Chapter title |
DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing
|
---|---|
Chapter number | 10 |
Book title |
Plant Gene Regulatory Networks
|
Published in |
Methods in molecular biology, June 2017
|
DOI | 10.1007/978-1-4939-7125-1_10 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7124-4, 978-1-4939-7125-1
|
Authors |
Filichkin, Sergei A., Megraw, Molly, Sergei A. Filichkin, Molly Megraw |
Editors |
Kerstin Kaufmann, Bernd Mueller-Roeber |
Abstract |
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. |
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