Hox Genes pp 197-208 | Cite as

Hox Transcriptomics in Drosophila Embryos

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1196)

Abstract

Hox proteins are evolutionarily conserved homeodomain containing transcription factors that specify segment identities along the anteroposterior axis of almost all bilaterian animals. They exert their morphogenetic role by transcriptionally regulating a large battery of downstream target genes. Therefore the dissection of transcriptional networks regulated by Hox proteins is an essential step towards a mechanistic understanding of how these transcription factors coordinate multiple developmental and morphogenetic processes. High-throughput techniques allowing whole-transcriptome mRNA expression profiling are powerful tools for the genome-wide identification of Hox downstream target genes in a variety of experimental settings. Here, we describe how to quantitatively identify Hox downstream genes in Drosophila embryos by performing a Hox transcriptome analysis using microarrays.

Key words

Hox Drosophila Transcription Microarray Transcriptome Expression profiling 

Notes

Acknowledgements

We would like to thank Jan U. Lohmann and Markus Schmid for sharing protocols with us.

References

  1. 1.
    Lewis EB (1978) A gene complex controlling segmentation in Drosophila. Nature 276:565–570PubMedCrossRefGoogle Scholar
  2. 2.
    McGinnis W, Krumlauf R (1992) Homeobox genes and axial patterning. Cell 68:283–302PubMedCrossRefGoogle Scholar
  3. 3.
    Hombría JC-G, Lovegrove B (2003) Beyond homeosis—HOX function in morphogenesis and organogenesis. Differentiation 71:461–476. doi: 10.1046/j.1432-0436.2003.7108004.x PubMedCrossRefGoogle Scholar
  4. 4.
    Pearson JC, Lemons D, McGinnis W (2005) Modulating Hox gene functions during animal body patterning. Nat Rev Genet 6:893–904. doi: 10.1038/nrg1726 PubMedCrossRefGoogle Scholar
  5. 5.
    Hueber SD, Lohmann I (2008) Shaping segments: Hox gene function in the genomic age. Bioessays 30:965–979. doi: 10.1002/bies.20823 PubMedCrossRefGoogle Scholar
  6. 6.
    Polychronidou M, Lohmann I (2013) Cell-type specific cis-regulatory networks: insights from Hox transcription factors. Fly (Austin) 7:13–17. doi: 10.4161/fly.22939 CrossRefGoogle Scholar
  7. 7.
    Leemans R, Loop T, Egger B et al (2001) Identification of candidate downstream genes for the homeodomain transcription factor Labial in Drosophila through oligonucleotide-array transcript imaging. Genome Biol 2:RESEARCH0015PubMedCentralPubMedGoogle Scholar
  8. 8.
    Mohit P, Makhijani K, Madhavi MB et al (2006) Modulation of AP and DV signaling pathways by the homeotic gene Ultrabithorax during haltere development in Drosophila. Dev Biol 291:356–367. doi: 10.1016/j.ydbio.2005.12.022 PubMedCrossRefGoogle Scholar
  9. 9.
    Hersh BM, Nelson CE, Stoll SJ et al (2007) The UBX-regulated network in the haltere imaginal disc of D. melanogaster. Dev Biol 302:717–727. doi: 10.1016/j.ydbio.2006.11.011 PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Hueber SD, Bezdan D, Henz SR et al (2007) Comparative analysis of Hox downstream genes in Drosophila. Development 134:381–392. doi: 10.1242/dev.02746 PubMedCrossRefGoogle Scholar
  11. 11.
    Pavlopoulos A, Akam M (2011) Hox gene Ultrabithorax regulates distinct sets of target genes at successive stages of Drosophila haltere morphogenesis. Proc Natl Acad Sci U S A 108:2855–2860. doi: 10.1073/pnas.1015077108 PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Pavlopoulos A, Akam M (2007) Hox go omics: insights from Drosophila into Hox gene targets. Genome Biol 8:208. doi: 10.1186/gb-2007-8-3-208 PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Miller DF, Rogers BT, Kalkbrenner A et al (2001) Cross-regulation of Hox genes in the Drosophila melanogaster embryo. Mech Dev 102:3–16PubMedCrossRefGoogle Scholar
  14. 14.
    Barthelson RA, Lambert GM, Vanier C et al (2007) Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells. BMC Genomics 8:340. doi: 10.1186/1471-2164-8-340 PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Bonn S, Zinzen RP, Perez-Gonzalez A et al (2012) Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat Protoc 7:978–994. doi: 10.1038/nprot.2012.049 PubMedCrossRefGoogle Scholar
  16. 16.
    Steiner FA, Talbert PB, Kasinathan S et al (2012) Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res 22:766–777. doi: 10.1101/gr.131748.111 PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Centre for Organismal Studies (COS) HeidelbergUniversity of HeidelbergHeidelbergGermany

Personalised recommendations