Human and Macaque Transcriptomes: A Comparison

Abstract

The initial deciphering of entire genomes from several mammalian species including human, chimpanzee and macaque has now been accomplished and the massive datasets are publicly available in the form of high‐quality draft sequences. As a direct result, the development and commercialization of an ever‐increasing number of sensitive tools to measure global gene expression (the ‘transcriptome’) is providing unique opportunities to evaluate and compare biological systems. One particularly important application is to use tissues derived from macaque models of toxicity and disease to infer responses in their human counterparts. Understanding the similarities and differences in how macaques and humans respond, at the functional genomic level, to perturbations in their environments has significant relevance in biomedical research.

Keywords: macaque; microarray; transcriptome; gene expression; genome

Figure 1.

Distribution of coding and noncoding sequence similarity between macaque and human. A histogram showing the degree of nucleotide sequence similarity between macaque and human for coding (dark bars) and noncoding (3′ UTR, light bars) transcribed sequence. Sequences (n=1180) were selected that cross a well‐defined stop codon and that provide concurrent sampling of 150 bp of sequence both proximal and distal to the stop. The best human match for each macaque sequence was identified using MEGABLAST. The high‐quality subset of these data (composed only of contiguous stretches of phred Q⩾20 bp, n=633) is plotted for both coding (squares) and noncoding (diamonds) sequence. Reproduced from Magness et al..

Figure 2.

Principal component analysis of primate whole blood tissue gene expression profiles. Gene expression levels for 54 000 probe pairs (representing 38 500 genes) were uploaded to Partek Pro 6.0 and analysed by principal component analysis (PCA). The GeneChip Operating System (GCOS) normalization algorithm (A, B) and the robust multiarray averaging (RMA) normalization algorithm (C, D) are shown for comparison. The ellipsoids (B, D) represent a two‐standard deviation space from the mean of each sample set. The axes correspond to principal component 1 (PC1, x‐axis), PC2 (y‐axis) and PC3 (z‐axis). Reproduced by permission of Dillman and Phillips .

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References

Bigger CB, Brasky KM and Lanford RE (2001) DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection. Journal of Virology 75: 7059–7066.

Byrne JA, Mitalipov SM, Clepper L and Wolf DP (2006) Transcriptional profiling of rhesus monkey embryonic stem cells. Biology of Reproduction 75: 908–915.

Carninci P (2006) Tagging mammalian transcription complexity. Trends in Genetics 22: 501–510.

Carninci P (2007) Constructing the landscape of the mammalian transcriptome. Journal of Experimental Biology 210: 1497–1506.

Carninci P, Kasukawa T, Katayama S et al. (2005) The transcriptional landscape of the mammalian genome. Science 309: 1559–1563.

Carninci P, Waki K, Shiraki T et al. (2003) Targeting a complex transcriptome: the construction of the mouse full‐length cDNA encyclopedia. Genome Research 13: 1273–1289.

Cheng J, Kapranov P, Drenkow J et al. (2005) Transcriptional maps of 10 human chromosomes at 5‐nucleotide resolution. Science 308: 1149–1154.

Chismar JD, Mondala T, Fox HS et al. (2002) Analysis of result variability from high‐density oligonucleotide arrays comparing same‐species and cross‐species hybridizations. Biotechniques 33: 516–522.

Costello CM, Mah N, Hasler R et al. (2005) Dissection of the inflammatory bowel disease transcriptome using genome‐wide cDNA microarrays. PLoS Medicine 2: e199.

Dillman III JF and Phillips CS (2005) Comparison of non‐human primate and human whole blood tissue gene expression profiles. Toxicological Sciences 87: 306–314.

Dukelow WR (1997) Ovulatory cycle characteristics in Macaca fascicularis. Journal of Medical Primatology 6: 33–42.

Fox KE and Harel D (2007) Beyond the gene. PLoS ONE 2: e1231.

Gibbs RA, Rogers J, Katze MG et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222–234.

Gingeras TR (2007) Origin of phenotypes: genes and transcripts. Genome Research 17: 682–690.

Gnatenko DV, Dunn JJ, McCorkle SR et al. (2003) Transcript profiling of human platelets using microarray and serial analysis of gene expression. Blood 101: 2285–2293.

Green KL, Szeliga KT, Bowen CA et al. (1999) Comparison of ethanol metabolism in male and female cynomolgus macaques (Macaca fascicularis). Alcohol Clinical and Experimental Research 23: 611–616.

Hacia JG, Makalowski W, Edgemon K et al. (1998) Evolutionary sequence comparisons using high‐density oligonucleotide arrays. Nature Genetics 18: 155–158.

Iizuka N, Oka M, Yamada‐Okabe H et al. (2003) Differential gene expression in distinct virologic types of hepatocellular carcinoma: association with liver cirrhosis. Oncogene 22: 3007–3014.

