Figure 2

Methylation of TIMP1. A. The genes in the region surrounding TIMP1 are shown with the gene name written above the line diagram for the gene (with vertical lines representing exons and small arrows showing transcriptional orientation). The number listed on the line below at the 5' end of the genes indicates the CpG island density. The TIMP1 and ZNF147 genes do not have enough CpG sites to qualify as a CpG island so there is no number listed. The SYN1, and PFC genes are listed in grey because these genes (which are expressed in a tissue-specific manner) were not examined in this study. The presence of repeat elements (SINE, LINE and LTR) is indicated by the vertical lines below the genes. This figure is based on data generated by the UCSC browser http://www.genome.ucsc.edu/ hg17 of NCBI Build 35. B. Somatic cell hybrids analysed for TIMP1 activity. In addition to the stable active X chromosomes that express TIMP1 and are unmethylated at the 5' end of the gene (Xa/+/U) there are several categories of inactive X chromosomes. Most inactive X chromosomes previously analysed do not express TIMP1 and are methylated (Xi/-/M). Other inactive X chromosomes express TIMP1 and are unmethylated (Xi/+/U), while an intermediary class of hybrids showed both DNA methylation and lower expression levels (Xi/+/M). Subcloning of these latter cells showed that they were unstable, giving rise to additional methylated expressing clones as well as methylated silent clones and expressing unmethylated clones. The arrows show approximate proportion of cells of each class derived from subcloning. Subclones further characterized are listed below, as are clones derived by 5-azacytidine treatment and their subclones (see Tables 1 and 2). C. DNA methylation of clones from four of the demethylated clones listed in Table 1. DNA from each clone was digested with Eco RI alone (U), Eco RI plus Hpa II (II) or Eco RI plus Hha I (I). Primers for the 5' end of TIMP1 and ARAF1 that flank Hpa II or Hha I methylation-sensitive restriction enzyme sites were used to assess methylation, while amplification of MIC2, which is unmethylated on both active and inactive X chromosomes, served as a control for complete digestion with the methylation-sensitive enzymes. D. Comparison of expression levels in subclones of two 'sibling' subclones of t11-az-10 differing in methylation states. The t11-az-10-7 and t11-az-10-10 clones are striped, with their subclones shown to their right. Methylation (dark fill) was observed for t11-az-10-7 and its subclones while t11-az-10-10 and its subclones were unmethylated (unfilled). All subclones continued to express both TIMP1 and ARAF1 as assayed by RT-PCR. Despite the relative stability of the methylated TIMP1+ culture, the TIMP1 expression level was significantly lower in the methylated cultures (p < 0.01). E. Methylation analysis by bisulphite treatment. The 5' end of the TIMP1 gene was sequenced after bisulfite conversion, which changes unmethylated Cs to Us but leaves methylated Cs unchanged. Therefore, the presence of a C indicates that the CpG was methylated. The following CpG sites were analyzed: Hha I sites (stars) at -3 and +31; and three other sites not analyzed by methylation-sensitive enzymes (circles) at +11, +17, +20. The Hpa II sites (triangles) at +61 and +81 were used in methylation-sensitive assays but were not reliably analysed by bisulphite sequencing. The open circles indicate unmethylated CpGs whereas the filled circles represent methylated CpGs. The shaded circles designate that both converted and unconverted bases were seen after sequencing, indicating that both methylated and unmethylated CpGs were present. Cell lines are listed, the male cells were GM7057 and the female cells were GM7059. t11-az-9-3 is a TIMP1^- subclone of t11-az-9.