specialization, promoting axial morphological diversification in bilaterian animals. Yet functionally specialized paralogous Hox proteins also continue performing ancient common functions. In this study, we investigate how highly divergent Hox proteins perform an identical function. This was achieved by comparing in Drosophila the mode of limb suppression by the central (Ultrabithorax and AbdominalA) and posterior class (AbdominalB) Hox proteins. Results highlight that Hox-mediated limb suppression relies on distinct modes of DNA binding and a distinct use of TALE cofactors. Control of common functions by divergent Hox proteins, at least in the case studied, relies on evolving novel molecular properties. Thus, changes in protein sequences not only provide the driving force for functional specialization of Hox paralogue proteins, but also provide means to perform common ancient functions in distinct ways.
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http://dx.doi.org/10.1371/journal.pgen.1003307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591290PMC
June 2013

The emerging role of acetylation in the regulation of autophagy.

Autophagy 2013 Jun 6;9(6):819-29. Epub 2013 Mar 6.

Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary.

Autophagy is an evolutionarily conserved catabolic process through which different components of the cells are sequestered into double-membrane cytosolic vesicles called autophagosomes, and fated to degradation through fusion with lysosomes. Autophagy plays a major function in many physiological processes including response to different stress factors, energy homeostasis, elimination of cellular organelles and tissue remodeling during development. Consequently, autophagy is strictly controlled and post-translational modifications such as phosphorylation and ubiquitination have long been associated with autophagy regulation. In contrast, the importance of acetylation in autophagy control has only emerged in the last few years. In this review, we summarize how previously identified histone acetylases and deacetylases modify key autophagic effector proteins, and discuss how this has an impact on physiological and pathological cellular processes.
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http://dx.doi.org/10.4161/auto.23908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672293PMC
June 2013

Antagonism versus cooperativity with TALE cofactors at the base of the functional diversification of Hox protein function.

PLoS Genet 2013 7;9(2):e1003252. Epub 2013 Feb 7.

CABD, CSIC/JA/Universidad Pablo de Olavide, Seville, Spain.

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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http://dx.doi.org/10.1371/journal.pgen.1003252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567137PMC
June 2013

Hox proteins display a common and ancestral ability to diversify their interaction mode with the PBC class cofactors.

PLoS Biol 2012 26;10(6):e1001351. Epub 2012 Jun 26.

Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR7288, CNRS, AMU, Parc Scientifique de Luminy, Case 907, Marseille, France.

Hox transcription factors control a number of developmental processes with the help of the PBC class proteins. In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide (HX). This paradigm is at the basis of the vast majority of experimental approaches dedicated to the study of Hox protein function. Here we questioned the unique and general use of the HX for PBC recruitment by using the Bimolecular Fluorescence Complementation (BiFC) assay. This method allows analyzing Hox-PBC interactions in vivo and at a genome-wide scale. We found that the HX is dispensable for PBC recruitment in the majority of investigated Drosophila and mouse Hox proteins. We showed that HX-independent interaction modes are uncovered by the presence of Meis class cofactors, a property which was also observed with Hox proteins of the cnidarian sea anemone Nematostella vectensis. Finally, we revealed that paralog-specific motifs convey major PBC-recruiting functions in Drosophila Hox proteins. Altogether, our results highlight that flexibility in Hox-PBC interactions is an ancestral and evolutionary conserved character, which has strong implications for the understanding of Hox protein functions during normal development and pathologic processes.
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http://dx.doi.org/10.1371/journal.pbio.1001351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383740PMC
October 2012

The MYST-containing protein Chameau is required for proper sensory organ specification during Drosophila thorax morphogenesis.

PLoS One 2012 6;7(3):e32882. Epub 2012 Mar 6.

Institut de Biologie du Développement de Marseille-Luminy, CNRS UMR6216/Université de la Méditerranée, Marseille, France.

The adult thorax of Drosophila melanogaster is covered by a stereotyped pattern of mechanosensory bristles called macrochaetes. Here, we report that the MYST containing protein Chameau (Chm) contributes to the establishment of this pattern in the most dorsal part of the thorax. Chm mutant pupae present extra-dorsocentral (DC) and scutellar (SC) macrochaetes, but a normal number of the other macrochaetes. We provide evidences that chm restricts the singling out of sensory organ precursors from proneural clusters and genetically interacts with transcriptional regulators involved in the regulation of achaete and scute in the DC and SC proneural cluster. This function of chm likely relies on chromatin structure regulation since a protein with a mutation in the conserved catalytic site fails to rescue the formation of supernumerary DC and SC bristles in chm mutant flies. This is further supported by the finding that mutations in genes encoding chromatin modifiers and remodeling factors, including Polycomb group (PcG) and Trithorax group (TrxG) members, dominantly modulate the penetrance of chm extra bristle phenotype. These data support a critical role for chromatin structure modulation in the establishment of the stereotyped sensory bristle pattern in the fly thorax.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032882PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295779PMC
August 2012

Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

PLoS Genet 2011 Oct 27;7(10):e1002302. Epub 2011 Oct 27.

Institut de Biologie du Développement de Marseille Luminy, UMR6216 CNRS, Parc Scientifique de Luminy, Case 907, Marseille, France.

Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.
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http://dx.doi.org/10.1371/journal.pgen.1002302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203194PMC
October 2011

Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay.

BMC Biol 2011 Jan 28;9. Epub 2011 Jan 28.

Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR 6216, CNRS, Université de la méditerranée, Parc Scientifique de Luminy, Case 907, 13288, Marseille Cedex 09, France.

