Molecular Characterization of the Pericentric Inversion That Causes Differences Between Chimpanzee Chromosome 19 and Human Chromosome 17 Hildegard Kehrer-Sawatzki,

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Molecular Characterization of the Pericentric Inversion That Causes Differences Between Chimpanzee Chromosome 19 and Human Chromosome 17 Hildegard Kehrer-Sawatzki, Bettina Schreiner, Simone Tänzer, Matthias Platzer, Stefan Müller, Horst Hameister The American Journal of Human Genetics Volume 71, Issue 2, Pages 375-388 (August 2002) DOI: 10.1086/341963 Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 1 Comparison of the G-banding pattern of human chromosome 17 and the homologous chromosomes in chimpanzees, orangutans, and gorillas. Gorillas have a unique reciprocal translocation t(4;19), which arose from the ancestral chromosomes equivalent to human chromosomes 5 and 17. Arrows indicate the parts homologous to human chromosome 17 involved in the pericentric inversion of chimpanzee 19, the paracentric inversion of orangutan chromosome 19, and the position of the gorilla t(4;19) breakpoints. GGO = Gorilla gorilla; PPY = Pongo pygmaeus; PTR = Pan troglodytes; HSA = Homo sapiens. The American Journal of Human Genetics 2002 71, 375-388DOI: (10.1086/341963) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 2 FISH with breakpoint-spanning human PAC clones RP5-1029K10 (A and B) and RP1-179H24 (E and F) and chimpanzee BACs RP43-134L13 (C and D) and RP43-141Q35 (G and H). A, C, E, and G, Results of hybridizations on chromosome preparations of chimpanzee lymphoblastoid cell lines. B, D, F, and H, Results of FISH on human lymphocyte metaphases. The American Journal of Human Genetics 2002 71, 375-388DOI: (10.1086/341963) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 3 Position of breakpoint-spanning human PAC clones and flanking BACs on human 17q21.3 (A) and human 17p13 (B). The FISH hybridization pattern of each BAC or PAC on chimpanzee chromosomes is given in italics above each horizontal line. The line represents the relative length of each clone. Vertical arrows point to the position of the breakpoints. The American Journal of Human Genetics 2002 71, 375-388DOI: (10.1086/341963) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 4 Structure of the breakpoint region on human 17q21.3 (A), chimpanzee 19q (B), human 17p13 (C), and chimpanzee 19p (D). The sequences with homology to human 17p13 are shown as blue lines, whereas regions of homology to 17q21.3 are in red. SmaI and EcoRI restriction sites are indicated. PCR products p40/41 and p210/211 were used as labeled probes in Southern blot hybridizations to isolate breakpoint-spanning SmaI fragments. Their positions are indicated by horizontal bars and the respective sizes of these fragments are added. The flanking genes, which have been identified by physical mapping and sequencing of cloned fragments overlapping the breakpoint-spanning SmaI fragments, are also indicated. E = EcoRI; S = SmaI. The American Journal of Human Genetics 2002 71, 375-388DOI: (10.1086/341963) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 5 Breakpoints on human 17p13 and 17q21.3. A, Repeat organization of the regions that harbor the inversion breakpoints on human 17p13 and human 17q21.3 as determined by the Repeat Masker program. The breakpoints were found in regions rich in repeats such as Alu elements (including a free right arm Alu-monomer [FRAM]), medium reiteration-frequency repeats (MER), parts of LINEs (L1, L2, L1MC3, and L1Mec), and LTR-element family members/mammalian retrotransposon-like superfamily (MLT1K and MSTA). The breakpoint is indicated by a double-headed arrow. B, Aligned sequences of human 17q21.3 in red letters and human 17p13 in blue letters and the respective sequences from chimpanzee 19p and 19q spanning the inversion breakpoints. The pentamer repeat GGGGT at the breakpoints is underlined. The 26-bp core sequence of the AluSq-element is marked by a box. At the human 17p breakpoint, a sequence with 83% similarity to the consensus topoisomerase IIv cleavage site is highlighted in yellow. The American Journal of Human Genetics 2002 71, 375-388DOI: (10.1086/341963) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 6 Distance and orientation of the genes flanking the pericentric inversion breakpoints on human 17q21.3 (A), on human 17p13 (B), in chimpanzee 19p (C), and in chimpanzee 19q (D). Thick arrows indicate the transcription orientation of each gene. The American Journal of Human Genetics 2002 71, 375-388DOI: (10.1086/341963) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 7 Evaluation of replication timing of sequences flanking the pericentric inversion breakpoints with BACs and PACs from human 17q21.3 (RP1-81K2 and RP11-613C6) and from human 17p13 (RP11-404G1 and RP11-1D5) as FISH probes (see fig. 3 for position of BACs relative to the breakpoint). The percentage of two doublet signals was determined in BrdU-labeled S-phase nuclei of fibroblastlike cells from chimpanzee (chimpanzee cell line CP132) and primary human foreskin fibroblasts. FISH analysis was also performed with BAC RP11-133K23 as reference probe for a late-replicating genomic region and with BAC RP11-869B15 for an early-replicating genomic region. D/D = two doublets; HSA = Homo sapiens; PTR = Pan troglodytes. The American Journal of Human Genetics 2002 71, 375-388DOI: (10.1086/341963) Copyright © 2002 The American Society of Human Genetics Terms and Conditions