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NicE-seq: high resolution open chromatin profiling.

ABSTRACT: 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.

SUBMITTER: Ponnaluri VKC

PROVIDER: S-EPMC5488340 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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NicE-seq: high resolution open chromatin profiling.

Ponnaluri V K Chaithanya VKC Zhang Guoqiang G Estève Pierre-Olivier PO Spracklin George G Sian Stephanie S Xu Shuang-Yong SY Benoukraf Touati T Pradhan Sriharsa S

Genome biology 20170628 1

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, c ...[more]

PMID: 28655330

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NicE-seq: high resolution open chromatin profiling

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