G. Balavoine, R. De-rosa, and A. Adoutte, Hox clusters and bilaterian phylogeny, Molecular Phylogenetics and Evolution, vol.24, issue.3, pp.366-373, 2002.
DOI : 10.1016/S1055-7903(02)00237-3

A. Bassett and J. Liu, CRISPR/Cas9 and Genome Editing in Drosophila, Journal of Genetics and Genomics, vol.41, issue.1, pp.7-19, 2014.
DOI : 10.1016/j.jgg.2013.12.004

M. Berger, G. Badis, A. Gehrke, S. Talukder, A. Philippakis et al., Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences, Cell, vol.133, issue.7, pp.1266-1276, 2008.
DOI : 10.1016/j.cell.2008.05.024

N. Bertrand, M. Roux, L. Ryckebüschryckeb¨ryckebüsch, K. Niederreither, P. Dolí-e et al., Hox genes define distinct progenitor sub-domains within the second heart field, Developmental Biology, vol.353, issue.2, pp.266-274, 2011.
DOI : 10.1016/j.ydbio.2011.02.029

J. Bischof, M. Björklundbj¨björklund, E. Furger, C. Schertel, J. Taipale et al., A versatile platform for creating a comprehensive UAS-ORFeome library in Drosophila, Development, vol.140, issue.11, pp.2434-2442, 2013.
DOI : 10.1242/dev.088757

J. Bischof, R. Maeda, M. Hediger, F. Karch, and K. Basler, An optimized transgenesis system for Drosophila using germ-line-specific ??C31 integrases, Proceedings of the National Academy of Sciences, vol.104, issue.9, pp.3312-3317, 2007.
DOI : 10.1073/pnas.0611511104

M. Blaxter, Revealing the Dark Matter of the Genome, Science, vol.330, issue.6012, pp.1758-1759, 2010.
DOI : 10.1126/science.1200700

S. Bondos, D. Catanese, . Jr, X. Tan, A. Bicknell et al., Hox Transcription Factor Ultrabithorax Ib Physically and Genetically Interacts with Disconnected Interacting Protein 1, a Double-stranded RNA-binding Protein, Journal of Biological Chemistry, vol.279, issue.25, pp.26433-26444, 2004.
DOI : 10.1074/jbc.M312842200

S. Bondos, X. Tan, and K. Matthews, Physical and Genetic Interactions Link Hox Function with Diverse Transcription Factors and Cell Signaling Proteins, Molecular & Cellular Proteomics, vol.5, issue.5, pp.824-834, 2006.
DOI : 10.1074/mcp.M500256-MCP200

M. Boube, B. Hudry, C. Immarigeon, Y. Carrier, S. Bernat-fabre et al., Drosophila melanogaster Hox Transcription Factors Access the RNA Polymerase II Machinery through Direct Homeodomain Binding to a Conserved Motif of Mediator Subunit Med19, PLoS Genetics, vol.130, issue.5, 2014.
DOI : 10.1371/journal.pgen.1004303.s009

URL : https://hal.archives-ouvertes.fr/hal-01107398

K. Brayer, V. Lynch, and G. Wagner, Evolution of a derived protein-protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation, Proceedings of the National Academy of Sciences, vol.108, issue.32, pp.414-420, 2011.
DOI : 10.1073/pnas.1100990108

V. Brodu, P. Elstob, and A. Gould, abdominal A specifies one cell type in Drosophila by regulating one principal target gene, Development, vol.129, pp.2957-2963, 2002.

M. Buljan, G. Chalancon, A. Dunker, A. Bateman, S. Balaji et al., Alternative splicing of intrinsically disordered regions and rewiring of protein interactions, Current Opinion in Structural Biology, vol.23, issue.3, 2013.
DOI : 10.1016/j.sbi.2013.03.006

S. Chan, H. Krumlauf, R. Mann, and R. , An extradenticle-induced conformational change in a HOX protein overcomes an inhibitory function of the conserved hexapeptide motif, The EMBO Journal, vol.15, pp.2476-2487, 1996.

