Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples

Hypertranscription occurs at targets of oncogene transcription factors in aggressive human cancers. However, detection relies on mRNAs which are heavily processed and have variable half-lives, and on accurate cell number estimations. Here we apply FFPE-CUTAC on slides and curls to quantify hypertranscription at regulatory elements and replication-coupled histone genes. We used FFPE-CUTAC, a modification of the CUT&Tag chromatin profiling strategy, whereby antibody-targeted controlled integration of DNA sequencing adapters at sites of paused RNA Polymerase II or between nucleosomes flanking open chromatin sites produces libraries for paired-end sequencing from Formalin-Fixed Paraffin-Embedded (FFPE) sections.