Profiling the epigenome at home

Steven Henikoff; Jorja G. Henikoff

We previously introduced CUT&Tag for efficient low-cost genome-wide chromatin profiling and showed that it provides high-resolution profiles for epitopes on nucleosomes, transcription factors and RNA Polymerase II with especially low signal-to-noise Fig. 7 : H3 lysine trimethylation data aligned to TSSs and ERVs. a) Heatmaps ordered by normalized counts (the scaled fraction of total counts at each basepair) and average plots showing that these four H3 tail trimethylations are mostly non-overlapping genome-wide when aligned around transcriptional start sites (TSSs). b) Heatmaps of the four H3 tail trimethylations aligned around the midpoints of the 50,707 annotated ERV elements on human Chromosome 1 and ordered top-to-bottom by decreasing element size. For clarity, the top segment of the H3K9me3 panel is expanded in the panel to the right to reveal a cluster of ~2-kb elements. K-means clustering of the 2-kb region centered around the midpoints all Chromosome 1 ERV elements separated the ERVs into a heavily H3K9trimethylated Cluster I (11%), a weakly H3K9-trimethylated Cluster II (27%) and Cluster III with background levels of H3K9 trimethylation (62%). The copyright holder for this preprint (which was not peer-reviewed) is the .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 characteristics (Kaya-Okur et al., 2019) . We showed that CUT&Tag is highly versatile not only in the range of chromatin features it can profile, but also in the read-out platforms it is suitable for, including in plate format for low-cell-number samples and nanowell dispensing for on the order of 1000 single cells. Since our original CUT&Tag publication in April, 2019, we have distributed >600 pA-Tn5 aliquots to laboratories around the world, and during that time our original protocol has been the most popular of the ~6000 protocols on Protocols.io (Lenny Teytelman, personal communication). Because CUT&Tag requires that cells or nuclei remain intact throughout the procedure, there are no harsh treatments or toxic chemicals required, which makes the protocol inherently safe and appropriate for being performed in a home utility area. Therefore, we expect that CUT&Tag@home will be welcomed by a substantial cohort of users, whether they are able to work in the lab or can only work at home subject to COVID-19 restrictions.