Hox protein interactions: screening and network building.

Computational Biology/methods; Databases, Protein; High-Throughput Screening Assays; Homeodomain Proteins/metabolism; Protein Binding; Protein Interaction Mapping/methods; Protein Interaction Maps; Reproducibility of Results; Two-Hybrid System Techniques; Yeasts/metabolism

Abstract :

[en] Understanding the mode of action of Hox proteins requires the identification of molecular and cellular pathways they take part in. This includes to characterize the networks of protein-protein interactions involving Hox proteins. In this chapter we propose a strategy and methods to map Hox interaction networks, from yeast two-hybrid and high-throughput yeast two-hybrid interaction screening to bioinformatic analyses based on the software platform Cytoscape.

Disciplines :

Biochemistry, biophysics & molecular biology

Author, co-author :

Bergiers, Isabelle

Lambert, Barbara

Daakour, Sarah ; Université de Liège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Biologie cell. et moléc.

Twizere, Jean-Claude ; Université de Liège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Biologie cell. et moléc.

Rezsohazy, Rene

Language :

English

Title :

Hox protein interactions: screening and network building.

Publication date :

2014

Journal title :

Methods in Molecular Biology

ISSN :

1064-3745

eISSN :

1940-6029

Publisher :

Humana Press, Clifton, United States - New Jersey

Volume :

1196

Pages :

319-48

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 22 February 2016

Statistics

Number of views

77 (6 by ULiège)

