title: A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana.
abstract: 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.
authors.affiliation: University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, 14476, Germany; Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany.
authors.forename: Mohammad Amin
authors.initials: MA
authors.lastname: Omidbakhshfard
authors.forename: Flavia Vischi
authors.initials: FV
authors.lastname: Winck
authors.forename: Samuel
authors.initials: S
authors.lastname: Arvidsson
authors.forename: Diego M
authors.initials: DM
authors.lastname: Riaño-Pachón
authors.forename: Bernd
authors.initials: B
authors.lastname: Mueller-Roeber
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics / Q000302:isolation & purification*; D005557:Formaldehyde / Q000494:pharmacology*; D020043:Genes, Essential; D018745:Genome, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D008967:Molecular Biology / Q000379:methods*; D016133:Polymerase Chain Reaction; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D013010:Sonication
chemical_list: D018744:DNA, Plant; D005557:Formaldehyde
keywords: Arabidopsis thaliana; FAIRE-qPCR; FAIRE-seq; chromatin; cis-regulatory elements; epigenomics; gene expression; gene regulatory network; transcription factor