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NicE-seq: high resolution open chromatin profiling
- Ponnaluri, V. K. Chaithanya, Zhang, Guoqiang, Estève, Pierre-Olivier, Spracklin, George, Sian, Stephanie, Xu, Shuang-yong, Benoukraf, Touati, Pradhan, Sriharsa
- Genome biology 2017 v.18 no.1 pp. 122
- DNA methylation, DNA-directed RNA polymerase, chromatin, deoxyribonuclease I, genome, regulatory sequences, transcription (genetics), transcription factors
- Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking enzyme assisted sequencing) for high-resolution open chromatin profiling on both native and formaldehyde-fixed cells. NicE-seq captures and reveals open chromatin sites (OCSs) and transcription factor occupancy at single nucleotide resolution, coincident with DNase hypersensitive and ATAC-seq sites at a low sequencing burden. OCSs correlate with RNA polymerase II occupancy and active chromatin marks, while displaying a contrasting pattern to CpG methylation. Decitabine-mediated hypomethylation of HCT116 displays higher numbers of OCSs.