Number of downloads

2 (0 by ULiège)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

OpenCitations

OpenAlex citations

Bibliography

Forlani S, Lawson KA, Deschamps J (2003) Acquisition of Hox codes during gastrulation and axial elongation in the mouse embryo. Development 130:3807–3819
Mallo M, Wellik DM, Deschamps J (2010) Hox genes and regional patterning of the vertebrate body plan. Dev Biol 344:7–15
Wellik DM (2009) Hox genes and vertebrate axial pattern. Curr Top Dev Biol 88:257–278
Zakany J, Duboule D (2007) The role of Hox genes during vertebrate limb development. Curr Opin Genet Dev 17:359–366
Chen F, Capecchi MR (1999) Paralogous mouse Hox genes, Hoxa9, Hoxb9, and Hoxd9, function together to control development of the mammary gland in response to pregnancy. Proc Natl Acad Sci U S A 96:541–546
Garin É, Lemieux M, Coulombe Y et al (2006) Stromal Hoxa5 function controls the growth and differentiation of mammary alveolar epithelium. Dev Dyn 235:1858–1871
Wellik DM (2011) Hox genes and kidney development. Pediatr Nephrol 26:1559–1565
Di-Poi N, Zakany J, Duboule D (2007) Distinct roles and regulations for HoxD genes in metanephric kidney development. PLoS Genet 3:e232
Aubin J, Dery U, Lemieux M et al (2002) Stomach regional specification requires Hoxa5- driven mesenchymal-epithelial signaling. Development 129:4075–4087
Zacchetti G, Duboule D, Zakany J (2007) Hox gene function in vertebrate gut morphogenesis: the case of the caecum. Development 134:3967–3973
Boucherat O, Montaron S, Berube-Simard FA, Aubin J, Philippidou P, Wellik DM, Dasen JS, Jeannotte L (2013) Partial functional redundancy between Hoxa5 and Hoxb5 paralog genes during lung morphogenesis. Am J Physiol Lung Cell Mol Physiol 304:L817–830
Mandeville I, Aubin J, LeBlanc M et al (2006) Impact of the loss of Hoxa5 function on lung alveogenesis. Am J Pathol 169:1312–1327
Zaffran S, Kelly RG (2012) New developments in the second heart field. Differentiation 84:17–24
Oury F, Murakami Y, Renaud JS et al (2006) Hoxa2- and rhombomere-dependent development of the mouse facial somatosensory map. Science 313:1408–1413
Geisen MJ, Di Meglio T, Pasqualetti M et al (2008) Hox Paralog Group 2 Genes Control the Migration of Mouse Pontine Neurons through Slit-Robo Signaling. PLoS Biol 6:e142
Di Bonito M, Narita Y, Avallone B, Sequino L, Mancuso M, Andolfi G, Franze AM, Puelles L, Rijli FM, Studer M (2013) Assembly of the auditory circuitry by a Hox genetic network in the mouse brainstem. PLoS Genet 9:e1003249
Di Meglio T, Kratochwil CF, Vilain N et al (2013) Ezh2 orchestrates topographic migration and connectivity of mouse precerebellar neurons. Science 339:204–207
Antonchuk J, Sauvageau G, Humphries RK (2002) HOXB4-induced expansion of adult hematopoietic stem cells ex vivo. Cell 109:39–45
Argiropoulos B, Humphries RK (2007) Hox genes in hematopoiesis and leukemogenesis. Oncogene 26:6766–6776
McGonigle GJ, Lappin TR, Thompson A (2008) Grappling with the HOX network in hematopoiesis and leukemia. Front Biosci 13:4297–4308
Cillo C (2007) Deregulation of the Hox Gene Network and Cancer. In: Papageorgiou S (ed) Hox gene expression. Springer, New York, pp 121–133
Paul D, Bridoux L, Rezsohazy R, Donnay I (2011) HOX genes are expressed in bovine and mouse oocytes and early embryos. Mol Reprod Dev 78:436–449
Graba Y, Aragnol D, Pradel J (1997) Drosophila Hox complex downstream targets and the function of homeotic genes. Bioessays 19:379–388
Akin ZN, Nazarali AJ (2005) Hox genes and their candidate downstream targets in the developing central nervous system. Cell Mol Neurobiol 25:697–741
Chen H, Rubin E, Zhang H et al (2005) Identification of transcriptional targets of HOXA 5. J Biol Chem 280:19373–19380
Lei H, Wang H, Juan AH, Ruddle FH (2005) The identification of Hoxc8 target genes. Proc Natl Acad Sci U S A 102:2420–2424
Svingen T, Tonissen KF (2006) Hox transcription factors and their elusive mammalian gene targets. Heredity 97:88–96
Makki N, Capecchi MR (2011) Identification of novel Hoxa1 downstream targets regulating hindbrain, neural crest and inner ear development. Dev Biol 357:295–304
Donaldson IJ, Amin S, Hensman JJ, Kutejova E, Rattray M, Lawrence N, Hayes A, Ward CM, Bobola N (2012) Genome-wide occupancy links Hoxa2 to Wnt-beta-catenin signaling in mouse embryonic development. Nucleic Acids Res 40:3990–4001
Merabet S, Pradel J, Graba Y (2005) Getting a molecular grasp on Hox contextual activity. Trends Genet 21:477–480
Merabet S, Sambrani N, Pradel J, Graba Y (2010) Regulation of Hox activity: insights from protein motifs. Adv Exp Med Biol 689:3–16
Rezsohazy R (2014) Non-transcriptional interactions of Hox proteins: inventory, facts, and future directions. Dev Dyn 243:117–131
Vidalain P, Boxem M, Ge H et al (2004) Increasing specificity in high-throughput yeast two-hybrid experiments. Methods 32:363–370
Dreze M, Monachello D, Lurin C et al (2010) High-quality binary interactome mapping. Methods Enzymol 470:281–315
Lemmens I, Lievens S, Tavernier J (2010) Strategies towards high-quality binary protein interactome maps. J Proteomics 73: 1415–1420
Eyckerman S, Verhee A, der Heyden JV et al (2001) Design and application of a cytokinereceptor- based interaction trap. Nat Cell Biol 3:1114–1119
Kodama Y, Hu CD (2012) Bimolecular fl uorescence complementation (BiFC): a 5-year update and future perspectives. Biotechniques 53:285–298
Hudry B, Viala S, Graba Y, Merabet S (2011) Visualization of protein interactions in living Drosophila embryos by the bimolecular fl uorescence complementation assay. BMC Biol 9:5
Koh GC, Porras P, Aranda B et al (2012) Analyzing protein-protein interaction networks. J Proteome Res 11:2014–2031
Cusick ME, Klitgord N, Vidal M, Hill DE (2005) Interactome: gateway into systems biology. Hum Mol Genet 14(suppl_2):R171–181
Lambert B, Vandeputte J, Remacle S et al (2012) Protein interactions of the transcription factor Hoxa 1. BMC Dev Biol 12:29
Bergiers I, Bridoux L, Nguyen N et al (2013) The Homeodomain Transcription Factor Hoxa2 Interacts with and Promotes the Proteasomal Degradation of the E3 Ubiquitin Protein Ligase RCHY 1. PLoS One 8:e80387
Vidal M, Braun P, Chen E et al (1996) Genetic characterization of a mammalian proteinprotein interaction domain by using a yeast reverse two-hybrid system. Proc Natl Acad Sci U S A 93:10321–10326
Vidal M, Brachmann RK, Fattaey A et al (1996) Reverse two-hybrid and one-hybrid systems to detect dissociation of proteinprotein and DNA-protein interactions. Proc Natl Acad Sci U S A 93(19):10315–10320
James P, Halladay J, Craig EA (1996) Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144:1425–1436
Rual JF, Hirozane-Kishikawa T, Hao T et al (2004) Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res 14:2128–2135
Wiemann S, Arlt D, Huber W et al (2004) From ORFeome to biology: a functional genomics pipeline. Genome Res 14:2136–2144
Rual J-F, Venkatesan K, Hao T et al (2005) Towards a proteome-scale map of the human protein–protein interaction network. Nature 437:1173–1178
Lamesch P, Li N, Milstein S et al (2007) hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 89:307–315
Simonis N, Rual JF, Lemmens I et al (2012) Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses. Retrovirology 9:26
Orchard S (2012) Molecular interaction databases. Proteomics 12:1656–1662
del-Toro N, Dumousseau M, Orchard S et al (2013) A new reference implementation of the PSICQUIC web service. Nucleic Acids Res 41:W601–606
Lambert B, Vandeputte J, Desmet PM et al (2010) Pentapeptide insertion mutagenesis of the Hoxa1 protein: mapping of transcription activation and DNA-binding regulatory domains. J Cell Biochem 110:484–496
Van Roey K, Orchard S, Kerrien S et al (2013) Capturing cooperative interactions with the PSI-MI format. Database, bat066
Aranda B, Blankenburg H, Kerrien S et al (2011) PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods 8:528–529
van Iersel MP, Pico AR, Kelder T et al (2010) The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics 11:5
Scardoni G, Petterlini M, Laudanna C (2009) Analyzing biological network parameters with CentiScaPe. Bioinformatics 25:2857–2859
Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2