GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86088/primaryOK200GenomicsGallus gallusGenome binding/occupancy profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86088GEOGSEfalseGenome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF [ChIP-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.2016/12/31GSE86088GSM2293349GSM2293367GSM2293388GSM2293366GSM2293369GSM2293368GSM2293385GSM2293363GSM2293362GSM2293384GSM2293365GSM2293387GSM2293386GSM2293364GSM2293381GSM2293380GSM2293383GSM2293361GSM2293382GSM2293360GSM2293359GSM2293356GSM2293378GSM2293377GSM2293355GSM2293358GSM2293379GSM2293357GSM2293374GSM2293352GSM2293373GSM2293351GSM2293376GSM2293354GSM2293353GSM2293375GSM2293370GSM2293350GSM2293372GSM229337121476SRP08300486088Gallus gallus