A ChIP-on-chip tiling array approach detects functional histone-free regions associated with boundaries at vertebrate HOX genes.
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.
Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Uppal Road, Hyderabad, Andhra Pradesh 500007, India.
Surabhi
S
Srivastava
Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Uppal Road, Hyderabad, Andhra Pradesh 500007, India.
Divya Tej
DT
Sowpati
Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Uppal Road, Hyderabad, Andhra Pradesh 500007, India.
Hita Sony
HS
Garapati
Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Uppal Road, Hyderabad, Andhra Pradesh 500007, India.
Deepika
D
Puri
Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Uppal Road, Hyderabad, Andhra Pradesh 500007, India.
Jyotsna
J
Dhawan
Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Uppal Road, Hyderabad, Andhra Pradesh 500007, India.
Rakesh K
RK
Mishra
ChIP, chromatin immunoprecipitation; ChIP-on-chip; Chromatin domain boundary; DTT, dithiothreitol; Enhancer blocking; GAF, GAGA binding factor; GAGA factor; HFR, histone-free region; HS, hypersensitive; Histone H3; Hox; NLR, normalized log ratio; PMSF, phenylmethanesulfonylfluoride