ArticleBMC genomics2019
Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 40 citations in OpenAlex.
- Spatially Resolved, Integrated Single-Cell Multiomic Profiling of the Transcriptome and Epigenomic Targets in Frozen Tissue Sections.Journal of visualized experiments : JoVE · 2026Article
- Review
- Analysis of DNA Methylation in Gliomas: Assessment of Preanalytical Variables.Laboratory investigation; a journal of technical methods and pathology · 2024Article
- Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain.eLife · 2024Article
- A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes.Laboratory investigation; a journal of technical methods and pathology · 2024Article
- Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag.Nature communications · 2023Article
- Titration-based normalization of antibody amount improves consistency of ChIP-seq experiments.BMC genomics · 2023Article
- Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer.Proteome science · 2022Article
- The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues.International journal of molecular sciences · 2022Review
- FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers.Nucleic acids research · 2021Article
- Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections.Molecular systems biology · 2021Article
- RNF20 and RNF40 regulate vitamin D receptor-dependent signaling in inflammatory bowel disease.Cell death and differentiation · 2021Article
- Proteome profiling of formalin-fixed, paraffin-embedded lung adenocarcinoma tissues using a tandem mass tag-based quantitative proteomics approach.Oncology letters · 2021Article
- Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential.Cancers · 2021Article
- FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues.Nature protocols · 2020Article
- Translational Opportunities for Microfluidic Technologies to Enable Precision Epigenomics.Analytical chemistry · 2020Article
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundEpigenetic 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.
resultsDuring 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.
conclusionsThis 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.
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