Genome architecture of the CCL3/CCL3L locus in humans and chimpanzees. (A) Log2 ratio distributions of the WGTP clones Chr17tp-10G9 and Chr17tp-6G12 from the human 17q12 locus for humans (top) and chimpanzees (bottom; ref., reference). (B) Sequence annotation of this locus based on the human reference genome (hg18), with locations of the WGTP clones and fosmids used in this study. We compared two human samples and Clint to NA10851 by aCGH with a human oligonucleotide platform covering the 17q12 locus with a median spacing of 50 bp. The high-resolution profiles are concordant with the WGTP results displayed in A: NA18916 shows an increase in CCL3L1 copy number together with a decrease in TBC1D3 copy number compared with NA10851, while NA19108 shows relative copy number gains for both genes. In contrast, no difference in CCL3L1 copy number can be detected between Clint and NA10851. Instead, a high-fold relative copy number loss of the TBC1D3 gene is identified in Clint, thus explaining the CND loss detected with the WGTP platform. (C) Absolute CCL3L1 copy number measurement by fiber-FISH, using probes containing CCL3 (green), CCL3L1 (red), and a DNA segment between these two genes (in white). NA10851 carries a single copy of CCL3L1 per chromosome, while NA18916 carries one copy of CCL3L1 on one chromosome, but two copies on the other chromosome. For Pt205 and Pt296, no DNA fiber shows green and red signals together, suggesting that CCL3 and CCL3L1 are not adjacent genes in chimpanzee. In addition, we observed only single red signals for these two chimpanzee individuals, with no evidence of tandem CCL3L1 duplication. (D) Interphase-FISH with probes containing CCL3 (green) and CCL3L1 (red). In NA10851 cells, the signals corresponding to CCL3 and CCL3L1 cannot be discriminated spatially. In contrast, gaps between the red and green signals can be observed in chimpanzee nuclei, confirming major structural differences in the architecture of the CCL3L1 locus between human and chimpanzee. These results are concordant with the published sequence of chimpanzee chromosome 17 (panTro2 assembly), where a single copy of CCL3L1 is present at 19.41 Mb and CCL3 is mapped at 21.07 Mb.
