Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome

Gene

Volumn 399, Issue 1, 2007, Pages 1-10

  Sakate, Ryuichi ^a,b   Suto, Yumiko ^c   Imanishi, Tadashi ^b   Tanoue, Tetsuya ^d   Hida, Munetomo ^e   Hayasaka, Ikuo ^d   Kusuda, Jun ^f   Gojobori, Takashi ^b,g   Hashimoto, Katsuyuki ^f,h   Hirai, Momoki ^e  

^a Japan Biological Information Research Center   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c Research and Development Department   (Japan)

^d SANWA KAGAKU KENKYUSHO CO LTD   (Japan)

^e TOKYO WOMEN'S MEDICAL UNIVERSITY   (Japan)

^f NATIONAL INSTITUTE OF BIOMEDICAL INNOVATION   (Japan)

^g NATIONAL INSTITUTE OF GENETICS   (Japan)

^h NATIONAL INSTITUTE OF INFECTIOUS DISEASES   (Japan)

Author keywords

Bioinformatics; Full length cDNA; Gene structure; Human evolution; Sequence analysis

Indexed keywords

COMPLEMENTARY DNA; GENE PRODUCT; NUCLEOTIDE; TRANSCRIPTOME;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ALU SEQUENCE; ANIMAL TISSUE; ARTICLE; CHIMPANZEE; DNA SEQUENCE; EXON; GENE CONTROL; GENE DELETION; GENE INSERTION; GENE MAPPING; HUMAN; HUMAN GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; RNA SPLICING; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION TERMINATION; TRANSPOSON;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ALU ELEMENTS; ANIMALS; CHROMOSOME MAPPING; DNA TRANSPOSABLE ELEMENTS; DNA, COMPLEMENTARY; GENOME, HUMAN; HUMANS; PAN TROGLODYTES; TRANSCRIPTION, GENETIC; VARIATION (GENETICS);

PAN;

EID: 34447535256     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2007.04.013     Document Type: Article

References (37)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
2. Anzai T., et al. Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 7708-7713
3. Brett D., Pospisil H., Valcarcel J., Reich J., and Bork P. Alternative splicing and genome complexity. Nat. Genet. 30 (2002) 29-30
4. Britten R.J. Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 13633-13635
5. Chen F.C., Vallender E.J., Wang H., Tzeng C.S., and Li W.H. Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences. J. Heredity 92 (2001) 481-489
6. Dorus S., et al. Accelerated Evolution of Nervous System Genes in the Origin of Homo sapiens. Cell 119 (2004) 1027-1040
7. Frith M.C., et al. Evolutionary turnover of mammalian transcription start sites. Genome Res. 16 (2006) 713-722
8. Fujiyama A., et al. Construction and analysis of a human-chimpanzee comparative clone map. Science 295 (2002) 131-134
9. He L., and Hannon G.J. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev., Genet. 5 (2004) 522-531
10. Hedges D.J., Callinan P.A., Cordaux R., Xing J., Barnes E., and Batzer M.A. Differential alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Res. 14 (2004) 1068-1075
11. Hellmann I., Zollner S., Enard W., Ebersberger I., Nickel B., and Paabo S. Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13 (2003) 831-837
12. Hida M., et al. Construction and preliminary characterization of full-length enriched cDNA libraries for nonhuman primates. Primate Res. 16 (2000) 95-110
13. Imanishi T., et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2 (2004) 856-875
14. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431 (2004) 931-945
15. Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16 (2000) 418-420
16. Keightley P.D., Lercher M.J., and Eyre-Walker A. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 3 (2005) e42
17. Kent W.J. BLAT - the BLAST-like alignment tool. Genome Res. 12 (2002) 656-664
18. Khaitovich P., et al. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309 (2005) 1850-1854
19. Kimura K., et al. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res. 16 (2006) 55-65
20. Kuroki Y., et al. Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat. Genet. 38 (2006) 158-167
21. Lee R.C., Feinbaum R.L., and Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 (1993) 843-854
22. Maquat L.E. Nonsense-mediated mRNA decay. Curr. Biol. 12 (2002) R196-R197
23. Maruyama K., and Sugano S. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138 (1994) 171-174
24. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
25. Okazaki Y., et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420 (2002) 563-573
26. Olson M.V., and Varki A. Sequencing the chimpanzee genome: insights into human evolution and disease. Nat. Rev. Genet. 4 (2003) 20-28
27. Osada N., et al. Substitution rate and structural divergence of 5'UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs. Mol. Biol. Evol. 22 (2005) 1976-1982
28. Ota T., and Nei M. Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site. Mol. Biol. Evol. 11 (1994) 613-619
29. Rice P., Longden I., and Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16 (2000) 276-277
30. Saitou N. Reconstruction of molecular phylogeny of extant hominoids from DNA sequence data. Am. J. Phys. Anthropol. 84 (1991) 75-85
31. Saitou N., and Ueda S. Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates. Mol. Biol. Evol. 11 (1994) 504-512
32. Sakate R., et al. Analysis of 5'-end sequences of chimpanzee cDNAs. Genome Res. 13 (2003) 1022-1026
33. Sham P.C., and Curtis D. Monte Carlo tests for associations between disease and alleles at highly polymorphic loci. Ann. Hum. Genet. 59 Pt 1 (1995) 97-105
34. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (2005) 69-87
35. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
36. Watanabe H., et al. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429 (2004) 382-388
37. Yunis J.J., Sawyer J.R., and Dunham K. The striking resemblance of high-resolution G-banded chromosomes of man and chimpanzee. Science 208 (1980) 1145-1148