Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles

Nat Med. 2016 Jun;22(6):685-91. doi: 10.1038/nm.4085. Epub 2016 Apr 25.


Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Carcinoma / genetics
  • Carcinoma, Transitional Cell / genetics
  • Chromatin Immunoprecipitation
  • Colorectal Neoplasms / genetics
  • Enhancer Elements, Genetic / genetics*
  • Epigenesis, Genetic
  • Formaldehyde
  • Gene Expression Profiling
  • Heterografts
  • High-Throughput Nucleotide Sequencing
  • Histone Code / genetics*
  • Humans
  • MCF-7 Cells
  • Mice
  • Neoplasms / genetics*
  • Paraffin Embedding
  • RNA, Messenger / metabolism*
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA
  • Tissue Fixation
  • Transcriptome
  • Urinary Bladder Neoplasms / genetics


  • RNA, Messenger
  • Formaldehyde