Retrotransposons and regulatory suites

BioEssays

Volumn 27, Issue 2, 2005, Pages 122-125

  Shapiro, James A ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

AMINO ACID SEQUENCE; ANIMAL CELL; BLASTOCYST; CELL DIFFERENTIATION; CELL MATURATION; DNA LIBRARY; EMBRYO; EXON; GENE LOCUS; MOUSE; NONHUMAN; OOCYTE; PREIMPLANTATION EMBRYO; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MOTIF; RETROPOSON; REVIEW;

ANIMALS; BLASTOCYST; CELL DIFFERENTIATION; DNA, COMPLEMENTARY; EXONS; GENE EXPRESSION REGULATION; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE LIBRARY; GENOME; MODELS, GENETIC; OOCYTES; RETROELEMENTS; RNA;

EID: 14344252402     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20192     Document Type: Review

References (32)

1. Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, et al. 2004. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell 7:597-606.
2. International Human Genome Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
3. McClintock B. 1987. Discovery And Characterization of Transposable Elements: The Collected Papers of Barbara McClintock. New York: Garland Press.
4. Smit AF. 1993. Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic Acids Res 21:1863-1872.
5. Brosius J. 1999. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115-134.
6. Schramke V, Allshire R. 2003. Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301:1069-1074.
7. Britten RJ. 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205:177-182.
8. Jordan IK, Rogozin IB, Glazko GV, Koonin EV. 2003. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet 19:68-72.
9. Shapiro JA, Sternberg Rv. 2004. Why repetitive DNA is essential to genome function. Biol Revs 80: In press.
10. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471-476.
11. Han JS, Szak ST, Boeke JD. 2004. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429:268-274.
12. Keeton EK, Fletcher TM, Baumann CT, Hager GL, Smith CL 2002. Glucocorticoid receptor domain requirements for chromatin remodeling and transcriptional activation of the mouse mammary tumor virus promoter in different nucleoprotein contexts. J Biol Chem 277:28247-28255.
13. Gerasimova TI, Byrd K, Corces VG. 2000. A chromatin insulator determines the nuclear localization of DNA. Mol Cell 6:1025-1035.
14. Wyrick JJ, Aparicio JG, Chen T, Barnett JD, Jennings EG, et al. 2001. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: High-resolution mapping of replication origins. Science 14:2357-2360.
15. Shapiro JA. 1999. Genome system architecture and natural genetic engineering in evolution. In: Caporale L, editor. Molecular Strategies for Biological Evolution. Ann NY: Acad Sci 870:23-35.
16. Shapiro JA. 2002. Genome Organization and Reorganization in Evolution: Formatting for Computation and Function. In: Speybroeck LV, de Vijver GV, de Waele D, editors. From Epigenesis to Epigenetics: The Genome in Context. Ann NY: Acad Sci 981:111-134.
17. Shapiro JA. 1984. Observations on the formation of clones containing araB-lacZ cistron fusions. Molec Gen Genet 194:79-90.
18. Shapiro JA. 1997. