Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples

Mirco Fanelli, Stefano Amatori, Iros Barozzi, Matias Soncini, Roberto Dal Zuffo, Gabriele Bucci, Maria Capra, Micaela Quarto, Gaetano Ivan Dellino, Ciro Mercurio, Myriam Alcalay, Giuseppe Viale, Pier Giuseppe Pelicci, Saverio Minucci

Research output: Contribution to journalArticle


Epigenetic alterations in the pattern of DNA and histone modifications play a crucial role in cancer development. Analysis of patient samples, however, is hampered by technical limitations in the study of chromatin structure from pathology archives that usually consist of heavily fixed, paraffin-embedded material. Here, we present a methodology [pathology tissue-ChIP (PAT-ChIP)] to extract and immunoprecipitate chromatin from paraffin-embedded patient samples up to several years old. In a pairwise comparison with canonical ChIP, PAT-ChIP showed a high reproducibility of results for several histone marks and an identical ability to detect dynamic changes in chromatin structure upon pharmacological treatment. Finally, we showed that PAT-ChIP can be coupled with high-throughput sequencing (PAT-ChIP-Seq) for the genome-wide analysis of distinct chromatin modifications. PAT-ChIP therefore represents a versatile procedure and diagnostic tool for the analysis of epigenetic alterations in cancer and potentially other diseases.

Original languageEnglish
Pages (from-to)21535-21540
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number50
Publication statusPublished - Dec 14 2010


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