ArticleNature medicine2016
Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.
Article in Nature medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 76 citations in OpenAlex.
- scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.Nature communications · 2025Article
- Improved ChIP Sequencing for H3K27ac Profiling and Super-Enhancer Analysis Assisted by Fluorescence-Activated Sorting of Formalin-Fixed Paraffin-Embedded Tissues.Biological procedures online · 2025Article
- Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.Epigenomes · 2024Review
- EZH2 mutations in follicular lymphoma distort H3K27me3 profiles and alter transcriptional responses to PRC2 inhibition.Nature communications · 2024Article
- Article
- 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
- Integrative approaches based on genomic techniques in the functional studies on enhancers.Briefings in bioinformatics · 2023Review
- Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag.Nature communications · 2023Article
- Nutritional Epigenetics in Cancer.Advances in nutrition (Bethesda, Md.) · 2022Review
- FFPE-ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin-Fixed Paraffin-Embedded Samples.Current protocols · 2022Article
- A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples.Bio-protocol · 2022Article
- HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples.Genome biology · 2022Article
- The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues.International journal of molecular sciences · 2022Review
- Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples.Genome research · 2022Article
- Analysis of Enhancers and Transcriptional Networks in Thermogenic Adipocytes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Chromatin Immunoprecipitation Assays on Medulloblastoma Cell Line DAOY.Methods in molecular biology (Clifton, N.J.) · 2022Article
- 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
- Hybrid Stomach-Intestinal Chromatin States Underlie Human Barrett's Metaplasia.Gastroenterology · 2021Article
- A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation.Genome research · 2021Article
Corrections and comments
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Authors and funding
23 authors at 6 institutions in 2 countries.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.