NicE-seq: high resolution open chromatin profiling

被引:34
作者
Ponnaluri, V. K. Chaithanya [1 ]
Zhang, Guoqiang [1 ]
Esteve, Pierre-Olivier [1 ]
Spracklin, George [1 ]
Sian, Stephanie [2 ]
Xu, Shuang-yong [1 ]
Benoukraf, Touati [2 ]
Pradhan, Sriharsa [1 ]
机构
[1] New England Biolabs Inc, 240 Cty Rd, Ipswich, MA 01938 USA
[2] Natl Univ Singapore, Canc Sci Inst Singapore, Singapore 117599, Singapore
来源
GENOME BIOLOGY | 2017年 / 18卷
关键词
Open chromatin; NicE-seq; Transcription factor occupancy; DNA methylation; TRANSCRIPTION FACTORS; HYPERSENSITIVE SITES; DNA DEMETHYLATION; REGIONS; BINDING; GENES; READS;
D O I
10.1186/s13059-017-1247-6
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
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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页数:15
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