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

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-emb...

Full description

Saved in:
Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2010-12, Vol.107 (50), p.21535-21540
Main Authors: Fanelli, Micro, Amatori, Stefano, Barozzi, Iros, Soncini, Matias, Zuffo, Roberto Dal, Bucci, Gabriele, Capra, Maria, Quarto, Micaela, Dellino, Gaetano Ivan, Mercurio, Ciro, Alcalay, Myriam, Viale, Giuseppe, Pelicci, Pier Giuseppe, Minucci, Saverio, Dawid, Igor B.
Format: Article
Language:English
Subjects:
Animals
Biological Sciences
Chromatin
Chromatin Immunoprecipitation - methods
Datasets
DNA
Epigenetics
Epigenomics - methods
Genomics
High-Throughput Nucleotide Sequencing - methods
Histones
Humans
Molecular structure
Neoplasms - genetics
Neoplasms - pathology
Pathology
Patients
Promoter regions
Protein Processing, Post-Translational
Proteins
Sequence Analysis, DNA - methods
Stem cells
Tissue Fixation - methods
Tissue samples
Tissues
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1007647107