SOX9 Is an Activator and Repressor in Chondrocytes Figure 7. Differential presence of SOX9-GLI sites in proliferating and hypertrophic phase-specific genes. (A) Position, orientation, and spacing of the conserved linked SOX9 (COL2C1 and COL2C2) and GLI binding sites within the inter- and intra-genic regions of genes preferentially expressed in proliferating (PC) or hypertrophic (HC) chondrocytes. Numbers between the sites indicate the length of nucleotide spacing. Conservation indicates the percentage of nucleotides and species conserved in the alignments spanning the SOX9 and GLI sites. The alignments were based on multiz30way in UCSC genome browser and were simplified to only include sequences from mouse (M), human (H), chimpanzee (P), canine (D), bovine (C), and opossum (O) genome. Genes tested but found negative include HC genes Bmp6, Cdkn1c, Loxl4, Spp1, and Vegfa as well as PC genes Acan, Bmp7, Col2a1, Col9a1, Col9a2, Col9a3, Col11a1, Col11a2, Fgfr3, Fos, Mia1, and Sox9. (B) Left panel: Venn diagram showing frequency of genes in the genome that contain perfectly conserved SOX9, GLI, or linked SOX9-GLI sites within the inter- and intra-genic regions. SOX9 and GLI sites co-exist but are not linked in the majority of genes. Right panel: Number of HC, PC and all genes in the mouse genome with conserved SOX9-GLI sites and p-values from hypergeometric test (HT, for the over-representation of positive HC and PC genes compared to the genome) and one-tailed Fisher’s exact test (FET, for the difference in number of positive genes between HC and PC group). The test was based on all genes in the mouse genome (32,120 genes). See also Figure S3 for alignment data of the linked sites. doi:10.1371/journal.pgen.1002356.g007 PLoS Genetics | www.plosgenetics.org 12 November 2011 | Volume 7 | Issue 11 | e1002356