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Kehrer-Sawatzki and Cooper, Human Mutation HUMAN MUTATION Supplementary Material Online Page S 1 Supplementary Material for the article: Kehrer-Sawatzki and Cooper, Human Mutation Understanding the Recent Evolution of the Human Genome; Insights from Human-Chimpanzee Genome Comparisons Hildegard Kehrer-Sawatzki and David N. Cooper Supplementary Tables S1-S4 and Supplementary Figures S1-S3 Supplementary Table S1: Divergence between humans and chimpanzees in different genic regions Genic regions Divergence in % All nucleotides Without CpGs Reference 5'UTR 5’UTR Coding sequence Coding sequence Exon-intron junctions 3'UTR 3'UTR Intronic 1.12 ± 0.04 1.00 ± 0.10 0.45 ± 0.01 0.51 ± 0.02 0.85 ± 0.02 0.86 ± 0.016 0.93 ± 0.09 1.20 ± 0.014 Hellmann et al. 2003a a Shi et al. 2003a b Hellmann et al. 2003a Shi et al. 2003a Shi et al. 2003a Hellmann et al. 2003a Shi et al. 2003a Hellmann et al. 2003a a: b: 0.77 ± 0.035 0.28 ± 0.008 0.63 ± 0.014 0.80 ± 0.012 Hellmann et al. 2003a investigated 5055 genes Shi et al. 2003a analysed 127 genes 1 Kehrer-Sawatzki and Cooper, Human Mutation HUMAN MUTATION Supplementary Material Online Page S 3 Supplementary Table S2: Cancer-related genes with codon insertions/deletions in humans as compared to chimpanzee (according to Puente et al. 2006) Gene Gene description CCNE1 FANCC FGFR1 HOXD11 ATP2C1 Cyclin E1 Fanconi anemia complementation group C Fibroblast growth factor receptor 1 Homeobox D11 ATPase, Ca++ transporting, type 2C, member 1 AF4/FMR2 family, member 1 Myeloid /lymphoid or mixed-lineage leukaemia translocated to, 3 Meningioma 1 AFF1 MLLT3 MN1 PML CASC5 ASPSCR1 Chromosome Amino acid(s) inserted 19q13.1 9q22.3 8p11.2-11.1 2q31.1 3q22.1 type Serine (S) Glutamine (Q) Aspartic acid (D) Glycine (G) Glutamic acid (E) 4q21 9p22 Codons inserted in poly(Q) poly(D) poly(G) poly(E) chimpanzee Serine (S) 2 Serines (S) poly(S) 22q12.1 4 Glutamines (Q) poly(Q) 15q22 15q14 17q25 Glycine (G), Phenylalanine (F) Arginine (R) Glutamic acid (E), Arginine (R) ATF1 DEK RNF2 Acute promyelocytic leukaemia Cancer susceptibility candidate 5 Alveolar soft part sarcoma chromosome region, candidate 1 Activating transcription factor 1 DEK oncogene (DNA binding) Ring finger protein 2 12q13 6p23 1q25.3 EP300 E1A binding protein p300 22q13.2 LMO2 AFF1 MYST4 11p13 4q21 10q22.2 NUMA1 LIM domain only 2 AF4/FMR2 family, member 1 Histone acetyltransferase (monocytic leukaemia) 4 Nuclear mitotic apparatus protein Alanine (A) Glutamic acid (E) Leucine (L), Arginine + Aspartic acid (RD) Methionine, Glutamine, Glutamine (MQQ) Glycine (G) Serine (S) 2+1 Glutamic acid (E) SMO ZNF38 Smoothened homologue (Drosophila) Zinc finger protein 38 7q32.3 7q22.1 11q13 Alanine (A)+ Alanine (A)+ Isoleucine (I)+ Glycine (G) Leucine (L) Glutamine (Q) in repeat Polymorphic in humans humans poly(ER) poly(E) poly(RD) poly(G) poly(S) poly(E) poly(L) poly(Q) 3 Kehrer-Sawatzki and Cooper, Human Mutation HUMAN MUTATION Supplementary Material Online Page S 4 Supplementary Table S3: Human chromosomes that are distinguished by pericentric inversions from their chimpanzee homologues and the results of breakpoint analyses HSA chromosome 1 Fixed in the chimpanzee lineagea b Segmental duplications Reference for breakpoint found at