Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq

Jian Zhong, Zhenqing Ye, Chad R. Clark, Samuel W. Lenz, Justin H Nguyen, Huihuang D Yan, Keith D Robertson, Gianrico Farrugia, Zhiguo Zhang, Tamas Ordog, Jeong Heon Lee

Research output: Contribution to journalArticle

Abstract

Background: Epigenetic dysregulation is involved in the etiology and progression of various human diseases. Formalin-fixed paraffin-embedded (FFPE) samples represent the gold standard for archiving pathology samples, and thus FFPE samples are a major resource of samples in clinical research. However, chromatin-based epigenetic assays in the clinical settings are limited to fresh or frozen samples, and are hampered by low chromatin yield in FFPE samples due to the lack of a reliable and efficient chromatin preparation method. Here, we introduce a new chromatin extraction method from FFPE tissues (Chrom-EX PE) for chromatin-based epigenetic assays. Results: During rehydration of FFPE tissues, applying a tissue-level cross-link reversal into the deparaffinized tissue at 65 °C dramatically increased chromatin yield in the soluble fraction. The resulting chromatin is compatible with targeted ChIP-qPCR and genome-wide ChIP-seq approaches. The chromatin prepared by Chrom-EX PE showed a gradual fragmentation pattern with varying incubation temperature. At temperatures below 37 °C, the majority of soluble chromatin is over 1 kb. The soluble chromatin prepared in the range of 45-60 °C showed a typical nucleosomal pattern. And the majority of chromatin prepared at 65 °C is close to mononucleosomal size. These observations indicate that chromatin preparation from FFPE samples can be controlled for downstream chromatin-based epigenetic assays. Conclusions: This study provided a new method that achieves efficient extraction of high-quality chromatin suitable for chromatin-based epigenetic assays with less damage on chromatin. This approach may provide a way to circumvent the over-fixed nature of FFPE tissues for future technology development.

Original languageEnglish (US)
Article number249
JournalBMC genomics
Volume20
Issue number1
DOIs
StatePublished - Mar 29 2019

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Paraffin
Formaldehyde
Chromatin
Epigenomics
Temperature
Fluid Therapy

Keywords

  • ChIP-seq
  • Chromatin extraction
  • FFPE tissues

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq. / Zhong, Jian; Ye, Zhenqing; Clark, Chad R.; Lenz, Samuel W.; Nguyen, Justin H; Yan, Huihuang D; Robertson, Keith D; Farrugia, Gianrico; Zhang, Zhiguo; Ordog, Tamas; Lee, Jeong Heon.

In: BMC genomics, Vol. 20, No. 1, 249, 29.03.2019.

Research output: Contribution to journalArticle

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AU - Nguyen, Justin H

AU - Yan, Huihuang D

AU - Robertson, Keith D

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AU - Zhang, Zhiguo

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AU - Lee, Jeong Heon

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