%0 Book Section %B Methods Mol Biol %D 2017 %T DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing %A Filichkin, S. A. %A Megraw, M. %X

Identifying cis-regulatory elements is critical in understanding the direct and indirect interactions that occur within gene regulatory networks. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high-throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. Yet, challenges still remain in processing recalcitrant tissues that have low DNA content. Here, we describe DNase I SIM (for Simplified In-nucleus Method), a protocol that simplifies and facilitates generation of DNase-seq libraries from plant tissues for high-resolution mapping of DNase I hypersensitive sites. By removing steps requiring the use of gel agarose plugs in DNase-seq, DNase I SIM reduces the time required to perform the protocol by at least 2 days, while also making possible the processing of difficult plant tissues including plant roots.

%B Methods Mol Biol %V 1629 %P 141-154 %@ 1940-6029 (Electronic)1064-3745 (Linking) %G eng %U https://link.springer.com/protocol/10.1007/978-1-4939-7125-1_10 %! Methods in molecular biology (Clifton, N.J.)