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Combining ATAC-seq with Nuclei Sorting for Discovery of Cis-regulatory Regions in Plant Genomes

Overview
Specialty Biochemistry
Date 2016 Dec 2
PMID 27903897
Citations 138
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Abstract

Summary: Application of ATAC-seq to sorted nuclei identifies accessible regions genome-wide.

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References
1.
He H, Meyer C, Hu S, Chen M, Zang C, Liu Y . Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods. 2013; 11(1):73-78. PMC: 4018771. DOI: 10.1038/nmeth.2762. View

2.
Davie K, Jacobs J, Atkins M, Potier D, Christiaens V, Halder G . Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet. 2015; 11(2):e1004994. PMC: 4334524. DOI: 10.1371/journal.pgen.1004994. View

3.
Giresi P, Kim J, McDaniell R, Iyer V, Lieb J . FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2006; 17(6):877-85. PMC: 1891346. DOI: 10.1101/gr.5533506. View

4.
Piper J, Elze M, Cauchy P, Cockerill P, Bonifer C, Ott S . Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data. Nucleic Acids Res. 2013; 41(21):e201. PMC: 3834841. DOI: 10.1093/nar/gkt850. View

5.
Kaiserli E, Jenkins G . UV-B promotes rapid nuclear translocation of the Arabidopsis UV-B specific signaling component UVR8 and activates its function in the nucleus. Plant Cell. 2007; 19(8):2662-73. PMC: 2002606. DOI: 10.1105/tpc.107.053330. View