Background: Protein interactions control the regulatory networks underlying developmental processes. The understanding of developmental complexity will, therefore, require the characterization of protein interactions within their proper environment. The bimolecular fluorescence complementation (BiFC) technology offers this possibility as it enables the direct visualization of protein interactions in living cells. However, its potential has rarely been applied in embryos of animal model organisms and was only performed under transient protein expression levels.

Results: Using a Hox protein partnership as a test case, we investigated the suitability of BiFC for the study of protein interactions in the living Drosophila embryo. Importantly, all BiFC parameters were established with constructs that were stably expressed under the control of endogenous promoters. Under these physiological conditions, we showed that BiFC is specific and sensitive enough to analyse dynamic protein interactions. We next used BiFC in a candidate interaction screen, which led to the identification of several Hox protein partners.

Conclusion: Our results establish the general suitability of BiFC for revealing and studying protein interactions in their physiological context during the rapid course of Drosophila embryonic development.
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http://dx.doi.org/10.1186/1741-7007-9-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041725PMC
January 2011

Selection of distinct Hox-Extradenticle interaction modes fine-tunes Hox protein activity.

Proc Natl Acad Sci U S A 2011 Feb 24;108(6):2276-81. Epub 2011 Jan 24.

Institut de Biologie du Développement de Marseille Luminy, Centre National de la Recherche Scientifique, Université de la Méditerranée, 13288 Marseille Cedex 09, France.

Hox genes encode transcription factors widely used for diversifying animal body plans in development and evolution. To achieve functional specificity, Hox proteins associate with PBC class proteins, Pre-B cell leukemia homeobox (Pbx) in vertebrates, and Extradenticle (Exd) in Drosophila, and were thought to use a unique hexapeptide-dependent generic mode of interaction. Recent findings, however, revealed the existence of an alternative, UbdA-dependent paralog-specific interaction mode providing diversity in Hox-PBC interactions. In this study, we investigated the basis for the selection of one of these two Hox-PBC interaction modes. Using naturally occurring variations and mutations in the Drosophila Ultrabithorax protein, we found that the linker region, a short domain separating the hexapeptide from the homeodomain, promotes an interaction mediated by the UbdA domain in a context-dependent manner. While using a UbdA-dependent interaction for the repression of the limb-promoting gene Distalless, interaction with Exd during segment-identity specification still relies on the hexapeptide motif. We further show that distinctly assembled Hox-PBC complexes display subtle but distinct repressive activities. These findings identify Hox-PBC interaction as a template for subtle regulation of Hox protein activity that may have played a major role in the diversification of Hox protein function in development and evolution.
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http://dx.doi.org/10.1073/pnas.1006964108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038764PMC
February 2011

Regulation of Hox activity: insights from protein motifs.

Adv Exp Med Biol 2010 ;689:3-16

Institute of Developmental Biology of Marseille Luminy, University of the Mediterranean, Marseille, France.

Deciphering the molecular bases of animal body plan construction is a central question in developmental and evolutionary biology. Genome analyses of a number of metazoans indicate that widely conserved regulatory molecules underlie the amazing diversity of animal body plans, suggesting that these molecules are reiteratively used for multiple purposes. Hox proteins constitute a good example of such molecules and provide the framework to address the mechanisms underlying transcriptional specificity and diversity in development and evolution. Here we examine the current knowledge of the molecular bases of Hox-mediated transcriptional control, focusing on how this control is encoded within protein sequences and structures. The survey suggests that the homeodomain is part of an extended multifunctional unit coordinating DNA binding and activity regulation and highlights the need for further advances in our understanding of Hox protein activity.
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http://dx.doi.org/10.1007/978-1-4419-6673-5_1DOI Listing
September 2010

Control of DNA replication: a new facet of Hox proteins?

Bioessays 2010 Sep;32(9):800-7

UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris 7, Paris, France.

Hox proteins are well-known as developmental transcription factors controlling cell and tissue identity, but recent findings suggest that they are also part of the cell replication machinery. Hox-mediated control of transcription and replication may ensure coordinated control of cell growth and differentiation, two processes that need to be tightly and precisely coordinated to allow proper organ formation and patterning. In this review we summarize the available data linking Hox proteins to the replication machinery and discuss the developmental and pathological implications of this new facet of Hox protein function.
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http://dx.doi.org/10.1002/bies.201000048DOI Listing
September 2010

Reiterative use of signalling pathways controls multiple cellular events during Drosophila posterior spiracle organogenesis.

Dev Biol 2010 Jul 18;343(1-2):18-27. Epub 2010 Apr 18.

Institut de Biologie du Développement de Marseille Luminy, IBDML, CNRS, Université de la Méditerranée, Parc Scientifique de Luminy, Case 907 13288 Marseille Cedex 09, France.

Organogenesis proceeds in multiple steps and events that need to be coordinated in time and space. Yet the genetic and molecular control of such coordination remains poorly understood. In this study we have investigated the contribution of three signalling pathways, Wnt/Wingless (Wg), Hedgehog (Hh), and epidermal growth factor receptor (EGFR), to posterior spiracle morphogenesis, an organ that forms under Abdominal-B (AbdB) control in the eighth abdominal segment. Using targeted signalling inactivation, we show that these pathways are reiteratively used to control multiple cellular events during posterior spiracle organogenesis, including cell survival and maintenance of cell polarity and adhesion required for tissue integrity. We propose that the reiterative use of the Wg, Hh, and EGFR signalling pathways serves to coordinate in time and space the sequential deployment of events that collectively allow proper organogenesis.
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http://dx.doi.org/10.1016/j.ydbio.2010.04.001DOI Listing
July 2010
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