the breakpoints characterization + Szamalek et al. 2006a 4 + Kehrer-Sawatzki et al. (2005a) 5 + Szamalek et al. (2005) 9 + +c Kehrer-Sawatzki et al. (2005b) 12 + + 15 + +d Kehrer-Sawatzki et al. (2005c) Shimada et al. (2005) Locke et al. (2003a) 16 + + Goidts et al. (2005) 17 + Kehrer-Sawatzki et al. (2002) 18 b + Goidts et al. (2004) Dennehey et al. (2004) a: As determined by using other hominoids as an outgroup and summarized in Kehrer-Sawatzki et al. (2005a) The inversions of chromosomes 1 and 18 were fixed in the human lineage and are therefore human-specific. c: Segmental duplications were identified at the inversion breakpoint in 9p12. Adjacent to the breakpoint in 9q, -satellites were detected. d: Breakpoints were not precisely characterized but narrowed down to regions of segmental duplications. b: 4 Kehrer-Sawatzki and Cooper, Human Mutation HUMAN MUTATION Supplementary Material Online Page S 5 Supplementary Table S4: Inversions identified owing to their involvement in human disease Disease/ syndrome (gene involved) Localization Size of inversion Frequency of the inversion in % in Reference transmitting parents (patients) controls 25-33 5 Osborne et al. 2001 Scherer et al. 2005 Williams-Beuren syndrome 7q11.23 1.5Mb Angelman syndrome 15q11-q13 4Mb 67 9 Gimelli et al. 2003 Sotos syndrome (NSD1) 5q35.3 1.9Mb 100 67-75 Visser et al. 2005 Recurrent translocation t(4;8)(p16;p23) Wolf-Hirschhorn syndromea 4p16 8p23 nd nd 100 12.5 26b Giglio et al. 2001, 2002 Haemophilia A (F8) Xq28 400kb (40) - Antonarakis et al. 1995 Hunter syndrome (idunorate 2-sulphatase, IDS) Xq28 90kb (13) - Bondeson et al. 1995 Familial juvenile nephronophthisis (NPHP1) 2q13 330kb 1.3 Saunier et al. 2000 48kb 33 Small et al. 1997 Emery-Dreifuss muscular dystrophy (EMD) Xq28 nd: not defined a: parents of individuals with t(4;8)(p16;p23) were shown to be heterozygous carriers of inversions at both 4p16 and 8p23. In the offspring of carriers, unbalanced karyotypes lead to Wolf-Hirschhorn syndrome if the der(4) chromosome is inherited. Patients with unbalanced der(8) show a milder spectrum of dysmorphic features. b: 2.5% are double heterozygotes. 5 Kehrer-Sawatzki and Cooper, Human Mutation HUMAN MUTATION Supplementary Material Online Page S 6 1 2 p33 4 p23-24 8 12 22 p15.1 p12 q12.3 q21.3 57 genes, from CARD10 to PMM1 14 genes, from ELAV4 to GPX7 UNC5D, FKSG2 ARHGAP15, GTDC1, ZFHX1B 10genes, from PAMC1 to ATB2B1 Supplementary Figure S1: Six human chromosomal regions with strong evidence for ‘selective sweeps’ as indicated by low diversity in humans compared to the divergence in chimpanzee according to Mikkelsen et al. (2005). On chromosome 4, no genes were identified in the corresponding region. 6 Kehrer-Sawatzki and Cooper, Human Mutation HUMAN MUTATION Supplementary Material Online Page S 7 Supplementary Figure S2: Frequency of lineage-specific Alu insertions in human and chimpanzee genomes among all transposon insertions (total numbers of transposon insertions in humans: n= 7786 and n= 2933 in chimpanzee) according to Mills et al. (2005). 7 Kehrer-Sawatzki and Cooper, Human Mutation HUMAN MUTATION Supplementary Material Online Page S 9 Supplementary Figure S3: Frequency of inter- and intrachromosomal duplications on human chromosomes according to Zhang et al. (2005). 9