FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues
Open Access
- 1 August 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Protocols
- Vol. 15 (8), 2503-2518
- https://doi.org/10.1038/s41596-020-0340-6
Abstract
This protocol describes a ChIP-seq procedure optimized for profiling H3K27 acetylation in archived formalin-fixed, paraffin-embedded (FFPE) tissues sampled through whole or macrodissected sectioning or from punched cores. Fixed-tissue ChIP-seq for H3K27 acetylation (H3K27ac) profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in formalin-fixed, paraffin-embedded (FFPE) tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65 degrees C in a higher concentration of detergent and a minimized sonication step, to produce robust genome-wide H3K27ac maps from clinical samples. FiTAc-seq generates high-quality enhancer landscapes and super-enhancer (SE) annotation in numerous archived FFPE samples from distinct tumor types. This approach will be of great interest for both basic and clinical researchers. The entire protocol from FFPE blocks to sequence-ready library can be accomplished within 4 d.Funding Information
- Associació per a la recerca oncològica
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (R37CA222574, 2PO1CA163227)
- Ministerio de Economía y Competitividad (PI18-01604)
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