CUTAC for FFPEs v2

Résumé

For more than a century, Formalin Fixed Paraffin Embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our single-tube CUTAC protocol are sufficient to produce high-resolution maps of paused RNA Polymerase II (RNAPII) at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identifyand mapregulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq.Our simple workflowsmakepossible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.Version 2 includes improvements in both the on-slide and bead options and extension of the improved bead option to curls.

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