D. Coiffier, B. Charroux, and S. Kerridge, Common functions of central and posterior Hox genes for the repression of head in the trunk of Drosophila, Development, vol.135, issue.2, pp.291-300, 2008.
DOI : 10.1242/dev.009662

P. Cunha, T. Sandmann, E. Gustafson, L. Ciglar, M. Eichenlaub et al., Combinatorial Binding Leads to Diverse Regulatory Responses: Lmd Is a Tissue-Specific Modulator of Mef2 Activity, PLoS Genetics, vol.29, issue.7, 2010.
DOI : 10.1371/journal.pgen.1001014.s008

L. De-navas, D. Foronda, M. Suzanne, S. Herrero, and E. , A simple and efficient method to identify replacements of P-lacZ by P-Gal4 lines allows obtaining Gal4 insertions in the bithorax complex of Drosophila, Mechanisms of Development, vol.123, issue.11, pp.860-867, 2006.
DOI : 10.1016/j.mod.2006.07.010

L. Fasano, R. ¨. , L. Corécor´coré, N. Alexandre, E. Vola et al., The gene teashirt is required for the development of Drosophila embryonic trunk segments and encodes a protein with widely spaced zinc finger motifs, Cell, vol.64, issue.1, pp.63-79, 1991.
DOI : 10.1016/0092-8674(91)90209-H

J. Finnerty, The origins of axial patterning in the metazoa: how old is bilateral symmetry?, The International Journal of Developmental Biology, vol.47, pp.523-529, 2003.

N. Foos, C. Maurel-zaffran, M. Matémat´maté, R. Vincentelli, M. Hainaut et al., A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/PBC Interaction Mode, Structure, vol.23, issue.2, pp.270-279, 2015.
DOI : 10.1016/j.str.2014.12.011

URL : https://hal.archives-ouvertes.fr/hal-01439016

D. Foronda, B. Estrada, L. De-navas, S. Herrero, and E. , Requirement of abdominal-A and Abdominal-B in the developing genitalia of Drosophila breaks the posterior downregulation rule, Development, vol.133, issue.1, pp.117-127, 2005.
DOI : 10.1242/dev.02173

R. Galant, C. Walsh, and S. Carroll, Hox repression of a target gene: extradenticle-independent, additive action through multiple monomer binding sites, Development, vol.3126, pp.3115-3126, 2002.

B. Gebelein, J. Culi, H. Ryoo, W. Zhang, and R. Mann, Specificity of Distalless Repression and Limb Primordia Development by Abdominal Hox Proteins, Developmental Cell, vol.3, issue.4, pp.487-498, 2002.
DOI : 10.1016/S1534-5807(02)00257-5

I. Ghosh, A. Hamilton, and L. Regan, Antiparallel Leucine Zipper-Directed Protein Reassembly:?? Application to the Green Fluorescent Protein, Journal of the American Chemical Society, vol.122, issue.23, pp.5658-5659, 2000.
DOI : 10.1021/ja994421w

J. Gnerer, K. Venken, and H. Dierick, Gene-specific cell labeling using MiMIC transposons, Nucleic Acids Research, vol.43, issue.8, pp.1-13, 2015.
DOI : 10.1093/nar/gkv113

A. Grienenberger, S. Merabet, J. Manak, I. Iltis, A. Fabre et al., Tgf?? signaling acts on a Hox response element to confer specificity and diversity to Hox protein function, Development, vol.130, issue.22, pp.5445-5455, 2003.
DOI : 10.1242/dev.00760

A. Hammonds, C. Bristow, W. Fisher, R. Weiszmann, S. Wu et al., Spatial expression of transcription factors in Drosophila embryonic organ development, Genome Biology, vol.14, issue.12, 2013.
DOI : 10.1093/bioinformatics/btl143

H. Hsiao, K. Gonzalez, D. Catanese, . Jr, K. Jordy et al., The Intrinsically Disordered Regions of the Drosophila melanogaster Hox Protein Ultrabithorax Select Interacting Proteins Based on Partner Topology, PLoS ONE, vol.4, issue.10, 2014.
DOI : 10.1371/journal.pone.0108217.s006

