TY  - JOUR
A1  - Omidbakhshfard, Mohammad Amin
A1  - Winck, Flavia Vischi
A1  - Arvidsson, Samuel Janne
A1  - Riano-Pachon, Diego M.
A1  - Müller-Röber, Bernd
T1  - A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana
T2  - Journal of integrative plant biology
N2  - 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.
KW  - Arabidopsis thaliana
KW  - chromatin
KW  - cis-regulatory elements
KW  - epigenomics
KW  - FAIRE-qPCR
KW  - FAIRE-seq
KW  - gene expression
KW  - gene regulatory network
KW  - transcription factor
Y1  - 2014
UR  - https://publishup.uni-potsdam.de/frontdoor/index/index/docId/37805
SN  - 1672-9072
SN  - 1744-7909
VL  - 56
IS  - 6
SP  - 527
EP  - 538
PB  - Wiley-Blackwell
CY  - Hoboken
ER  -