Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo

Baëza, Manon; Viala, Séverine; Heim, M; Dard, Amélie; Hudry, Bruno; Duffraisse, Marilyne; Rogulja-Ortmann, Ana; Brun, Catherine; Merabet, Samir

doi:10.7554/elife.06034

Cited by 52 publications

(79 citation statements)

References 76 publications

(107 reference statements)

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“…As in our case the adjacency of Hox/Pbx binding site may identify other transcription factors that work with the Hox proteins. Because Hox proteins can interacts with many transcription factors (e.g., abd-A binds to 35; Baeza et al, 2015), they may facilitate the activation of target genes by a wide range of transcription factors.…”

Section: Discussionmentioning

confidence: 99%

Hox Proteins Act as Transcriptional Guarantors to Ensure Terminal Differentiation

2015

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Summary Cell differentiation usually occurs with high fidelity, yet the expression of many transcription factors is variable. Using the touch receptor neurons (TRNs) in C. elegans, we found that the Hox proteins CEH-13/lab and EGL-5/Abd-B overcome this variability by facilitating the activation of the common TRN fate determinant mec-3 in the anterior and posterior TRNs, respectively. CEH-13 and EGL-5 increase the probability of mec-3 transcriptional activation by the POU-homeodomain transcription factor UNC-86 using the same Hox/Pbx binding site. Mutation of ceh-13 and egl-5 resulted in an incomplete (~40%) loss of the TRN fate in respective TRNs, which correlates with quantitative mRNA measurements showing two distinct modes (all or none) of mec-3 transcription. Therefore, Hox proteins act as transcriptional “guarantors” to ensure reliable and robust gene expression during terminal neuronal differentiation. Guarantors do not activate gene expression by themselves but promote full activation of target genes regulated by other transcription factors.

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Section: Discussionmentioning

confidence: 99%

Hox Proteins Act as Transcriptional Guarantors to Ensure Terminal Differentiation

2015

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“…Overall our work revealed an astonishing level of functional diversity for a short conserved peptide motif, ranging from transcriptional regulation with generic or tissuespecific cofactors (11) to context-dependent nuclear export. Thus, the HX motif and its immediate surrounding region constitute a privileged platform for diversifying Hox protein function during development and evolution.…”

Section: Introductionmentioning

confidence: 92%

Role of a versatile peptide motif in controlling Hox nuclear export and autophagy in theDrosophilafat body

Duffraisse

Paul

Hudry

et al. 2019

Preprint

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Hox proteins are major regulators of embryonic development, acting in the nucleus to regulate the expression of their numerous downstream target genes. By analyzing deleted forms of the Drosophila Hox protein Ultrabithorax (Ubx), we revealed the presence of an unconventional Nuclear Export Signal (NES) that overlaps with the highly conserved hexapeptide (HX) motif. This short linear motif was originally described as mediating the interaction with the PBC proteins, a generic and crucial class of Hox transcriptional cofactors in development and cancer. Here we show that the HX motif is involved in the interaction with the major CRM1/Embargoed exportin protein. This novel role was found in several Drosophila and human Hox proteins. We provide evidence that HX-dependent Hox nuclear export is tightly regulated in the Drosophila fat body to control the onset of autophagy. Our results underline the high molecular versatility of a unique short peptide motif for controlling context-dependent activity of Hox proteins at both transcriptional and non-transcriptional levels.consensus distribution of hydrophobic residues (indicated below the graph). NetNES predicts a putative NES with a good confidence score in the region upstream of the HX (magenta peak). E. BiFC between wild type or HX-mutated VC-Scr fusion protein and VN-Emb, as indicated. Fusion proteins are expressed with the Antennapedia (Antp)-Gal4 driver. Graphs on the right show the statistical quantification of BiFC signal in the nucleus (N) and cytoplasm (C) of epidermal cells of stage 10 live embryos. The HX mutation affects the Scr-Emb interaction only in the cytoplasm. F. Genetic interaction between Scr and Emb. The co-expression of cold HA-Emb triggers Scr in the cytoplasm except if the HX motif is mutated. Quantification is performed as described in the Figure 2. Expanded View 5. Analysis of Drosophila and human Hox protein sequences withNetNES. The sequence of putative NESs is provided when the prediction score was good enough (magenta peak above the red line threshold). No NES was predicted in Antp and AbdB. NES were predicted in the N-terminal region of Dfd and Scr, and in the homeodomain (HD) of AbdA, HOXB4, HOXA5, HOXA7 and HOXA9. Expanded View 6. Analysis of Drosophila and human Hox protein sequences withLocNES. The sequence of putative NESs is provided when the prediction score was good enough. NESs were predicted only in Antp, AbdA and AbdB. Of note, one of the NES predicted in AbdB contains the derived HX motif (corresponding to a single W residue: bolded and red). Expanded View 7. Conservation of the non-canonical NES covering the HX motif in Dfd (A) and Scr (B) proteins from invertebrate and vertebrate species. Dm: Drosophila melanogaster. Am: Apis melifera. Bm: Bombyx mori. Tc: Tribolium castaneaum. Csa: Cupiennus salei. Mm: Mus musculus. Dr: Danio rerio. Nv: Nasonia vitripennis. Red arrowheads highlight hydrophobic residues of the putative NESs. Expanded View 8. The HX motif of human HOXA5 is part of a NES mediating CRM1dependent export in live H...

