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.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Ponnaluri VKC,Zhang G,Estève PO,Spracklin G,Sian S,Xu SY,Benoukraf T,Pradhan Sdoi
10.1186/s13059-017-1247-6subject
Has Abstractpub_date
2017-06-28 00:00:00pages
122issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-017-1247-6journal_volume
18pub_type
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