Plant Functional Genomics pp 71-89

Part of the Methods in Molecular Biology book series (MIMB, volume 1284) | Cite as

Genome-Wide Mapping of DNase I Hypersensitive Sites in Plants

Abstract

Genomic regions associated with regulatory proteins are known to be highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion followed by high-throughput DNA sequencing (DNase-seq). DNase-seq has become a powerful technique for genome-wide mapping of chromatin accessibility in eukaryotes with a sequenced genome. We have developed a DNase-seq procedure in plants. This procedure was adapted from the protocol originally developed for mammalian cell lines. It includes plant nuclei isolation, digestion of purified nuclei with DNase I, recovery of DNase-trimmed DNA fragments, DNase-seq library development, Illumina sequencing and data analysis. We also introduce a barcoding system for library preparation. We have conducted DNase-seq in both Arabidopsis thaliana and rice, and developed genome-wide open chromatin maps in both species. These DHS datasets have been used to detect footprints from regulatory protein binding and to reveal genome-wide nucleosome positioning patterns.

Key words

Chromatin accessibility Open chromatin cis-Regulatory DNA elements DNase I hypersensitive sites DNase-seq 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of HorticultureUniversity of Wisconsin-MadisonMadisonUSA

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