Long noncoding RNA HOTTIP cooperates with CCCTC-binding factor to coordinate HOXA gene expression

The spatiotemporal control of HOX gene expression is dependent on positional identity and often correlated to their genomic location within each loci. Maintenance of HOX expression patterns is under complex transcriptional and epigenetic regulation, which is not well understood. Here we demonstrate that HOTTIP, a lincRNA transcribed from the 5′ edge of the HOXA locus, physically associates with the CCCTC-binding factor (CTCF) that serves as an insulator by organizing HOXA cluster into disjoint domains, to cooperatively maintain the chromatin modifications of HOXA genes and thus coordinate the transcriptional activation of distal HOXA genes in human foreskin fibroblasts. Our results reveal the functional connection of HOTTIP and CTCF, and shed light on lincRNAs in gene activation and CTCF mediated chromatin organization. •HOTTIP is required for activation of distal HOXA genes but its role is restricted by CTCF boundary.•HOTTIP and CTCF coordinate to specify the pattern of histone modifications on HOXA genes in foreskin fibroblasts.•HOTTIP RNA acts as a new interaction partner of CTCF.