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Updated: May 27, 2026
An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
Published on: April 5, 2018
Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue
Mirco Fanelli1, Stefano Amatori, Iros Barozzi
1Department of Biomolecular Sciences, Molecular Pathology Lab 'PaoLa', University of Urbino 'Carlo Bo', Fano, Italy. mirco.fanelli@uniurb.it
Insights
Pathology tissue chromatin immunoprecipitation (PAT-ChIP) enables epigenetic analysis of archival formalin-fixed, paraffin-embedded (FFPE) samples. This 4-day protocol allows genome-wide studies of histone modifications and transcription factor binding from FFPE tissues.
Area of Science:
- Epigenetics
- Molecular Biology
- Pathology
Background:
- Formalin-fixed, paraffin-embedded (FFPE) samples are the standard for long-term pathology sample storage.
- Analyzing FFPE samples for epigenetic information is challenging due to sample preservation methods.
- High-throughput analysis of FFPE-derived chromatin is crucial for retrospective studies.
Purpose of the Study:
- To describe a novel technique, pathology tissue chromatin immunoprecipitation (PAT-ChIP), for chromatin extraction from FFPE samples.
- To enable high-throughput epigenetic analyses, such as ChIP-seq, on FFPE-derived chromatin.
- To facilitate the use of archival FFPE samples for epigenetic biomarker discovery.
Main Methods:
- Development and detailed explanation of the PAT-ChIP protocol for chromatin preparation from FFPE tissues.
- Optimization of reagents and troubleshooting steps for robust chromatin extraction.
- Adaptation of existing techniques for PAT-ChIP-sequencing (PAT-ChIP-seq) workflow.
Main Results:
- A 4-day protocol for PAT-ChIP was established, yielding good-quality chromatin from FFPE samples.
- PAT-ChIP allows for the first time genome-wide analysis of histone modifications and transcription factor binding from FFPE samples.
- The technique is applicable to archival FFPE samples, even those stored for several years.
Conclusions:
- PAT-ChIP provides a robust method for epigenetic analysis of FFPE samples.
- This technique unlocks the potential of pathology archives for epigenetic research and biomarker identification.
- PAT-ChIP-seq facilitates retrospective epigenetic studies and the discovery of novel epigenetic targets.
Abstract:
Formalin-fixed, paraffin-embedded (FFPE) samples represent the gold standard for storage of pathology samples. Here we describe pathology tissue chromatin immunoprecipitation (PAT-ChIP), a technique for extraction and high-throughput analysis, by techniques such as ChIP-seq, of chromatin derived from FFPE samples. Technically, the main challenge of PAT-ChIP is the preparation of good-quality chromatin from FFPE samples. Here we provide a detailed explanation of the methodology used, the choice of reagents and the troubleshooting steps required to establish a robust chromatin preparation procedure. Other steps have also been adapted from existing techniques to optimize their use for PAT-ChIP-seq. The protocol requires 4 d from the start to the end of the PAT-ChIP procedure. PAT-ChIP provides, for the first time, the chance to perform analyses of histone modifications and transcription factor binding on a genome-wide scale using patient-derived FFPE samples. This technique therefore allows the immediate use of pathology archives (even those that are several years old) for epigenetic analyses and the identification of candidate epigenetic biomarkers or targets.
