ArticlePlant methods2015
Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana.
Article in Plant methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Epigenetics and plant hormone dynamics: a functional and methodological perspective.Journal of experimental botany · 2024Review
- The ChIP-Hub Resource: Toward plantEncode.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Genome-wide mapping of DNase I hypersensitive sites in pineapple leaves.Frontiers in genetics · 2023Article
- Quality control and evaluation of plant epigenomics data.The Plant cell · 2022Article
- Prediction of condition-specific regulatory genes using machine learning.Nucleic acids research · 2020Article
- Review
- Pioneer Factors in Animals and Plants-Colonizing Chromatin for Gene Regulation.Molecules (Basel, Switzerland) · 2018Review
- Time to build on good design: Resolving the temporal dynamics of gene regulatory networks.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome.Plant physiology · 2018Article
- Computational Methods for Assessing Chromatin Hierarchy.Computational and structural biotechnology journal · 2018Review
- A transcription factor hierarchy defines an environmental stress response network.Science (New York, N.Y.) · 2016Article
- Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.The Plant cell · 2016Review
- Genome-wide epigenomic profiling for biomarker discovery.Clinical epigenetics · 2016Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundIdentifying 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.
resultsBy 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.
conclusionThis protocol simplifies and facilitates generation of DNase-seq libraries from plant tissues for high resolution mapping of DNase I hypersensitive sites.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.