B. Hudry, S. Remacle, M. Delfini, R. Rezsohazy, Y. Graba et al., Hox Proteins Display a Common and Ancestral Ability to Diversify Their Interaction Mode with the PBC Class Cofactors, PLoS Biology, vol.121, issue.6, 2012.
DOI : 10.1371/journal.pbio.1001351.s013

URL : https://hal.archives-ouvertes.fr/hal-00843467

B. Hudry, S. Viala, Y. Graba, and S. Merabet, Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay, BMC Biology, vol.9, issue.1, pp.1741-7007, 2011.
DOI : 10.1186/1741-7007-9-5

URL : https://hal.archives-ouvertes.fr/hal-00848904

I. Der-rieden, P. Mainguy, G. Woltering, J. Durston, and A. , Homeodomain to hexapeptide or PBC-interaction-domain distance: size apparently matters, Trends in Genetics, vol.20, issue.2, pp.76-79, 2004.
DOI : 10.1016/j.tig.2003.12.001

L. Kammermeier, S. Sprecher, M. ¨. , M. Miller, D. Kaufman et al., Hox gene crossregulatory interactions in the embryonic brain of Drosophila, Mechanisms of Development, vol.121, pp.527-536, 2004.

T. Kerppola, Bimolecular Fluorescence Complementation (BiFC) Analysis as a Probe of Protein Interactions in Living Cells, Annual Review of Biophysics, vol.37, issue.1, pp.465-487, 2008.
DOI : 10.1146/annurev.biophys.37.032807.125842

Y. Kodama and C. Hu, Bimolecular fluorescence complementation (BiFC): A 5-year update and future perspectives, BioTechniques, vol.53, issue.5, pp.285-298, 2012.
DOI : 10.2144/000113943

T. Kondo, Y. Hashimoto, K. Kato, S. Inagaki, S. Hayashi et al., Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA, Nature Cell Biology, vol.49, issue.6, pp.660-665, 1595.
DOI : 10.1266/ggs.81.129

E. Kvon, G. Stampfel, Y. Cuna, J. Dickson, B. Stark et al., HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature, Genes & Development, vol.26, issue.9, pp.908-913, 2012.
DOI : 10.1101/gad.188052.112

B. Lambert, J. Vandeputte, S. Remacle, I. Bergiers, N. Simonis et al., Protein interactions of the transcription factor Hoxa1, BMC Developmental Biology, vol.12, issue.1, pp.29-39, 2012.
DOI : 10.1186/1471-213X-12-29

C. Landry, E. Levy, A. Rabbo, D. Tarassov, K. Michnick et al., Extracting Insight from Noisy Cellular Networks, Cell, vol.155, issue.5, pp.983-989, 2013.
DOI : 10.1016/j.cell.2013.11.003

G. Lee, L. Donaldson, M. Pufall, H. Kang, I. Pot et al., The Structural and Dynamic Basis of Ets-1 DNA Binding Autoinhibition, Journal of Biological Chemistry, vol.280, issue.8, pp.7088-7099, 2005.
DOI : 10.1074/jbc.M410722200

O. Lee, H. Kim, Q. He, H. Baek, D. Yang et al., Genomewide YFP fluorescence complementation screen identifies new regulators for telomere signaling in human cells, Molecular & Cellular Proteomics, vol.10, 2011.

X. Li, S. Macarthur, R. Bourgon, D. Nix, D. Pollard et al., Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm, PLOS Biology, vol.6, 2008.

