NicE-seq: high resolution open chromatin profiling.
V K Chaithanya PonnaluriGuoqiang ZhangPierre-Olivier EstèveGeorge SpracklinStephanie SianShuang-Yong XuTouati BenoukrafSriharsa PradhanPublished in: Genome biology (2017)
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.
Keyphrases
- single cell
- transcription factor
- genome wide
- rna seq
- dna methylation
- high resolution
- minimally invasive
- dna damage
- gene expression
- dna binding
- induced apoptosis
- cell cycle arrest
- acute myeloid leukemia
- mass spectrometry
- healthcare
- genome wide identification
- oxidative stress
- bone marrow
- high speed
- signaling pathway
- social media
- mesenchymal stem cells
- ionic liquid