TGF-? signaling acts on a Hox response element to confer specificity and diversity to Hox protein function

Stanford University, Palo Alto, California, United States
Development (Impact Factor: 6.46). 12/2003; 130(22):5445-55. DOI: 10.1242/dev.00760
Source: PubMed


Hox proteins play fundamental roles in generating pattern diversity during development and evolution, acting in broad domains but controlling localized cell diversification and pattern. Much remains to be learned about how Hox selector proteins generate cell-type diversity. In this study, regulatory specificity was investigated by dissecting the genetic and molecular requirements that allow the Hox protein Abdominal A to activate wingless in only a few cells of its broad expression domain in the Drosophila visceral mesoderm. We show that the Dpp/Tgfbeta signal controls Abdominal A function, and that Hox protein and signal-activated regulators converge on a wingless enhancer. The signal, acting through Mad and Creb, provides spatial information that subdivides the domain of Abdominal A function through direct combinatorial action, conferring specificity and diversity upon Abdominal A activity.

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Available from: Samir Merabet, Jan 14, 2015
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    • "Beside the highly conserved and generic HX and HD, very few protein signatures have been identified and functionally analyzed in Hox proteins (Merabet et al., 2009). Genomic sequence divergence over short evolutionary distance, for example between D. melanogaster and D. virilis, is sufficient to identify conserved blocks likely to act as cisregulatory regions (Grienenberger et al., 2003; Manak et al., 1994). Fig. 4. Ng-Lab can perform some of the Dm-Lab functions. "
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    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. Copyright © 2015. Published by Elsevier Ireland Ltd.
    Full-text · Article · Jul 2015 · Mechanisms of development
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    • "By comparison, low-throughput analyses focusing on individual Hox activities were more successful in revealing context-specific cofactors, as exemplified with the Drosophila AbdA and Deformed (Dfd) proteins (Fig. 3). In these studies, context-specific cofactors such as zinc finger TFs (Suzuki et al., 2003; Robertson et al., 2004; Mahaffey, 2005), nuclear effectors of signalling pathways (Grieder et al., 1997; Mann and Affolter, 1998; Bai et al., 2000; Saleh et al., 2000; Yang et al., 2000; Marty et al., 2001; Merabet et al., 2002; Grienenberger et al., 2003; Bondos, 2006; Li et al., 2006; Walsh and Carroll, 2007), and cell-specific TFs (Gebelein et al., 2004; Gong et al., 2007; Li- Kroeger et al., 2008; Stobe et al., 2009; Witt et al., 2010) were described to distinguish , regionalize, or specify Hox transcriptional activities, respectively. However, considered together, few studies have dissected interactions on physiological target enhancers (Zappavigna et al., 1996; Prevot et al., 2000; Di Rocco et al., 2001; Gebelein et al., 2004; Hersh and Carroll, 2005; Pan et al., 2005; Gong et al., 2007; Taghli- Lamallem et al., 2007; Li-Kroeger et al., 2008; Williams et al., 2008; Stobe et al., 2009; Witt et al., 2010; Sorge et al., 2012). "
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    ABSTRACT: Background: Hox proteins are key developmental regulators involved in almost every embryonic tissue for specifying cell fates along longitudinal axes or during organ formation. It is thought that the panoply of Hox activities relies on interactions with tissue-, stage-, and/or cell-specific transcription factors. High-throughput approaches in yeast or cell culture systems have shown that Hox proteins bind to various types of nuclear and cytoplasmic components, illustrating their remarkable potential to influence many different cell regulatory processes. However, these approaches failed to identify a relevant number of context-specific transcriptional partners, suggesting that these interactions are hard to uncover in non-physiological conditions. Here we discuss this problematic. Results: In this review, we present intrinsic Hox molecular signatures that are probably involved in multiple (yet specific) interactions with transcriptional partners. We also recapitulate the current knowledge on Hox cofactors, highlighting the difficulty to tracking context-specific cofactors through traditional large-scale approaches. Conclusion: We propose experimental approaches that will allow a better characterisation of interaction networks underlying Hox contextual activities in the next future.
    Full-text · Article · Jan 2014 · Developmental Dynamics
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    • "To test the separate and distinct contributions of Hox, I–HD and NK-2 TF binding sites to mesodermal gene regulation, we used the complete spectrum of DNA binding preferences compiled from PBM data to identify and to selectively generate by in vitro mutagenesis nonbinding versions of predicted Hox, I–HD and NK-2 recognition sequences in a number of well-characterized mesodermal enhancers, while simultaneously preserving to the greatest extent possible the pattern of binding sequences for other classes of HD TFs (see Figures 1 and S1-S4) [5,26]. In addition, experiments were designed to minimize the number of nucleotide changes in each enhancer sequence, which varied from 0.402% to 4.98% of total nucleotides changed (average = 3%), which is comparable to the number of nucleotide changes in enhancer sequences in previous investigations of Hox function, which varied from 0.66% to 5.4% of total nucleotides changed (average = 3.2%) [16,29,30,31,32,33,34]. A representative example is shown in Figure 1 in which the PBM-derived enrichment scores (E-scores) of different HD classes are mapped along a segment of the Ndg enhancer, with the horizontal black line representing a threshold binding E-score > 0.31, which we previously showed optimally separated bound from unbound sequences (see Materials and Methods) [5]. "
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    ABSTRACT: Homeodomain (HD) proteins are a large family of evolutionarily conserved transcription factors (TFs) having diverse developmental functions, often acting within the same cell types, yet many members of this family paradoxically recognize similar DNA sequences. Thus, with multiple family members having the potential to recognize the same DNA sequences in cis-regulatory elements, it is difficult to ascertain the role of an individual HD or a subclass of HDs in mediating a particular developmental function. To investigate this problem, we focused our studies on the Drosophila embryonic mesoderm where HD TFs are required to establish not only segmental identities (such as the Hox TFs), but also tissue and cell fate specification and differentiation (such as the NK-2 HDs, Six HDs and identity HDs (I-HDs)). Here we utilized the complete spectrum of DNA binding specificities determined by protein binding microarrays (PBMs) for a diverse collection of HDs to modify the nucleotide sequences of numerous mesodermal enhancers to be recognized by either no or a single subclass of HDs, and subsequently assayed the consequences of these changes on enhancer function in transgenic reporter assays. These studies show that individual mesodermal enhancers receive separate transcriptional input from both I-HD and Hox subclasses of HDs. In addition, we demonstrate that enhancers regulating upstream components of the mesodermal regulatory network are targeted by the Six class of HDs. Finally, we establish the necessity of NK-2 HD binding sequences to activate gene expression in multiple mesodermal tissues, supporting a potential role for the NK-2 HD TF Tinman (Tin) as a pioneer factor that cooperates with other factors to regulate cell-specific gene expression programs. Collectively, these results underscore the critical role played by HDs of multiple subclasses in inducing the unique genetic programs of individual mesodermal cells, and in coordinating the gene regulatory networks directing mesoderm development.
    Full-text · Article · Jul 2013 · PLoS ONE
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