CUT&Tag overcomes biases of ChIP and establishes chromatin patterns for repetitive genomic loci

New <i>in situ</i> chromatin profiling methods, such as CUT&Tag, have streamlined studies of chromatin features by eliminating the need for up-front purification, but we find that some features are not equally detectable when comparing with previous methods. ChIP-Seq and CUT&Tag identify similar chromatin enrichment profiles for genic loci, such as promoters, but major differences are detected at heterochromatin-associated regions. Unlike ChIP-Seq, CUT&Tag detects robust levels of H3K9me3 over a substantial number of repetitive elements, with especially high sensitivity over evolutionarily young retrotransposons. For example, mouse IAPEz-int elements exhibit strong enrichment using CUT&Tag but underrepresentation using ChIP-Seq. Additionally, several euchromatin-associated proteins, such as RUNX1, co-purify with insoluble heterochromatin in ChIP studies, but are detectible at repetitive elements when applying <i>in situ</i> fragmentation methods. Our study reveals that the current understanding of chromatin states is extensively incomplete, and newer <i>in situ</i> chromatin fragmentation-based techniques are preferred for investigating repetitive elements and retrotransposons.