International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.

Jacquelin B, Mayau V, Brysbaert G et al. (2007) Long oligonucleotide microarrays for African green monkey gene expression profile analysis. FASEB Journal 21: 1–10.

Kampa D, Cheng J, Kapranov P et al. (2004) Novel RNAs identified from an in‐depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research 14: 331–342.

Kim VN (2006) Small RNAs just got bigger: piwi‐interacting RNAs (piRNAs) in mammalian testes. Genes & Development 20: 1993–1997.

Kocabas AM, Crosby J, Ross PJ et al. (2006) The transcriptome of human oocytes. Proceedings of the National Academy of Sciences of the USA 103: 14027–14032.

Liu SM, Xavier R, Good KL et al. (2006) Immune cell transcriptome datasets reveal novel leukocyte subset‐specific genes and genes associated with allergic processes. Journal of Allergy and Clinical Immunology 118: 496–503.

Lu C, Tej SS, Luo S et al. (2005) Elucidation of the small RNA component of the transcriptome. Science 309: 1567–1569.

Magness CL, Fellin PC, Thomas MJ et al. (2005) Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human. Genome Biology 6: R60.

Marvanová M, Ménager J, Bezard E et al. (2003) Microarray analysis of nonhuman primates: validation of experimental models in neurological disorders. FASEB Journal 17: 929–931.

Mineno J, Okamoto S, Ando T et al. (2006) The expression profile of microRNAs in mouse embryos. Nucleic Acids Research 34: 1765–1771.

Pennisi E (2001) The human genome. Science 291: 1177–1180.

Schena M, Shalon D, Davis RW and Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470.

Shi L, Reid LH, Jones WD et al. (2006) The MicroArray Quality Control (MAQC) project shows inter‐ and intraplatform reproducibility of gene expression measurements. Nature Biotechnology 24: 1151–1161.

Slatter JG, Templeton IE, Castle JC et al. (2006) Compendium of gene expression profiles comprising a baseline model of the human liver drug metabolism transcriptome. Xenobiotica 36: 938–962.

Spindel ER, Pauley MA, Jia Y et al. (2005) Leveraging human genomic information to identify nonhuman primate sequences for expression array development. BioMed Central Genomics 6: 1–8.

The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799–816.

Vahey MT, Nau ME, Taubman M et al. (2003) Patterns of gene expression in peripheral blood mononuclear cells of rhesus macaques infected with SIVmac251 and exhibiting differential rates of disease progression. AIDS Research and Human Retroviruses 19: 369–387.

Venter JC, Adams MD, Myers EW et al. (2001) The sequence of the human genome. Science 291: 1304–1351.

Walker J and Rigley K (2000) Gene expression profiling in human peripheral blood mononuclear cells using high‐density filter‐based cDNA microarrays. Journal of Immunological Methods 239: 167–179.

Walker SJ, Wang Y, Grant KA et al. (2006) Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates. Journal of Neuroscience Methods 152: 179–189.

Wallace JC, Korth MJ, Paeper B et al. (2007) High‐density rhesus macaque oligonucleotide microarray design using early stage rhesus genome sequence information and human genome annotations. BioMed Central Genomics 8: 1–10.

Whitney AR, Diehn M, Popper SJ et al. (2003) Individuality and variation in gene expression patterns in human blood. Proceedings of the National Academy of Sciences of the USA 100: 1896–1901.

Ylostalo J, Randall AC, Myers TA et al. (2005) Transcriptome profiles of host gene expression in a monkey model of human malaria. Journal of Infectious Diseases 191: 400–409.

Zou J, Young S, Zhu F et al. (2002) Microarray profile of differentially expressed genes in a monkey model of allergic asthma. Genome Biology 3: 1–13.

Further Reading

Brett D, Pospisil H, Valcarcel J et al. (2002) Alternative splicing and genome complexity. Nature Genetics 30: 29–30.

Caceres M, Lachuer J, Zapala MA et al. (2003) Elevated gene expression levels distinguish human from non‐human primate brains. Proceedings of the National Academy of Sciences of the USA 100: 13030–13035.

Enard W, Khaitovich P, Klose J et al. (2002) Intra‐ and interspecific variation in primate gene expression patterns. Science 296: 340–343.

Khaitovich P, Weiss G, Lachmann M et al. (2004) A neutral model of transcriptome evolution. PLoS Biology 2: E132.

Osada N, Hirata M, Tanuma R et al. (2005) Substitution rate and structural divergence of 5′UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs. Molecular Biology and Evolution 22: 1976–1982.

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Walker, Stephen J(Jul 2008) Human and Macaque Transcriptomes: A Comparison. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020771]