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

New in situ 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 in situ fragmentation methods. Our study reveals that the current understanding of chromatin states is extensively incomplete, and newer in situ chromatin fragmentation-based techniques are preferred for investigating repetitive elements and retrotransposons.