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NicE-seq: high resolution open chromatin profiling

by Estève, Pierre-Olivier , Spracklin, George , Zhang, Guoqiang , Sian, Stephanie , Ponnaluri, V. K. Chaithanya , Pradhan, Sriharsa , Xu, Shuang-yong , Benoukraf, Touati

in 5-aza-2'-deoxycytidine / Animal Genetics and Genomics / Binding sites / Bioinformatics / Biomedical and Life Sciences / Cell cycle / Cell division / Chromatin / Chromatin - genetics / Chromosomes / Colorectal cancer / CpG islands / CpG Islands - genetics / Deoxyribonuclease / deoxyribonuclease I / Deoxyribonuclease I - genetics / Deoxyribonucleic acid / DNA / DNA methylation / DNA Methylation - genetics / DNA polymerase / DNA-directed RNA polymerase / E coli / Enzymes / Epigenetics / Evolutionary Biology / Gene expression / genome / Genome, Human - genetics / Genomes / HCT116 Cells / Human Genetics / Humans / Labeling / Life Sciences / Method / Methods / Microbial Genetics and Genomics / Molecular weight / NicE-seq / Nicking endonuclease / Open chromatin / Plant Genetics and Genomics / Proteins / Regulatory Elements, Transcriptional - genetics / Regulatory sequences / RNA Polymerase II - genetics / Stem cells / transcription (genetics) / Transcription factor occupancy / Transcription factors / Transposase / Transposases - genetics

2017

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NicE-seq: high resolution open chromatin profiling

by Estève, Pierre-Olivier , Spracklin, George , Zhang, Guoqiang , Sian, Stephanie , Ponnaluri, V. K. Chaithanya , Pradhan, Sriharsa , Xu, Shuang-yong , Benoukraf, Touati

2017

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NicE-seq: high resolution open chromatin profiling

by Estève, Pierre-Olivier , Spracklin, George , Zhang, Guoqiang , Sian, Stephanie , Ponnaluri, V. K. Chaithanya , Pradhan, Sriharsa , Xu, Shuang-yong , Benoukraf, Touati

2017

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Journal Article

NicE-seq: high resolution open chromatin profiling

Estève, Pierre-Olivier,

Spracklin, George,

Zhang, Guoqiang,

Sian, Stephanie,

Ponnaluri, V. K. Chaithanya,

Pradhan, Sriharsa,

Xu, Shuang-yong,

Benoukraf, Touati

2017

Overview

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.

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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

5-aza-2'-deoxycytidine

/ Animal Genetics and Genomics

/ Binding sites

/ Bioinformatics

/ Biomedical and Life Sciences

/ Cell cycle

/ Cell division