ArticleMethods (San Diego, Calif.)2009
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).
Article in Methods (San Diego, Calif.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers.
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Who cites it
132 citing papers in PubMed.
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- Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.Epigenomes · 2024Review
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- Unwrap RAP1's Mystery at Kinetoplastid Telomeres.Biomolecules · 2024Review
- Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin.Scientific reports · 2023Article
- Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Review
- Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Pioneer factors as master regulators of the epigenome and cell fate.Nature reviews. Molecular cell biology · 2022Review
- Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns.International journal of molecular sciences · 2022Article
- NicE-C efficiently reveals open chromatin-associated chromosome interactions at high resolution.Genome research · 2022Article
- Chromatin Dynamics in Digestive System Cancer: Commander and Regulator.Frontiers in oncology · 2022Review
- Mapping open chromatin by ATAC-seq in bread wheat.Frontiers in plant science · 2022Article
- Differential ATAC-seq and ChIP-seq peak detection using ROTS.NAR genomics and bioinformatics · 2021Article
- A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility.Nature protocols · 2021Review
72 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The binding of sequence-specific regulatory factors and the recruitment of chromatin remodeling activities cause nucleosomes to be evicted from chromatin in eukaryotic cells. Traditionally, these active sites have been identified experimentally through their sensitivity to nucleases. Here we describe the details of a simple procedure for the genome-wide isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). We also provide protocols for different methods of detecting FAIRE-enriched DNA, including use of PCR, DNA microarrays, and next-generation sequencing. FAIRE works on all eukaryotic chromatin tested to date. To perform FAIRE, chromatin is crosslinked with formaldehyde, sheared by sonication, and phenol-chloroform extracted. Most genomic DNA is crosslinked to nucleosomes and is sequestered to the interphase, whereas DNA recovered in the aqueous phase corresponds to nucleosome-depleted regions of the genome. The isolated regions are largely coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, enhancers, insulators, and active promoters. Given its speed and simplicity, FAIRE has utility in establishing chromatin profiles of diverse cell types in health and disease, isolating DNA regulatory elements en masse for further characterization, and as a screening assay for the effects of small molecules on chromatin organization.
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