No Formaldehyde, No Problem for New Genome-Wide Chip Method

Transcription factors (TFs) interpret regulatory information encoded in genomes to direct gene expression, thereby influencing essentially every cellular process. Mutations in TFs or the DNA sequences recognized by TFs are often found in human diseases (Lee and Young, 2013; Maurano et al., 2012). Mapping the genome-wide distributions of TF recognition sites is thus of significant interest for understanding basic cellular processes as well as the potential bases of many diseases. The gold-standard method for surveying protein-genome interactions is chromatin immunoprecipitation (ChIP), which has been combined with hybridization to tiled microarrays (ChIPchip) or high-throughput sequencing (ChIP-seq) to give whole-genome pictures of protein binding. ChIP generally involves the treatment of cells with formaldehyde (X-ChIP), which covalently fixes protein-DNA and protein-protein interactions. Cells are then disrupted and chromatin is solubilized via sonication. While X-ChIP-chip and X-ChIP-seq studies have yielded many important insights, there are limitations associated with these techniques. For example, formaldehyde crosslinking preferentially generates protein-protein crosslinks (O’Neill and Turner, 2003) and can lead to false-positive ChIP signals due to crosslinking to the transcription machinery at highly expressed loci (Teytelman et al., 2013). Native ChIP (N-ChIP), which does not use formaldehyde crosslinking, may offer solutions to some of these issues.