Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag

Steven Henikoff (), Jorja G. Henikoff, Kami Ahmad, Ronald M. Paranal, Derek H. Janssens, Zachary R. Russell, Frank Szulzewsky, Sita Kugel and Eric C. Holland
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Steven Henikoff: Fred Hutchinson Cancer Center
Jorja G. Henikoff: Fred Hutchinson Cancer Center
Kami Ahmad: Fred Hutchinson Cancer Center
Ronald M. Paranal: Fred Hutchinson Cancer Center
Derek H. Janssens: Fred Hutchinson Cancer Center
Zachary R. Russell: Fred Hutchinson Cancer Center
Frank Szulzewsky: Fred Hutchinson Cancer Center
Sita Kugel: Fred Hutchinson Cancer Center
Eric C. Holland: Fred Hutchinson Cancer Center

Nature Communications, 2023, vol. 14, issue 1, 1-17

Abstract: Abstract 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 CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.

Date: 2023
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DOI: 10.1038/s41467-023-41666-z

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