D. Li-kroeger, L. Witt, H. Grimes, T. Cook, and B. Gebelein, Hox and Senseless Antagonism Functions as a Molecular Switch to Regulate EGF Secretion in the Drosophila PNS, Developmental Cell, vol.15, issue.2, pp.298-308, 2008.
DOI : 10.1016/j.devcel.2008.06.001

V. Lynch, A. Tanzer, Y. Wang, F. Leung, B. Gellersen et al., Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals, Proceedings of the National Academy of Sciences, vol.105, issue.39, pp.14928-14933, 2008.
DOI : 10.1073/pnas.0802355105

E. Magny, J. Pueyo, F. Pearl, M. Cespedes, J. Niven et al., Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames, Science, vol.341, issue.6150, pp.1116-1120, 2013.
DOI : 10.1126/science.1238802

R. Mann, K. Lelli, and R. Joshi, Chapter 3 Hox Specificity, Current Topics in Developmental Biology, vol.88, issue.09, pp.63-101, 2009.
DOI : 10.1016/S0070-2153(09)88003-4

O. Medina-martinez and R. Ram?, In vivo mutagenesis of the Hoxb8 hexapeptide domain leads to dominant homeotic transformations that mimic the loss-of-function mutations in genes of the Hoxb cluster, Developmental Biology, vol.264, 2003.

S. Merabet and A. Dard, Tracking context-specific transcription factors regulating hox activity, Developmental Dynamics, vol.15, issue.1, pp.16-23, 2014.
DOI : 10.1002/dvdy.24002

S. Merabet and B. Hudry, On the border of the homeotic function: Re-evaluating the controversial role of cofactor-recruiting motifs, BioEssays, vol.10, issue.(Suppl 1), pp.499-507, 2011.
DOI : 10.1002/bies.201100019

S. Merabet, Z. Kambris, M. Capovilla, B. ´. , H. Pradel et al., The Hexapeptide and Linker Regions of the AbdA Hox Protein Regulate Its Activating and Repressive Functions, Developmental Cell, vol.4, issue.5, pp.761-768, 2003.
DOI : 10.1016/S1534-5807(03)00126-6

URL : https://hal.archives-ouvertes.fr/hal-00311055

S. Merabet, M. Saadaoui, N. Sambrani, B. Hudry, J. Pradel et al., A unique Extradenticle recruitment mode in the Drosophila Hox protein Ultrabithorax, Proceedings of the National Academy of Sciences, vol.104, issue.43, pp.16946-16951, 2007.
DOI : 10.1073/pnas.0705832104

URL : https://hal.archives-ouvertes.fr/hal-00311042

S. Merabet, B. Hudry, M. Saadaoui, and Y. Graba, Classification of sequence signatures: a guide to Hox protein function, BioEssays, vol.65, issue.5, pp.500-511, 2009.
DOI : 10.1002/bies.200800229

URL : https://hal.archives-ouvertes.fr/hal-00409168

S. Merabet, I. Litim-mecheri, D. Karlsson, R. Dixit, M. Saadaoui et al., Insights into Hox Protein Function from a Large Scale Combinatorial Analysis of Protein Domains, PLoS Genetics, vol.411, issue.10, 2011.
DOI : 10.1371/journal.pgen.1002302.s011

URL : https://hal.archives-ouvertes.fr/inserm-00711704

C. Moorman, L. Sun, J. Wang, E. De-wit, W. Talhout et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster, Proceedings of the National Academy of Sciences of, pp.12027-12032, 2006.
DOI : 10.1073/pnas.0605003103

M. Morell, P. Czihal, R. Hoffmann, L. Otvos, F. Avií-es et al., Monitoring the interference of protein-protein interactions in vivo by bimolecular fluorescence complementation: the DnaK case, PROTEOMICS, vol.273, issue.17, pp.3433-3442, 2008.
DOI : 10.1002/pmic.200700739

K. Mukherjee, B. ¨. , and T. , Comprehensive Analysis of Animal TALE Homeobox Genes: New Conserved Motifs and Cases of Accelerated Evolution, Journal of Molecular Evolution, vol.155, issue.2, pp.137-153, 2007.
DOI : 10.1007/s00239-006-0023-0

V. Neduva and R. Russell, Linear motifs: Evolutionary interaction switches, FEBS Letters, vol.120, issue.15, pp.3342-3345, 2005.
DOI : 10.1016/j.febslet.2005.04.005

M. Noyes, R. Christensen, A. Wakabayashi, G. Stormo, M. Brodsky et al., Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites, Cell, vol.133, issue.7, pp.1277-1289, 2008.
DOI : 10.1016/j.cell.2008.05.023

