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.
Highlights
The mammalian genome is largely packaged into chromatin consisting primarily of DNA, proteins, and RNA
We hypothesized that Nt.CviPII would be able to travel across the nuclear membrane and nick open chromatin regions inside the nucleus
The cells were scored for TexasRed-dATP incorporation and compared to DAPI for open chromatin index (OCI) measurement
Summary
The mammalian genome is largely packaged into chromatin consisting primarily of DNA, proteins, and RNA. This macromolecular structure is further condensed into larger folded structures, such as chromosomes, during cell division. The cell cycle phase and the transcriptional status of the cell influences the state of the chromatin. It often undergoes remodeling events for switching between closed and open conformations to provide accessibility to DNA-binding proteins, including transcription factors [1,2,3]. Studies identified nucleosome-depleted regions as being hypersensitive to DNase I and point to the association of these
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