DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing

  • Sergei A. Filichkin
  • Molly MegrawEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1629)


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.

Key words

DNase-seq DNase I hypersensitive sites Open chromatin Arabidopsis Roots Nuclei 



This work was supported by NIH grant GM097188 and startup funds from Oregon State University to M.M.


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Department of Botany and Plant PathologyOregon State UniversityCorvallisUSA
  2. 2.Center for Genome Research and BiocomputingOregon State UniversityCorvallisUSA
  3. 3.Department of Electrical Engineering and Computer ScienceOregon State UniversityCorvallisUSA

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