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Bioinformatics Dae-Soo Kim

The DNA Sequence of chimpanzee chromosome 22 and comparative analysis with its human ortholog, chromosome 21. Bioinformatics Dae-Soo Kim. Comparative analysis of Human and chimpanzee genome.

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Bioinformatics Dae-Soo Kim

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  1. The DNA Sequence of chimpanzee chromosome 22 and comparative analysis with its human ortholog, chromosome 21 Bioinformatics Dae-Soo Kim

  2. Comparative analysis of Human and chimpanzee genome • Human-chimp comparative genome research is essential for narrowing down the genetic change involved in the acquisitions of unique human features • We report the high quality DNA sequence of 33.3Mb of chimpanzee chromosome 22. • 1.44% of the chromosome consisted of single base substitutions in addition to nearly 68,000 INDEL • 83% of the 231 coding sequence show difference at the amino acid sequence level. MPL

  3. Introduction • Estimates of nucleotide substitution rates of aligned sequences were quite ranging from 1.23% by BAC end sequencing to about 2% by molecular analysis • Molecular analysis of HSA21 and its genes is of central medical interest because of trisomy 21, the most common genetic cause of metal retardation in the human population. MPL

  4. Mapping, sequencing and global view of chimpanzee chromosome 22 • Genomic DNA origination from three male chimpanzee individuals. • Sequence coverage of the euchromatic potion of the long arm of chromosome 22 is 98.6%. • Accuracy was calculated as 99.99% from the overlap clone sequence MPL

  5. Overall differences • The overall structural features of PTR22 are almost the same as those of HSA21. • About a 400kb or 1.2% difference in size with HSA21 being larger then PTR22 (ISRs;53.7% and simple repeats;9.54%) • The pericentromeric copy of a 200kb region found duplicated in HSA21 is missing in PTR22 • We also detected apparently human specific sequences (first intron PFKL of HSA21a) MPL

  6. Two large indel hot spots werw found around 9.5~11.5Mb and 16.5~17.5Mb from the centromere • We found large human insertion/chimpanzee deletions in the first introns of the NCAM2(~10kb)and GRIK1(~4kb) (Neural functions) • One of the largest structural changes identified here is a 54kb region located at 11.4Mb from the centromere in HSA21 but absent in PTR22.(flanked by HSAT5 satellite repeat and consists of 164 fragments from 64 different LTR) MPL

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  8. Base substitutions • The overall nucleotide substitution level in aligned regions between PTR22 and HSA21 is about 1.44%(excluding INDEL) • The most conserved region was around 12.5Mb corresponding to the distal boundary region of the gene desert. MPL

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  10. Repetitive elements • HSA21 is about 1.2% longer in size than PTR22 • Five LTR subfamilies LTR are more abundant in HSA21 • All MER4A1-int and MER83B-int elements are specific to HSA21 • All of the seven AluYb9’s found in HSA21 and the one in PTR22 are lineage specific • Although the AluYa8 subfamily is though to be a recent derivative of AluYa5 MPL

  11. Lineage specific insertions and deletions • We identified about 68,000 INDEL is total • Greater than 99% of the INDELs were shorter than 300bp • These site should be produced either through h-ins/p-dels or p-ins/h-dels • We tested 567 INDEL larger than 300bp in size using DNA samples from 5 human ,5chimpanzee ,1 gorilla, 2 orangutan • Insertions being mostly produced by the integration of Alu and L1 elements MPL

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  13. Lineage specific insertion Lineage specific deletion MPL

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  15. Deletions not being related to particular repetitive structures except for a few cases. • We found that most of the insertions 300-350bp in length were members of AluY family in both chromosome • Between 370-1000bp only a smaller number of insertions mostly L1 and LTR • We observed that the distribution of newly integrated Alu are quit different between HSA21 and PTR 22 (HSA21; 56% high G+C ,PTR22;70% low G+C) MPL

  16. Unlike the insertion, deletions do not exactly correspond to any ISR elements, indicating that deletion events are independent of ISRs. • The deletion of these elements may have also been generated by homologous recombination between these relatively short identical or similar flanking segments. • HSA21 gained 32kb but lost 39kb while PTR22 gained 25kb and lost 53kb(INDEL 300~5000bp) • PTR 22 has suffered more losses than HSA21 since speciation. MPL

  17. A neighbor joining analysis show that such AluY elements can be largely separated into chimp and human groups as expected(AluY was inserted after speciation) • Humans seem to have experienced such expansions more frequently and more recently than chimp MPL

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  19. Gene catalogue and structural characterization of coding sequences • We have annotated 284 protein coding genes and 98 pseudogenes for HSA21 and 272 genes and 89 pseudogenes for PTR22 • All the conserved pseudogenes showed the same size except for KRTAP21P1 which is non processed in HSA21 but processed in PTR22 • Six HSA21 genes showing hallmarks of retrogenes were not found in PTR 22 and are likely to have inserted during human evolution (H2BFS;histon family S,5 keratin associated protein) • The minimum nucleotide sequence identity is 83%(KRTAP6-3) and the maximum is 100% • We compared the human and chimp coding sequences in 231 genes (omitted 41) MPL

  20. Among the 231 genes associated to a canonical ORF 179 show a coding sequence of identical length in human and chimpanzee and exhibit similar intron-exon boundaries • 39genes shown an identical amino acid and nucleotide sequence between human and chimp (biological process 5, metabolic enzymes 5, signal transduction 8, protein folding 2) • One hundred and forty out of these 179 genes show amino acid replacements but no gross structural changes and expected. MPL

  21. Ka/Ks analysis • 10% of the genes had Ka/Ks rations >1 with the highest value being 3.37 for the human hair keratine associated protein • Relatively rapidly evolving genes may be estimated from Ka, Ka+Ks or just nucleotide divergence values. (3 KRTAP gene, KCNE1; potassium channel protein ,TCP10L;complex protein, B3GALT5;galctocyltransferase,IGSF5;immunoglobulin) MPL

  22. Promoter analysis • Computation analysis of the transcription factor binding site within the l-kb upstream region of each gene. • All of the specific TFBSs were caused by base substitution in either human or chimpanzee • These may mot clearly account for the expression changes observed in this study MPL

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  25. Conclusion This study shows for the first time a chromosome wide comparison between human and chimpanzee using high quality sequence. MPL

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