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

2010; National Academy of Sciences; Volume: 107; Issue: 50 Linguagem: Inglês

10.1073/pnas.1007647107

1091-6490

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

Genomics and Chromatin Dynamics

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.