CUT&Tag for High-Resolution Epigenomic Profiling From a Low Amount of Arabidopsis Tissue

The genome-wide profiling of chromatin states that are defined by different histone posttranslational modifications, known as epigenomic profiling, is crucial for understanding the epigenetic regulations of gene expression, both in animal and plant systems. CUT&Tag (Cleavage Under Targets and Tagmentation) is a novel enzyme-tethering method for epigenomic profiling, initially developed for mammalian cells. CUT&Tag has several advantages compared to the most commonly used epigenomic profiling methods such as chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). CUT&Tag allows epigenenomic profiling from a much smaller amount of starting material compared to ChIP-seq. Moreover, CUT&Tag relies on in situ DNA cleavage mediated by a transposase tethered to antibodies, while ChIP-seq typically involves nearly random DNA fragmentation. This fundamental difference raises the important question of whether CUT&Tag provides distinct advantages in terms of resolution and the precision of epigenomic profiles compared to ChIP-seq.

We profiled the genome-wide distribution of three histone modifications, H3K27me3, H3K4me3, and H3K27Ac, from a few seedlings of Arabidopsis that weighed around 0.01 g. We compared the CUT&Tag H3K27me3 profile with publicly available H3K27me3 profiles generated from ChIP-seq, and ChIPmentation, a ChIP-seq-based technique where MNase and Tn5 transposon are used to cleave the chromatin and prepare sequencing libraries, respectively. We showed that all these techniques capture the same broad lines of the epigenomes, but they also showed preferences toward different genomic features and revealed different sets of peaks. Analysis using the CUT&Tag datasets for the three histone modifications revealed their genomic locations and their relationship with the gene expression level, which are consistent with the expected effect of these histone marks on gene transcription. By comparing to the nucleosome occupancy data, we show that CUT&Tag reached resolution at the single-nucleosome level, which is similar to that of ChIPmentation, but higher than that of ChIP-seq. Moreover, both CUT&Tag and ChIPmentation data revealed an enrichment of H3K27me3 mark on exons, thus providing a deeper understanding of epigenome features that could not be resolved by ChIP-seq.

CUT&Tag is a valid, easy-to-perform, cost-effective, and reliable approach for efficient epigenomic profiling in Arabidopsis, compatible with limited amounts of plant tissue, and provides a higher resolution compared to that of ChIP-seq. Because the CUT&Tag protocol starting input is isolated nuclei, it is applicable to model and nonmodel plants.