Abstract
BackgroundAccessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development. Chromatin accessibility along with integrated multiomics approaches have been used for determining molecular subtypes of cancer in patient samples.ResultsOne-pot Universal NicE-seq (One-pot UniNicE-seq) is an improved accessible chromatin profiling method that negate DNA purification and incorporate sonication free enzymatic fragmentation before library preparation and is suited to a variety of mammalian cells. One-pot UniNicE-seq is versatile, capable of profiling 4% formaldehyde fixed chromatin in as low as 25 fixed cells. Accessible chromatin profile is more efficient on formaldehyde-fixed cells using one-pot UniNicE-seq compared to Tn5 transposon mediated methods, demonstrating its versatility.ConclusionOne-pot UniNicE-seq allows the entire process of accessible chromatin labeling and enrichment in one pot at 4% formaldehyde cross-linking conditions. It doesn’t require enzyme titration, compared to other technologies, since accessible chromatin is labelled with 5mC incorporation and deter degradation by nicking enzyme, thus opening the possibility for automation.
Highlights
Accessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development
Since formaldehyde is a potent genotoxic stress agent used for fixation of cells prior to accessible chromatin analysis, we investigated if DNA damage pathways are activated during formaldehyde cell fixation process
We used a series of formaldehyde concentrations ranging between 0.2 and 4% to fix HCT116 cells for 5, 10 and 20 min, and measured the accumulation of both pH2A.X foci and poly ADP-ribosylation
Summary
Accessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development. The cumulative influence of these protein factors determines the transcriptional state of the chromatin [2]. Upon biological and environmental signals, nuclear chromatin undergoes remodeling, providing accessibility to DNA-binding proteins including transcription factors to initiate gene expression. The chromatin accessibility landscape is gradually established during early human embryogenesis and was distinctive from mice [7]. To understand how these processes occur in vivo, chromatin accessibility snapshot would be of immense help. In a landmark study using genome-wide chromatin accessibility profiles of 410 tumor samples representing 23 cancer types
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