ChIP-seq for Gli1 and Gli2 in chondrosarcoma

Excessive Hedgehog signaling in chondrocytes is sufficient to cause formation of enchondroma-like lesions in mice which can progress to chondrosarcoma. To elucidate potential mechanisms through which activation of Hedgehog signaling contributes to cartilage tumor formation, we used chromatin immunoprecipitation and next generation sequencing to identify Gli1 and Gli2 target genes in primary human chondrosarcoma. In silico analyses were conducted to identify and characterize Gli1 and Gli2 binding regions, including de novo motif analysis, co-localization with additional transcription factors, distance to transcriptional start site, conservation between human and mouse, and supervised and unsupervised analyses of biological pathways and processes. Our results profile putative unique and overlapping target genes of Gli1 and Gli2 in chondrosarcoma. Overall design: Cells were cultured from a primary chondrosarcoma obtained following surgery. Cells were divided into three groups and treated with Shh ligand to stimulate the Hedgehog signaling pathway. Following fixation, DNA was immunoprecipitated using antibodies against Gli1, Gli2, and IgG (negative control), and subjected to sequencing.