A ChIP-on-chip tiling array approach detects functional histone-free regions associated with boundaries at vertebrate HOX genes

Abstract

Hox genes impart segment identity to body structures along the anterior–posterior axis and are crucial for proper development. A unique feature of the Hox loci is the collinearity between the gene position within the cluster and its spatial expression pattern along the body axis. However, the mechanisms that regulate collinear patterns of Hox gene expression remain unclear, especially in higher vertebrates. We recently identified novel histone-free regions (HFRs) that can act as chromatin boundary elements demarcating successive murine Hox genes and help regulate their precise expression domains (Srivastava et al., 2013). In this report, we describe in detail the ChIP-chip analysis strategy associated with the identification of these HFRs. We also provide the Perl scripts for HFR extraction and quality control analysis for this custom designed tiling array dataset.

Epigenetic mechanisms and boundaries in the regulation of mammalian Hox clusters

“…Interspersed between the peaks of histone H3 enrichment, we observed a distinctive pattern of gaps, which we defined as histone free regions or HFRs (Srivastava et al, 2013). Using a bioinformatics approach to map the extent and location of the HFRs (Srivastava et al, 2014), we showed that the gaps in H3 binding mapped precisely to the intergenic regions separating adjacent Hox genes. This is recapitulated here for the Hoxd cluster ( Fig.…”