Fig. 2
From: Molecular and computational approaches to map regulatory elements in 3D chromatin structure
Methods to map regulatory elements. a Simplified protocols of methods to identify regulatory elements using histone modifications are shown. ChIP-seq is performed in lysed cells, while CUT & RUN and CUT & TAG are performed in intact nuclei. b Simplified protocols of methods to map chromatin accessibility are shown. Cells are lysed, and the DNA is either fragmented with enzymes or through sonication. c Simplified protocols of methods to measure global DNA methylation levels are shown. Bisulfite sequencing uses bisulfite conversion followed by sequencing. NOMe-seq simultaneously detects endogenous DNA methylation levels (CpG) and chromatin accessibility (GpC). Bisulfite treatment converts unmethylated C into U, which is converted to T during PCR amplification. pA-MN: Protein A and micrococcal nuclease. pA-Tn5: Protein A and Tn5 transposase, M.CviPl: GpC Methyltransferase