Formaldehyde-assisted isolation of regulatory elements Sequencing (FAIRE-seq) is a method for directly detecting DNA sequences not occupied by nucleosomes. The principle is based on the fact that DNA-entangled nucleosomes and nucleosome-free bound DNA have different solubility in phenol and chloroform. Nucleosomes with entangled DNA are distributed at the junction of the two phases, while nucleosome-free DNA is distributed in the hydrophilic phase. Lifeasible provides FAIRE-seq technology service, which overcomes the sequence preference of MNase and DNase I to cut DNA. FAIRE directly enriches the region of activated chromatin, which can be directly applied to any type of cell or tissue, with no requirement for the starting state of the cells.

During FAIRE phenol-chloroform extraction, protein-uncrosslinked DNA is dissolved in the aqueous phase, while protein-bound DNA remains at the interface of the two phases, thus dividing whole genomic DNA into two parts (i.e., aqueous-phase and organic-phase DNA). The aqueous-phase DNA is then detected, and we commonly use fluorescent quantitative PCR, DNA microarray chips, and second-generation sequencing technologies.

Specific steps for FAIRE-seq

• Preparation of sequencing library. Firstly, purification and recovery, then PCR amplification and screening of DNA to create the final library.
• Use algorithms to clean the library by removing sequenced sequences through adapter filtering.
• Use algorithms to assess library quality, such as confidence score and nucleotide distribution.
• Use algorithms to map high-quality reads to the reference genome.
• Data visualization and searching for regions of the assay significantly enriched in the hairline view relative to the background.
• Use algorithms to evaluate crosslink-folding correlation coefficients.

Advantages

• Simple and highly reproducible protocol.
• Does not require antibodies.
• Does not require enzymes, such as DNase or MNase, avoiding the optimization and extra steps necessary for enzymatic processing.
• Does not require a single-cell suspension or nuclear isolation, so it is easily adapted for use on tissue samples.

Applications

• We combine three experimental techniques, ChIP-seq, DNase-seq, and FAIRE-seq, which can be used to reveal transcription factor binding sites, nucleosome distribution locations, open regions of chromatin, and the relationship between the three.
• We combined FAIRE-seq with DNase-seq technology to reveal the characteristics of open chromatin, which became a preferred method to study the regulation at the DNA level.

Lifeasible uses FAIRE-seq technology to identify chromatin accessibility and detect DNA sequences associated with regulatory activities on a genome-wide scale. You need to provide the sample, species information, target gene name and ID, etc., and we can complete the whole analysis process and deliver the lab report for you, including methods, results, and conclusions. Please feel free to contact us for your customized solution.

*If your organization requires the signing of a confidentiality agreement, please contact us by email.

For research use only, not intended for any clinical use.

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