CUT&Tag for high-resolution epigenomic profiling from a low amount of Arabidopsis tissue

Abstract

BackgroundThe genome-wide profiling of chromatin states that are defined by different histone post-translational 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, [1]) 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 less amount of starting material compared to ChIP-seq. CUT&Tag is based on the in situ cleavage of DNA by enzymes tethered to antibodies, while in ChIP-seq, the cleavage is done by a nearly random fragmentation step. In theory, this difference in the way of cleaving DNA allows CUT&Tag to reach a higher resolution compared to ChIP-seq. Therefore, CUT&Tag holds the potential to profile the genome-wide distribution at a high resolution even from a small amount of plant tissues. ResultsWe profiled the genome-wide distribution of three histone modifications, H3K27me3, H3K4me3 and H3K27Ac, from a few seedlings of Arabidopsis that weighed around 0.01 grams. By comparing the H3K27me3 profiles generated from ChIP-seq and CUT&Tag, we showed that CUT&Tag and ChIP-seq capture the same broad lines of the epigenomes, but they also 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 nucleosomal resolution, a much higher resolution than ChIP-seq. In the end, we presented that the increased resolution of CUT&Tag could better reveal the exon enrichment of histone modifications and the epigenetic states of the +1 nucleosome, showing benefits and advantages that this technique could bring to the field of plant epigenetics and chromatin study in general. ConclusionCUT&Tag is a valid, easy-to-perform, cost-effective, and reliable approach for efficient epigenomic profiling in Arabidopsis, even with limited amount of starting material and provides a higher resolution compared to ChIP-seq. Because the CUT&Tag protocol starting input is isolated nuclei, it is also applicable to other model and non-model plants.