J Integr Plant Biol. ›› 2014, Vol. 56 ›› Issue (6): 527-538.DOI: 10.1111/jipb.12151

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A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana

Mohammad Amin Omidbakhshfard1,2, Flavia Vischi Wink1†, Samuel Arvidsson1‡, Diego M. Riaño-Pachón3 and Bernd Mueller-Roeber1,2*   

  1. 1University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
    2Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
    3Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, Brazil
  • Received:2013-08-30 Accepted:2013-12-11 Published:2013-12-20
  • About author:Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
    LGC Genomics GmbH, Berlin, Germany
    *Correspondence E-mail: bmr@uni-potsdam.de


The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.


Omidbakhshfard MA, Winck FV, Arvidsson S, Riaño‐Pachón DM, Mueller‐Roeber B (2014) A step‐by‐step protocol for formaldehyde‐assisted isolation of regulatory elements from Arabidopsis thaliana. J Integr Plant Biol 56: 527–538. doi: 10.1111/jipb.12151

Key words: Arabidopsis thaliana, chromatin, cis-regulatory elements, epigenomics, FAIRE-qPCR, FAIRE-seq, gene expression, gene regulatory network

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