S. Padrick and M. Rosen, Physical Mechanisms of Signal Integration by WASP Family Proteins, Annual Review of Biochemistry, vol.79, issue.1, pp.707-735, 2010.
DOI : 10.1146/annurev.biochem.77.060407.135452

T. Pawson, G. Gish, and P. Nash, SH2 domains, interaction modules and cellular wiring, Trends in Cell Biology, vol.11, issue.12, pp.504-511, 2001.
DOI : 10.1016/S0962-8924(01)02154-7

F. Prince, T. Katsuyama, Y. Oshima, S. Plaza, D. Resendez-perez et al., The YPWM motif links Antennapedia to the basal transcriptional machinery, Development, vol.135, issue.9, pp.1669-1679, 2008.
DOI : 10.1242/dev.018028

M. Pufall and B. Graves, Autoinhibitory Domains: Modular Effectors of Cellular Regulation, Annual Review of Cell and Developmental Biology, vol.18, issue.1, pp.421-462, 2002.
DOI : 10.1146/annurev.cellbio.18.031502.133614

A. Saeed, N. Bhagabati, J. Braisted, W. Liang, V. Sharov et al., [9] TM4 Microarray Software Suite, Methods in Enzymology, vol.411, issue.06, pp.134-193, 2006.
DOI : 10.1016/S0076-6879(06)11009-5

P. Shannon, A. Markiel, O. Ozier, N. Baliga, J. Wang et al., Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks, Genome Research, vol.13, issue.11, pp.2498-2504, 2003.
DOI : 10.1101/gr.1239303

A. Stein and P. Aloy, Contextual Specificity in Peptide-Mediated Protein Interactions, PLoS ONE, vol.266, issue.7, 2008.
DOI : 10.1371/journal.pone.0002524.s005

D. Tawfik, Messy biology and the origins of evolutionary innovations, Nature Chemical Biology, vol.315, issue.10, pp.692-696, 2010.
DOI : 10.1038/nchembio.441

P. Tompa, N. Davey, T. Gibson, and M. Babu, A Million Peptide Motifs for the Molecular Biologist, Molecular Cell, vol.55, issue.2, pp.161-169, 2014.
DOI : 10.1016/j.molcel.2014.05.032

T. Trudeau, R. Nassar, A. Cumberworth, E. Wong, G. Woollard et al., Structure and Intrinsic Disorder in Protein Autoinhibition, Structure, vol.21, issue.3, pp.332-341, 2013.
DOI : 10.1016/j.str.2012.12.013

K. Van-roey, H. Dinkel, R. Weatheritt, T. Gibson, and N. Davey, The switches.ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces, Science Signaling, vol.6, issue.269, 2013.
DOI : 10.1126/scisignal.2003345

K. Van-roey, T. Gibson, and N. Davey, Motif switches: decision-making in cell regulation, Current Opinion in Structural Biology, vol.22, issue.3, pp.378-385, 2012.
DOI : 10.1016/j.sbi.2012.03.004

K. Van-roey, B. Uyar, R. Weatheritt, H. Dinkel, M. Seiler et al., Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation, Chemical Reviews, vol.114, issue.13, pp.6733-6778, 2014.
DOI : 10.1021/cr400585q

K. Venken, Y. He, R. Hoskins, and H. Bellen, P[acman]: A BAC Transgenic Platform for Targeted Insertion of Large DNA Fragments in D. melanogaster, Science, vol.314, issue.5806, pp.1747-1751, 2006.
DOI : 10.1126/science.1134426

C. Walsh and S. Carroll, Collaboration between Smads and a Hox protein in target gene repression, Development, vol.134, issue.20, pp.3585-3592, 2007.
DOI : 10.1242/dev.009522

J. Zakany and D. Duboule, The role of Hox genes during vertebrate limb development, Current Opinion in Genetics & Development, vol.17, issue.4, pp.359-366, 2007.
DOI : 10.1016/j.gde.2007.05.011