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“…In contrast to the RhoA element that mediates Abd-A specific transcriptional activation with Pax2, the DCRE contains two binding sites for the FoxG (Slp) with both Abd-A and Ubx in embryos, and at least Abd-A does so in a manner dependent on its ability to bind DNA [47]. Moreover, the thoracic Hox factor, Antp, failed to interact with Slp2 in BiFC assays, and we previously found that instead of mediating repression Antp stimulates the DMX leg enhancer in a DCRE-dependent manner via unknown mechanisms [35].…”

Section: Hox Specificity: Target Activation Vs Target Repressionmentioning

confidence: 99%

“…Altogether, these findings are consistent with Slp2 selectively working with Ubx and Abd-A on the DCRE to mediate abdominal repression. However, it should also be noted that of the five different Hox factors tested in BiFC assays, only Antp failed to interact significantly with Slp2 [47]. Thus, it is possible that the Slp/FoxG factors are directly integrated with several Hox factors and that the specificity of output will depend upon the presence of appropriately spaced/oriented DNA binding sites within the cis-regulatory modules.…”

Section: Hox Specificity: Target Activation Vs Target Repressionmentioning

confidence: 99%

Thecis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements inDrosophila

Zandvakili

Uhl

Campbell

et al. 2018

Preprint

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Hox genes encode a family of transcription factors that, despite having similar in vitro DNA binding preferences, regulate distinct genetic programs along the metazoan anterior-posterior axis. To better define mechanisms of Hox specificity, we compared and contrasted the ability of abdominal Hox factors to regulate two cis-regulatory elements within the Drosophila embryo. Both the Ultrabithorax (Ubx) and Abdominal-A (Abd-A) Hox factors form cooperative complexes with the Extradenticle (Exd) and Homothorax (Hth) transcription factors to repress the distal-less leg selector gene via the DCRE, whereas only Abd-A interacts with Exd and Hth on the RhoA element to activate a rhomboid serine protease gene that stimulates Epidermal Growth Factor secretion.By swapping binding sites between these elements, we found that the RhoA Exd/Hth/Hox site configuration that mediates Abd-A specific activation can also convey transcriptional repression by both Ubx and Abd-A when placed into the DCRE, but only in one orientation. We further show that the orientation and spacing of Hox sites relative to additional transcription factor binding sites within the RhoA and DCRE elements is critical to mediate appropriate cell-and segment-specific output. These results indicate that the interaction between Hox, Exd, and Hth neither determines activation vs repression specificity nor defines Ubx vs Abd-A specificity. Instead the precise integration of Hox sites with additional TF inputs is required for accurate transcriptional output.Taken together, these studies provide new insight into the mechanisms of Hox target and regulatory specificity as well as the constraints placed on regulatory elements to convey appropriate outputs. Author SummaryThe Hox genes encode a family of transcription factors that give cells within each region along the developing body plan a unique identity in animals from worms to mammals. Surprisingly, however, most of the Hox factors bind the same or highly similar DNA sequences. These findings raise a paradox: How can proteins that have highly similar DNA binding properties perform different functions in the animal by regulating different sets of target genes? In this study, we address this question by studying how two Hox factors regulate the expression of target genes that specify leg development and the making of liver-like cells in the developing fly. By comparing and contrasting how Hox target genes are activated and/or repressed, we found that the same Hox binding sites can mediate either activation or repression in a manner that depends upon context. In addition, we found that a Hox binding site that is normally regulated by only one Hox factor, can also be used by more than one Hox factor swapped into another target gene. These findings indicate that the specificity of a Hox factor to regulate target genes does not rely solely upon DNA binding specificity but also requires regulatory specificity.

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Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo

Cited by 52 publications

References 76 publications

Hox Proteins Act as Transcriptional Guarantors to Ensure Terminal Differentiation

Hox Proteins Act as Transcriptional Guarantors to Ensure Terminal Differentiation

Role of a versatile peptide motif in controlling Hox nuclear export and autophagy in theDrosophilafat body

Thecis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements inDrosophila

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