Formaldehyde-assisted isolation of regulatory elements

Abstract

Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) is based on locus-specific variations in the ability of protein components of chromatin to trap genomic DNA following formaldehyde treatment. This variation is mostly due to uneven nucleosome distribution since histones are the most abundant and highly crosslinkable components of chromatin. The method can identify and enrich for physically accessible DNA segments of the eukaryotic genome corresponding to known regulatory regions and regions that might have thus far unidentified structural role in the nuclear organization of chromatin. The enrichment patterns are cell type specific and thus might provide information about how transcriptional systems are organized and regulated in various tissues and how they might be disrupted in disease states. Analysis of a 268 kb region of chromosome 19 in human fibroblasts shown here demonstrates that while most DNA fragments detected by FAIRE correspond to sites of DNaseI hypersensitivity in active regions of chromatin, some are found in otherwise repressed chromatin domains and at other sites that are not found with other methods used to probe chromatin structure. Further exploration of FAIRE is warrented due to the simplicity of the protocol and recent advancements in massively parallel sequencing.

Keywords: DNase I sensitivity; FAIRE; chromatin structure; formaldehyde crosslinking; genome organization; nucleosome distribution; regulatory sequences; transcription.

Figure 1. Comparison of FAIRE with other techniques probing chromatin structure

A region of human chromosome 19 was analyzed using the UCSC genome browser (http://genome.ucsc.edu/) as described in the text. Numbers at the top of both panels indicate chromosomal coordinates. In both panels the positions of genes in the regions covered, as well as the locations of repeated sequences are indicated. Stars denote position of FAIRE signals that overlap with sites of DNase I hypersensitivity in inactive chromatin.