Dynamic evolution of endogenous retrovirus-derived genes expressed in bovine conceptuses during the period of placentation

Genome Biology and Evolution

Volumn 5, Issue 2, 2013, Pages 296-306

  Nakagawa, So ^a,b   Bai, Hanako ^c   Sakurai, Toshihiro ^c   Nakaya, Yuki ^d   Konno, Toshihiro ^c   Miyazawa, Takayuki ^d   Gojobori, Takashi ^a   Imakawa, Kazuhiko ^c  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b HARVARD UNIVERSITY   (United States)

^c UNIVERSITY OF TOKYO   (Japan)

^d KYOTO UNIVERSITY   (Japan)

Author keywords

Cow; Endogenous retrovirus; Envelope; RNA seq; Syncytin

Indexed keywords

BOVINAE; CANIS FAMILIARIS; EUTHERIA; MAMMALIA;

EID: 84876580989     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt007     Document Type: Article

References (54)

1. Andersson AC, et al. 2002. Developmental expression of HERV-R (ERV3) and HERV-K in human tissue. Virology 297:220-225.
2. Ashton-Beaucage D, et al. 2010. The exon junction complex controls the splicing of MAPK and other long intron-containing transcripts in Drosophila. Cell 143:251-262.
3. Baba K, et al. 2011. Identification of novel endogenous betaretroviruses which are transcribed in the bovine placenta. J Virol. 85:1237-1245.
4. Bachellerie JP, Cavaillé J, Hüttenhofer A. 2002. The expanding snoRNA world. Biochimie 84:775-790.
5. Bazer FW, Spencer TE, Johnson GA, Burghardt RC, Wu G. 2009. Comparative aspects of implantation. Reproduction 138:195-209.
6. Bé nit L, Dessen P, Heidmann T. 2001. Identification, phylogeny, and evolution of retroviral elements based on their envelope genes. J Virol. 75: 11709-11719.
7. Bovine Genome Sequencing and Analysis Consortium. 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522-528.
8. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973.
9. Chan PP, Lowe TM. 2009. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37:D93-D97.
10. Chang C, Chen PT, Chang GD, Huang CJ, Chen H. 2004. Functional characterization of the placental fusogenic membrane protein syncytin. Biol Reprod. 71:1956-1962.
11. Cornelis G, et al. 2012. Ancestral capture of syncytin-Car1, a fusogenic endogenous retroviral envelope gene involved in placentation and conserved in Carnivora. Proc Natl Acad Sci U S A. 109: E432-E441.
12. Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164-1165.
13. Dupressoir A, et al. 2005. Syncytin-A and syncytin-B, two fusogenic placenta-specific murine envelope genes of retroviral origin conserved in Muridae. Proc Natl Acad Sci U S A. 102:725-730.
14. Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol. 7: e1002195.
15. Edwards CA, et al. 2008. The evolution of the DLK1-DIO3 imprinted domain in mammals. PLoS Biol. 6:e135.
16. Esnault C, et al. 2008. A placenta-specific receptor for the fusogenic, endogenous retrovirus-derived, human syncytin-2. Proc Natl Acad Sci U S A. 105:17532-17537.
17. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
18. Finn RD, et al. 2010. The Pfam protein families database. Nucleic Acids Res. 38:D211-D222.
19. Goujon M, et al. 2010. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res. 38:W695-W699.
20. Harris JR. 1998. Placental endogenous retrovirus (ERV): structural, functional, and evolutionary significance. Bioessays 20:307-316.
21. Heidmann O, Vernochet C, Dupressoir A, Heidmann T. 2009. Identification of an endogenous retroviral envelope gene with fusogenic activity and placenta-specific expression in the rabbit: a new "syncytin" in a third order of mammals. Retrovirology 6:107.
22. Ideta A, Urakawa M, Aoyagi Y, Saeki K. 2007. Early development in utero of bovine nuclear transfer embryosusing early G1 and G0 phase cells. Cloning Stem Cells 9:571-580.
23. InternationalHuman Genome SequencingConsortium. 2004. Finishing the euchromatic sequence of the human genome. Nature 431:931-945.
24. Kaminuma E, et al. 2010. DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res. 38:D33-D38.
25. Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
26. Kim J, et al. 2012. Transcriptome landscape of the human placenta. BMC Genomics 13:115.
27. Kiss T. 2001. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 20:3617-3622.
28. Kiss T. 2002. Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109:145-148.
29. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 305:567-580.
30. Krysan DJ, Rockwell NC, Fuller RS. 1999. Quantitative characterization of furin specificity. Energetics of substrate discrimination using an internally consistent set of hexapeptidyl methylcoumarinamides. J Biol Chem. 274:23229-23234.
31. Kudaka W, Oda T, Jinno Y, Yoshimi N, Aoki Y. 2008. Cellular localization of placenta-specific human endogenous retrovirus (HERV) transcripts and their possible implication in pregnancy-induced hypertension. Placenta 29:282-289.
32. Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320.
33. Li F, Nellâker C, Yolken RH, Karlsson H. 2011. A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation. BMC Genomics 12:22.
34. Mi S, et al. 2000. Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 403:785-789.
35. Mortazavi A,Williams BA, McCue K, Schaeffer L,Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods. 5:621-628.
36. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
37. Nagaoka K, et al. 2003. Regulation of blastocyst migration, apposition, and initial adhesion by a chemokine, interferon gamma-inducible protein 10 kDa (IP-10), during early gestation. J Biol Chem. 278: 29048-29056.
38. Ng VL, Wood TG, Arlinghaus RB. 1982. Processing of the env gene products of Moloney murine leukaemia virus. J Gen Virol. 59:329-343.
39. Ono R, et al. 2001. A retrotransposon-derived gene, PEG10, is a novel imprinted gene located on human chromosome 7q21. Genomics 73: 232-237.
40. Ono R, et al. 2006. Deletion of Peg10, an imprinted gene acquired from a retrotransposon, causes early embryonic lethality. Nat Genet. 38: 101-106.
41. Palmarini M, Mura M, Spencer TE. 2004. Endogenous betaretroviruses of sheep: teaching new lessons in retroviral interference and adaptation. J Gen Virol. 85:1-13.
42. Rawn SM, Cross JC. 2008. The evolution, regulation, and function of placenta-specific genes. Annu Rev Cell Dev Biol. 24:159-181.
43. Sagata N, Yasunaga T, Ogawa Y, Tsuzuku-Kawamura J, Ikawa Y. 1984. Bovine leukemia virus: unique structural features of its long terminal repeats and its evolutionary relationship to human T-cell leukemia virus. Proc Natl Acad Sci U S A. 81:4741-4745.
44. Sakurai T, et al. 2009. Induction of endogenous interferon tau gene transcription by CDX2 and high acetylation in bovine nontrophoblast cells. Biol Reprod. 80:1223-1231.
45. Schuster SC. 2008. Next-generation sequencing transforms today's biology. Nat Methods. 5:16-18.
46. Sekita Y, et al. 2008. Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta. Nat Genet. 40: 243-248.
47. Shankar K, et al. 2012. RNA-seq analysis of the functional compartments within the rat placentation site. Endocrinology 153: 1999-2011.
48. Sperber GO, Airola T, Jern P, Blomberg J. 2007. Automated recognition of retroviral sequences in genomic data-RetroTector. Nucleic Acids Res. 35:4964-4976.
49. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
50. Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 57:758-771.
51. Suzuki S, et al. 2007. Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet. 3:e55.
52. Weiss RA. 2006. The discovery of endogenous retroviruses. Retrovirology 3:67.
53. Wildman DE, et al. 2006. Evolution of the mammalian placenta revealed by phylogenetic analysis. Proc Natl Acad Sci U S A. 103: 3203-3208.
54. Yoshioka K, et al. 2000. Determination of genes involved in the process of implantation: application of GeneChip to scan 6500 genes. Biochem Biophys Res Commun. 272:531-538.