FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.

By P. Giresi, Jonghwan Kim, Ryan McDaniell, V. Iyer, J. Lieb. Genome Research, 2007

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DNA segments that actively regulate transcription in vivo are typically characterized by eviction of nucleosomes from chromatin and are experimentally identified by their hypersensitivity to nucleases. Here we demonstrate a simple procedure for the isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements). To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray. FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters. Evidence for cell-type-specific patterns of FAIRE enrichment is also presented. FAIRE has utility as a positive selection for genomic regions associated with regulatory activity, including regions traditionally detected by nuclease hypersensitivity assays.

Subfields: Molecular Biology

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Citations in the corpus

Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. (2013, neutral): “…of TF clusters than other well established correlates, including histone H3 K27 acetylation, FAIRE or DNase I hypersensitivity (Creyghton et al., 2010; Giresi et al., 2007; Thurman et al., 2012; Figures 4E and S4; Table S4), suggesting that cohesin may have a role in cluster formation or function.”
Pioneer transcription factors: establishing competence for gene expression. (2011, methodology): “By combining FAIRE (formaldehyde-assisted isolation of regulatory elements) (Giresi et al. 2007) or DHS (DNasehypersensitive site) analysis with high-throughput sequencing, a global understanding of chromatin structure is evolving (Eeckhoute et al.”
Defining cell types and states with single-cell genomics (2015, background): “assays for accessibility (Crawford et al. 2006; Giresi et al. 2007; Hesselberth et al. 2009; Buenrostro et al. 2013).”
Linking disease associations with regulatory information in the human genome (2012, methodology): “The integrative analysis uses both DNase-seq and formaldehydeassisted isolation of regulatory elements (FAIRE) (Giresi et al. 2007) data to identify regions of open chromatin, and thus finds a slightly”
Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila (2014, background): “Integration of binding activities by Bcd-dependent enhancers Despite recent technical and computational advances (Crawford et al. 2006; Giresi et al. 2007; Heintzman et al. 2007; Visel et al. 2009; modEncode Consortium et al. 2010; Zhu et al. 2013), identifying active enhancers in genome sequences…”
A User's Guide to the Encyclopedia of DNA Elements (ENCODE) (2011, methodology): “Chromatin structure is also being profiled with the FAIRE technique [40,57,58], in which chromatin from formaldehyde-crosslinked cells is sonicated in a fashion similar to ChIP and then extracted with phenol, followed by sequencing of soluble DNA fragments.”
Latent enhancers activated by stimulation in differentiated cells. (2013, neutral): “79%) (Giresi et al., 2007), basal p300 (0.”
Targeted in situ genome-wide profiling with high efficiency for low cell numbers (2018, neutral): “For example, several methods, including DNase1 footprinting 14 , FAIRE-seq 15 , Sono-seq 16 , MNase-seq 17,18 and ATAC-seq 19 , are being used to map TF binding genome-wide using a sequencing readout.”
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules (2012, background): “FAIRE-seq relies on enhanced sensitivity to DNA breakage of nucleosome-depleted regions (Giresi et al. 2007; Nagy and Price 2009).”
The Ensembl Regulatory Build (2015, positive): “Regions of open chromatin can be mapped using formaldehyde-assisted isolation of regulatory elements (FAIRE) [19], nuclease digestion by DNase1 coupled with high-throughput sequencing (DNase-seq) [20] or assaying transposase-accessible chromatin (ATAC-seq) [21].”
PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls (2009, neutral): “There are also peaks in the signal maps for unstimulated and interferon-γ–stimulated HeLa S3 input DNA in the vicinity of promoters of known genes, which may correspond to regions of open chromati”
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. (2010, methodology): “For the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) experiment (Giresi et al., 2007), cells were crosslinked and sonicated as for ChIP experiments.”
Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo (2015, methodology): “We used formaldehyde-assisted isolation of regulatory elements (FAIRE) (Giresi et al. 2007; McKay and Lieb 2013) to performgenome-wide profiling of open chromatin in embryos lacking maternal Zld (zld).”
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007, methodology): “Three tiers of correlations were calculated: (1) tier 1: correlation among different technical replicas represented by different microarrays hybridized to the same sample; (2) tier 2: correlation among different biological replicas for the same cell line or tissue and (3) tier 3: correlation among d”
Ensembl regulation resources (2016, background): “For example, histone modifications and TF binding locations previously identified with chromatin immunoprecipitation followed by microarray hybridisation (ChIP-chip) (12) now generally employ high-throughput sequencing (ChIP-seq) (13, 14); DNA methylation is assayed with MeDIP (15) or bisul-phite se”