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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Acknowledgment
This work was supported by NIH grant GM097188 and startup funds from Oregon State University to M.M.
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Filichkin, S.A., Megraw, M. (2017). DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing. In: Kaufmann, K., Mueller-Roeber, B. (eds) Plant Gene Regulatory Networks. Methods in Molecular Biology, vol 1629. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7125-1_10
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DOI: https://doi.org/10.1007/978-1-4939-7125-1_10
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Publisher Name: Humana Press, New York, NY
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Online ISBN: 978-1-4939-7125-1
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