Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF [RNA-Seq]

The homeotic genes (Hox genes) encode transcription factors (HOX-TFs) that are key regulators of animal development. Single and compound deletion of Hox genes in mice revealed that they act in a partially redundant manner to pattern the vertebrate limb. Biochemical screens probing the sequence specificity of the DNA-binding domains showed that HOX-TFs recognize largely similar DNA sequences, but also emphasized the important role of co-factors in HOX DNA-binding. However, due to their high sequence homology and overlapping expression patterns, little is known about the genome-wide binding of these transcription factors Here, we set out to systematically compare the effects of the nine limb-bud expressed HOX-TFs on cell differentiation and gene regulation, and compare their genome-wide binding characteristics. We find that HOX-TFs induce distinct regulatory programs in transduced cells. Through genome-wide DNA binding profiling we find that the posterior HOX-TFs can be separated into two groups with distinct binding motifs and association with co-factors. Through this unexpected grouping, we characterize the CCCTC-binding factor (CTCF) as a novel co-factor of HOX-TFs and show that one, but not the other group of HOX-TFs binds to thousands of CTCF-occupied sites in the chicken genome. Overall design: Examination of the binding of 10 different transcription factors, a Cohesin subunit and an expression analysis (RNAseq analysis) in the chicken primary cell culture overexpression system.

20