Profiling the epigenome at home

Steven Henikoff; Jorja G. Henikoff

To illustrate the utility of our simple chromatin profiling approach, we chose antibodies to one dimethylated and four tri-methylated lysines on the Nterminal tail of Histone H3 that mark distinct chromatin features genome-wide. H3K4me3 preferentially marks nucleosomes immediately downstream of gene promoters and H3K4me2 also marks enhancers, H3K36me3 marks gene bodies, H3K27me3 marks regions of Polycomb developmental silencing (facultative heterochromatin) and H3K9me3 marks regions of constitutive heterochromatin. A representative region is shown (Figure 6) , with selected comparisons to illustrate specific chromatin features. A comparison between H3K4me2 and H3K4me3 shows the active housekeeping STRIP2 promoter marked by H3K4me3 and an enhancer just downstream marked by both modifications. These functional inferences are supported by an ATACseq track, which shows that both sites are accessible to Tn5 and by SuRE (Survey of Regulatory Elements), a massively parallel reporter survey for autonomous active regulatory elements in K562 cells (van Arensbergen et al., 2017) . Further downstream the STRIP2 gene body is heavily marked by H3K36me3, in contrast to the NRF1 gene The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.15.043083 doi: bioRxiv preprint encoding a transcription factor, where there is strong H3K4 di-and tri-methylation, but very little gene-body H3K36me3. This example illustrates the rich gene regulatory information that can be obtained by CUT&Tag.