Abstract
Sequences of the entire human genome reveal a relative richness in structure with repetitive elements, tandem repeats, inverted repeats, and palindrome structures. Focusing on structure, the evolution of X and Y chromosomes in primates is reviewed here, and the relationship between gene expression and gene structure on autosomes is explored. In a four-stratum scenario of mammalian sex chromosome evolution, a region of exceptionally low sequence divergence has been identified, and the reasons for this low sequence divergence are presented here. In addition, the construction of palindromes on the human Y chromosome is discussed in relationship to the emergence of genes in the male-specific region on the Y chromosome. Based on these observations, six of eight palindromes on the human Y chromosome are considered to have formed before the divergence of Old World monkeys and hominoids. The relationship between gene expression patterns and copy number variation illustrates the role of negative selection in the retention of high copy number to maintain the coordination of gene expression in a network of gene expression.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Abbreviations
- AMEL:
-
Amelogenin
- AMY1:
-
Amylase 1
- CD:
-
Chromodomain
- CMAH:
-
CMP-N-acetylneuraminic acid hydroxylase
- CNV:
-
Copy number variation
- CSP1:
-
Chimpanzee-specific palindrome 1
- DAZ:
-
Deleted in azoospermia
- ELN:
-
Tropoelastin
- HSAY:
-
Human (Homo sapiens) Y chromosome
- HSF:
-
Heat-shock transcription factor
- KAL:
-
Kallman syndrome
- LINEs:
-
Long interspersed elements
- MHC:
-
Major histocompatibility complex
- Myr:
-
Million years
- NWMs:
-
New World monkeys
- OWMs:
-
Old World monkeys
- PAR1:
-
Pseudo-autosomal region 1
- PTRY:
-
Chimpanzee (Pan troglodytes) Y chromosome
- RBM:
-
RNA-binding motif
- SINEs:
-
Short interspersed elements
- VC:
-
Variable charge
- XKR:
-
X Kell blood-related
References
Bailey JA, Yavor AM, Viggiano L et al (2002) Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. Am J Hum Genet 70:83–100
Bhowmick BK, Satta Y, Takahata N (2007) The origin and evolution of human ampliconic gene families and ampliconic structure. Genome Res 17:441–450
Blekhman R, Oshlack A, Gilad Y (2009) Segmental duplications contribute to gene expression differences between humans and chimpanzees. Genetics 182:627–630
Cheng Z, Ventura M, She X et al (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature (Lond) 437:88–93
Drummond-Borg M, Deeb SS, Motulsky AG (1989) Molecular patterns of X chromosome-linked color vision genes among 134 men of European ancestry. Proc Natl Acad Sci USA 86:983–987
Ebersberger I, Metzler D, Schwarz C et al (2002) Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet 70:1490–1497
Fu N, Drinnenberg I, Kelso J et al (2007) Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS One 2(2):e216
Groot PC, Mager WH, Frants RR (1991) Interpretation of polymorphic DNA patterns in the human alpha-amylase multigene family. Genomics 10:779–785
Hayakawa T, Satta Y, Gagneux P et al (2001) Alu-mediated inactivation of the human CMP-N-acetylneuraminic acid hydroxylase gene. Proc Natl Acad Sci USA 98:11399–11140
Hughes JF, Skaletsky H, Pyntikova T et al (2010) Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536–539
Iafrate AJ, Feuk L, Rivera MN et al (2004) Detection of large-scale variation in the human genome. Nat Genet 36:949–951
International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature (Lond) 409:860–921
Iwase M, Satta Y, Hirai Y et al (2003) The amelogenin loci span an ancient pseudoautosomal boundary in diverse mammalian species. Proc Natl Acad Sci USA 100:5258–5263
Iwase M, Satta Y, Hirai H et al (2010) Frequent gene conversion events between the X and Y homologous chromosomal regions in primates. BMC Evol Biol 10:225
Khaitovich P, Muetzel B, She X et al (2004) Regional patterns of gene expression in human and chimpanzee brains. Genome Res 14:1462–1473
Kuroda-Kawaguchi T, Skaletsky H, Brown LG et al (2001) The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men. Nat Genet 29(3):279–286
Kuroki Y, Toyoda A, Noguchi H et al (2006) Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat Genet 38:158–167
Lahn BT, Page DC (1999) Four evolutionary strata on the human X chromosome. Science 286:964–967
Lahn BT, Page DC (2000) A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. Hum Mol Genet 9:311–319
Li WH, Gu Z, Wang H et al (2001) Evolutionary analyses of the human genome. Nature (Lond) 409:847–849
Marques-Bonet T, Kidd JM, Ventura M et al (2009) A burst of segmental duplications in the genome of the African great ape ancestor. Nature (Lond) 457:877–881
Perry GH, Dominy NJ, Claw KG et al (2007) Diet and the evolution of human amylase gene copy number variation. Nat Genet 39:1256–1260
Ross MT, Grafham DV, Coffey AJ et al (2005) The DNA sequence of the human X chromosome. Nature (Lond) 434:325–337
Samonte RV, Eichler EE (2002) Segmental duplications and the evolution of the primate genome. Nat Rev Genet 3:65–72
Sawai H, Kawamoto Y, Takahata N et al (2004) Evolutionary relationships of major histocompatibility complex class I genes in simian primates. Genetics 166:1897–1907
Sinzelle L, Izsvák Z, Ivics Z (2009) Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cell Mol Life Sci 66:1073–1093
Skaletsky H, Kuroda-Kawaguchi T, Minx PJ et al (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature (Lond) 423:825–837
Szabó Z, Levi-Minzi SA, Christiano AM et al (1999) Sequential loss of two neighboring exons of the tropoelastin gene during primate evolution. J Mol Evol 49:664–671
Acknowledgments
The author thanks Drs. Mineyo Iwase and Hielim Kim for their help in the analysis and discussion. The findings presented here are from research supported in part by a grant (16107001) from the Japan Science Promotion Society (JSPS) and in part by a grant (17018032) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer
About this chapter
Cite this chapter
Satta, Y. (2012). Genome Structure and Primate Evolution. In: Hirai, H., Imai, H., Go, Y. (eds) Post-Genome Biology of Primates. Primatology Monographs. Springer, Tokyo. https://doi.org/10.1007/978-4-431-54011-3_10
Download citation
DOI: https://doi.org/10.1007/978-4-431-54011-3_10
Published:
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-54010-6
Online ISBN: 978-4-431-54011-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)