Advertisement

Chemical Genetic Screens Using Arabidopsis thaliana Seedlings Grown on Solid Medium

  • Thanh Theresa Dinh
  • Xuemei Chen
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1263)

Abstract

Genetic screening has been a powerful tool in identifying new genes in a pathway of interest (forward genetics) or attributing function to a particular gene via mutagenesis (reverse genetics). Small molecule-based chemical genetics is increasingly adapted in Arabidopsis research as a tool for similar purposes, i.e., to identify genes involved in certain biological processes and to dissect the biological roles of a gene. Chemical genetic screens have been successful in circumventing genetic redundancy to assign biological roles to a gene family as well as novel functions for well-known genes. Here, we describe how to screen Arabidopsis seedlings grown on solid medium with chemical compounds.

Key words

Chemical genetics Small molecules Genetic screens Arabidopsis seedlings Solid medium 

Notes

Acknowledgement

Research in the Chen lab is supported by funds from Howard Hughes Medical Institute, Gordon and Betty Moore Foundation (GBMF3046), National Institutes of Health (GM061146), and National Institutes of Food and Agriculture (2010-04209). T.T.D. was supported by the National Science Foundation ChemGen IGERT program (DGE0504249) and NIH NIAID, Molecular and Cellular Immunobiology (5T32 AI07290) fellowship.

References

  1. 1.
    Meyerowitz EM (1989) Arabidopsis, a useful weed. Cell 56:263–269PubMedCrossRefGoogle Scholar
  2. 2.
    Schultz EA, Haughn GW (1991) LEAFY, a homeotic gene that regulates inflorescence development in Arabidopsis. Plant Cell 3:771–781PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Weigel D et al (1992) LEAFY controls floral meristem identity in Arabidopsis. Cell 69:843–859PubMedCrossRefGoogle Scholar
  4. 4.
    Weigel D, Nilsson O (1995) A developmental switch sufficient for flower initiation in diverse plants. Nature 377:495–500PubMedCrossRefGoogle Scholar
  5. 5.
    Flachowsky H et al (2010) Overexpression of LEAFY in apple leads to a columnar phenotype with shorter internodes. Planta 231:251–263PubMedCrossRefGoogle Scholar
  6. 6.
    Radhamony RN, Prasad AM, Srinivasan R (2005) T-DNA insertional mutagenesis in Arabidopsis: a tool for functional genomics. Electron J Biotechnol 8(1). http://www.ejbiotechnology.info/content/vol8/issue1/full/4/
  7. 7.
    Okamoto M et al (2013) Activation of dimeric ABA receptors elicits guard cell closure, ABA-regulated gene expression, and drought tolerance. Proc Natl Acad Sci U S A 110:12132–12137PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Park SY et al (2009) Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324:1068–1071PubMedCentralPubMedGoogle Scholar
  9. 9.
    Robert S et al (2008) Endosidin1 defines a compartment involved in endocytosis of the brassinosteroid receptor BRI1 and the auxin transporters PIN2 and AUX1. Proc Natl Acad Sci U S A 105:8464–8469PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Drakakaki G et al (2011) Clusters of bioactive compounds target dynamic endomembrane networks in vivo. Proc Natl Acad Sci U S A 108:17850–17855PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    He W et al (2011) A small-molecule screen identifies L-kynurenine as a competitive inhibitor of TAA1/TAR activity in ethylene-directed auxin biosynthesis and root growth in Arabidopsis. Plant Cell 23:3944–3960PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Knoth C et al (2009) The synthetic elicitor 3,5-dichloroanthranilic acid induces NPR1-dependent and NPR1-independent mechanisms of disease resistance in Arabidopsis. Plant Physiol 150:333–347PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Dinh TT et al (2013) Generation of a luciferase-based reporter for CHH and CG DNA methylation in Arabidopsis thaliana. Silence 4:1PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Dinh TT, Gao L, Liu X, Chen X (2014) DNA topoisomerase IA promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. PLoS Genet 10:e1004446PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Dalmay T et al (2000) An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101:543–553PubMedCrossRefGoogle Scholar
  16. 16.
    Mourrain P et al (2000) Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101:533–542PubMedCrossRefGoogle Scholar
  17. 17.
    Peragine A et al (2004) SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 18:2368–2379PubMedCentralPubMedCrossRefGoogle Scholar
  18. 18.
    Dinh TT et al (2014) Genetic screens for floral mutants in Arabidopsis thaliana: enhancers and suppressors. Methods Mol Biol 1110:127–156PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Botany and Plant Sciences, Institute of Integrative Genome BiologyUniversity of CaliforniaRiversideUSA
  2. 2.Laboratory of Immunology and Vascular Biology, Department of PathologyStanford University School of MedicineStanfordUSA
  3. 3.Howard Hughes Medical InstituteUniversity of CaliforniaRiversideUSA

Personalised recommendations