{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86088/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"species":["Gallus gallus"],"gds_type":["Genome binding/occupancy profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86088"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF [ChIP-Seq]","description":"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.","dates":{"publication":"2016/12/31"},"accession":"GSE86088","cross_references":{"GSM":["GSM2293349","GSM2293367","GSM2293388","GSM2293366","GSM2293369","GSM2293368","GSM2293385","GSM2293363","GSM2293362","GSM2293384","GSM2293365","GSM2293387","GSM2293386","GSM2293364","GSM2293381","GSM2293380","GSM2293383","GSM2293361","GSM2293382","GSM2293360","GSM2293359","GSM2293356","GSM2293378","GSM2293377","GSM2293355","GSM2293358","GSM2293379","GSM2293357","GSM2293374","GSM2293352","GSM2293373","GSM2293351","GSM2293376","GSM2293354","GSM2293353","GSM2293375","GSM2293370","GSM2293350","GSM2293372","GSM2293371"],"GPL":["21476"],"SRA":["SRP083004"],"GSE":["86088"],"taxon":["Gallus gallus"]}}