Global discovery of primate-specific genes in the human genome (Proceedings of the National Academy of Sciences of the United States of America (2009) 106, 29, (12019-12024) DOI: 10.1073/pnas.0904569106);Global discovery of primate-specific genes in the human genome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 29, 2009, Pages 12019-12024

  Tay, Sen Kwan ^a,c   Blythe, Jason ^b   Lipovich, Leonard ^a,b  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

EST; Gene birth; Genomics; Reproduction

Indexed keywords

GENE PRODUCT; TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; DNA SEQUENCE; EXON; EXPRESSED SEQUENCE TAG; GENE DUPLICATION; GENE INSERTION; GENE SEQUENCE; HUMAN; HUMAN GENOME; MICROARRAY ANALYSIS; NONHUMAN; PHENOTYPE; PRIMATE; PRIORITY JOURNAL; REPRODUCTION; SPECIES DIFFERENTIATION; TELOMERE;

PRIMATES;

EID: 67749145754     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0907913106     Document Type: Erratum

References (47)

1. Varki A, Altheide TK (2005) Comparing the human and chimpanzee genomes: Searching for needles in a haystack. Genome Res 15:1746-1758.
2. Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87.
3. Rhesus Macaque Genome Sequencing and Analysis Consortium (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-234.
4. King M, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188:107-116.
5. Kehrer-Sawatzki H, Cooper DN (2006) Understanding the recent evolution of the human genome: Insights from human-chimpanzee genome comparisons. Hum Mutat 28:99-130.
6. Olson M, Varki A (2003) Sequencing the chimpanzee genome: Insights into human evolution and disease. Nat Rev Genet 1:20-28.
7. Nahon J (2003) Birth of 'human-specific' genes during primate evolution. Genetica 118:193-208.
8. Johnson R, et al. (2009) Regulation of neural macroRNAs by the transcriptional repressor REST. RNA 15:85-96.
9. Frith M, Pheasant M, Mattick JS (2005) The amazing complexity of the human transcriptome. Eur J Hum Genet 13:894-897.
10. Pang K, Frith MC, Mattick JS (2006) Rapid evolution of noncoding RNAs: Lack of conservation does not mean lack of function. Trends Genet 22:1-5.
11. Kent W (2002) BLAT - The BLAST-like alignment tool. Genome Res 12:656-664.
12. Schwartz S, et al. (2003) Human-mouse alignments with BLASTZ. Genome Res 13:103-107.
13. Schmieder S, et al. (2008) Primate-specific spliced PMCHL RNAs are non-protein coding in human and macaque tissues. BMC Evol Biol. 8:330.
14. Turner L, Hoekstra HE (2008) Causes and consequences of the evolution of reproductive proteins. Int J Dev Biol 52:769-780.
15. Levinson B, Kenwrick S, Lakich D, Hammonds G, Jr, Gitschier J (1990) A transcribed gene in an intron of the human factor VIII gene. Genomics 7:1-11.
16. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945.
17. Yu P, Ma D, Xu M (2005) Nested genes in the human genome. Genomics 86:414-422.
18. Bailey J, Yavor AM, Viggiano L, Misceo D, Horvath JE (2002) Human-specific duplication and mosaic transcripts: Recent paralogous structure of chromosome 22. Am J Hum Genet 70:83-100.
19. Mills R, Bennet A, Iskow RC, Devine SE (2007) Which transposable elements are active in the human genome? Trends Genet 23:183-191.
20. Makalowski W, Mitchell GA, Labuda, D (1994) Alu sequences in the coding regions of mRNA: A source of protein variability. Trends Genet 10:188-193.
21. Nekrutenko A, Li WH (2001) Transposable elements are found in a large number of human protein-coding genes. Trends Genet 17:619-621.
22. Sorek R, Ast G, Graur D (2002) Alu-containing exons are alternatively spliced. Genome Res 12:1060-1067.
23. Pannetier M, Renault L, Jolivet G, Cotinot C, Pailhoux E (2005) Ovarian-specific expression of a new gene regulated by the goat PIS region and transcribed by a FOXL2 bidirectional promoter. Genomics 85:715-726.
24. Dai H, et al. (2008) The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proc Natl Acad Sci USA 105:7478-7483.
25. Platts A, Dix DJ, Chemes HE, Thompson KE (2007) Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs. Hum Mol Genet 16:763-773.
26. Repping S, et al. (2006) High mutation rates have driven extensive structural polymorphism amony human Y chromosomes. Nat Genet 38:463-467.
27. Delbridge M, Graves JA (1999) Mammalian Y chromosome evolution and the male-specific functions of Y chromosome-borne genes. Rev Reprod 4:101-109.
28. Wu Q, Tommerup N, Ming Wang S, Hansen L (2006) A novel primate specific gene, CEI, is located in the homeobox gene IRXA2 promoter in Homo sapiens. Gene 371:167-173.
29. Takamatsu K, et al. (2002) Identification of two novel primate-specific genes in DSCR. DNA Res 9:89-97.
30. Marques A, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H (2005) Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 3:1970-1979.
31. Koonin E (2006) The origin of introns and their role in eukaryogenesis: A compromise solution to the introns-early versus introns-late debate? Bio Direct 1:22.
32. Pollard K, et al. (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genet 2:1599-1611.
33. Yang S, et al. (2008) Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. PLoS Genet 4:e3.
34. Bannert N, Kurth R (2004) Retro elements and the human genome: New perspectives on an old relation. PNAS 101:14572-14579.
35. Wang T, et al. (2007) Species-specific endogenous retroviruses shape the trancriptional network of human tumor suppressor protein p53. PNAS 104:18613-18618.
36. Brosius J, Gould SJ (1992) On "genomenclature": A comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". Proc Natl Acad Sci USA 89:10706-10710.
37. Long M, Betrán E, Thornton K, Wang W (2003) The origin of new genes: Glimpses from the young and old. Nat Rev Genet 4:865-875.
38. Emerson J, Kaessmann H, Betrán E, Long M (2004) Extensive gene traffic on the mammalian X chromosome. Science 303:537-540.
39. Vibranovski M, Zhang Y, Long M (2009) Out of the X chromosomal gene movement in the Drosophila genus. Genome Res 19:897-903.
40. Turner L, Hoekstra HE (2006) Adaptive evolution of fertilization proteins within a genus: Variation in ZP2 and ZP3 in deer mice (Peromyscus). Mol Biol Evol 23:1656-1669.
41. Lanz R, McKenna NJ, Onate SA, Albrecht U, Wong J (1999) A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 97:17-27.
42. Willingham A, et al. (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309:1570-1573.
43. Zhou Y, et al. (2007) Activation of p53 by MEG3 non-coding RNA. J Biol Chem 282:24731-24742.
44. Guttman M, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-227.
45. Toll-Riera M, et al. (2008) Origin of primate orphan genes: A comparative genomics approach. Mol Biol Evol 26:603-612.
46. 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.
47. Pollard K, et al. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443:167-172.