MPL The DNA Sequence of chim panzee chromosome 22 and comparative analysis wit h its human ortholog, ch romosome 21 Bioinformatics Dae-Soo Kim
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The DNA Sequence of chimpanzee chromosome 22 and comparative analysis with its human ortholog, ch
romosome 21
Bioinformatics
Dae-Soo Kim
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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.
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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.
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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
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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)
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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)
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Size (bp)*1
Unaligned sites*2 25,242 101,709
# of sequencing gaps 14
# of clone gaps*3 3
Estimated total clone gap size 73,108
G+C% 40.94%
CG dinucleotide 361,259
CpG islands 950
Nucleotide diversity 0.072% 0.14%
Repeats bp # bp #
SINEs 3,649,153 15,137 3,614,825 15,048
Young Alus *4 21,557 75 2,606 10
LINEs 5,853,821 8,737 5,736,911 8673
Young L1s *5 82,493 48 78,657 55
LTRs 3,621,501 7,282 3,550,807 7,180
Transposons 949,215 3,363 945,129 3,350
RNAs*6 8,830 100 8,722 99
Satellite 19,327 21 14,773 18
Others 30,452 38 34,776 43
Total 14,132,299 34,678 13,905,943 34,411
42.7% 42.4%
*1 Size of the contig data after the site where the first base of the PTR22q contig is aligned
*2 Regions extended into HSA21q clone gaps and subtelomeric unmatched regions
*3 Excluding pericentromeric and subtelomeric gaps
*4 AluYa5, AluYa8, AluYb8 and AluYb9
*5 L1HS and L1PA2*6 snRNA, scRNA, 5S rRNA, tRNA, 7SL RNA and other small RNA genes
358,450
885
HSA21q
33,127,944
2
41.01%
PTR22q
32,799,845
22
74,311
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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.
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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
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Lineage specific insertions and deletions
We identified about 68,000 INDEL is total Greater than 99% of the INDELs were shorter tha
n 300bp These site should be produced either through h-in
s/p-dels or p-ins/h-dels We tested 567 INDEL larger than 300bp in size u
sing DNA samples from 5 human ,5chimpanzee ,1 gorilla, 2 orangutan
Insertions being mostly produced by the integration of Alu and L1 elements
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Lineage specific insertion
Lineage specific deletion
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2.4 2.6 2.8 3 3.2 3.4 3.6
HSA21q insertion
PTR22q insertion
HSA21q deletion
PTR22q deletion
251 398 631 1000 1585 2512 3981
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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)
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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.
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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
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HSA21 120.AluY PTR22 033.AluY PTR22 097.AluY PTR22 075.AluY
PTR22 063.AluY PTR22 140.AluY
PTR22 058.AluY PTR22 153.AluY
PTR22 069.AluY PTR22 147.AluY
PTR22 096.AluY PTR22 010.AluY
HSA21 211.AluY PTR22 192.AluY
HSA21 172.AluY HSA21 197.AluYa5
HSA21 121.AluYa5 HSA21 045.AluYa5
HSA21 216.AluYa5 HSA21 017.AluYa5
HSA21 131.AluYa5 HSA21 166.AluYa5
PTR22 098.AluY HSA21 215.AluY
HSA21 201.AluY HSA21 148.AluY HSA21 188.AluY
HSA21 132.AluY HSA21 106.AluY
HSA21 208.AluY HSA21 218.AluYb8
HSA21 018.AluYb8 HSA21 034.AluYb8
HSA21 174.AluYb9 HSA21 135.AluYb9
HSA21 020.AluYb8 HSA21 036.AluYb8
HSA21 025.AluYb8 HSA21 187.AluYb8
HSA21 206.AluYb8 HSA21 076.AluYb8
HSA21 013.AluYb8 HSA21 168.AluYb8
HSA21 244.AluYb8 HSA21 213.AluY
PTR22 082.AluY HSA21 153.AluY
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0.01
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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)
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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.
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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)
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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
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Red: TF binding sites found only in human
Blue: TF binding sites found only in chimpanzee
Yellow: TF binding sites common in huamn, chimpanzee and mouse
Grey: TF binding sites common in human and mouse.
Position 1 locates 1000 bases upstream from the coding sequence of gene
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Conclusion
This study shows for the first time a chromosome wide comparison between human and chimpanzee using high quality sequence.