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Next-Generation Sequencing Applied to Flower Development: ChIP-Seq

  • Emmanuelle GracietEmail author
  • Diarmuid Seosamh Ó’Maoiléidigh
  • Frank WellmerEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1110)

Abstract

Over the past 20 years, classic genetic approaches have shown that the developmental program underlying flower formation involves a large number of transcriptional regulators. However, the target genes of these transcription factors, as well as the gene regulatory networks they control, remain largely unknown. Chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-Seq), which allows the identification of transcription factor binding sites on a genome-wide scale, has been successfully applied to a number of transcription factors in Arabidopsis. The ChIP-Seq procedure involves chemical cross-linking of proteins to DNA, followed by chromatin fragmentation and immunoprecipitation of specific protein–DNA complexes. The regions of the genome bound by a specific transcription factor can then be identified after next-generation sequencing.

Keywords

Arabidopsis Flower development ChIP-Seq Transcription factors 

Notes

Acknowledgements

Work in our laboratory is funded by grants from Science Foundation Ireland to F.W. and E.G.

References

  1. 1.
    Kaufmann K et al (2010) Regulation of transcription in plants: mechanisms controlling developmental switches. Nat Rev Genet 11(12):830–842PubMedCrossRefGoogle Scholar
  2. 2.
    Bowman JL et al (1991) Genetic interactions among floral homeotic genes of Arabidopsis. Development 112(1):1–20PubMedGoogle Scholar
  3. 3.
    Krizek BA, Fletcher JC (2005) Molecular mechanisms of flower development: an armchair guide. Nat Rev Genet 6(9):688–698PubMedCrossRefGoogle Scholar
  4. 4.
    Solomon MJ, Varshavsky A (1985) Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc Natl Acad Sci U S A 82(19):6470–6474PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11(1):31–46PubMedCrossRefGoogle Scholar
  6. 6.
    Johnson DS et al (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316(5830):1497–1502PubMedCrossRefGoogle Scholar
  7. 7.
    Kaufmann K et al (2010) Orchestration of floral initiation by APETALA1. Science 328(5974):85–89PubMedCrossRefGoogle Scholar
  8. 8.
    Yant L et al (2010) Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. Plant Cell 22(7):2156–2170PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Wuest SE et al (2012) Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA. Proc Natl Acad Sci U S A 109(33):13452–13457PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Gerstein MB et al (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489(7414):91–100PubMedCrossRefGoogle Scholar
  11. 11.
    Morohashi K, Grotewold E (2009) A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors. PLoS Genet 5(2):e1000396PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Kaufmann K et al (2009) Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biol 7(4):e1000090PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Mathieu J et al (2009) Repression of flowering by the miR172 target SMZ. PLoS Biol 7(7):e1000148PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Deal RB, Henikoff S (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell 18(6):1030–1040PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  1. 1.Smurfit Institute of GeneticsTrinity CollegeDublinIreland
  2. 2.Smurfit Institute of GeneticsTrinity College DublinDublinIreland

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