Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Plant Methods
Jason S CumbieMolly Megraw

Abstract

Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. 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. While this method was originally developed for human cell lines, later adaptations made the processing of plant tissues possible. Challenges still remain in processing recalcitrant tissues that have low DNA content. By removing steps requiring the use of gel agarose plugs in DNase-seq, we were able to significantly reduce the time required to perform the protocol by at least 2 days, while also making possible the processing of difficult plant tissues. We refer to this simplified protocol as DNase I SIM (for simplified in-nucleus method). We were able to successfully create DNase-seq libraries for both leaf and root tissues in Arabidopsis using DNase I SIM. This protocol simplifies and facilitates generation of DNase-seq libraries from plant tissues for high resolution mapping of DNase I hypersensitive sites.

References

Dec 29, 2000·Nature·UNKNOWN Arabidopsis Genome Initiative
Sep 28, 2006·PLoS Genetics·Gregory J HoganJason D Lieb
Sep 12, 2008·Bioinformatics·Alan P BoyleTerrence S Furey
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Nov 24, 2011·Genome Research·Wenli ZhangJiming Jiang
Dec 21, 2011·Methods in Molecular Biology·Kairong Cui, Keji Zhao
Jul 4, 2013·Current Protocols in Molecular Biology·Sam JohnJohn A Stamatoyannopoulos
Nov 5, 2013·Nature Methods·Jeff VierstraJohn A Stamatoyannopoulos
Mar 29, 2014·Methods in Molecular Biology·Jason M Rizzo, Satrajit Sinha
Sep 16, 2014·Cell Reports·Alessandra M SullivanJohn A Stamatoyannopoulos
Dec 5, 2014·Epigenetics & Chromatin·Maria Tsompana, Michael J Buck
Mar 12, 2015·Methods in Molecular Biology·Wenli Zhang, Jiming Jiang

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Citations

Aug 2, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Xuelei LaiChloe Zubieta
Aug 2, 2019·Plant, Cell & Environment·James Ronald, Seth J Davis
Apr 25, 2020·Nucleic Acids Research·Qi SongSong Li
Nov 30, 2016·Clinical Epigenetics·René A M DirksHendrik Marks
Jun 7, 2018·Proceedings of the National Academy of Sciences of the United States of America·Kathleen Greenham, C Robertson McClung
Oct 15, 2021·The Plant Cell·Robert J SchmitzBlake C Meyers

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Datasets Mentioned

BETA
PRJNA285928

Methods Mentioned

BETA
MNase-seq
mechanical shearing
transgenic
affinity purification
confocal microscopy
fluorescence
transgenics

Software Mentioned

Seq
R language
R
GBrowse
INTACT
bowtie

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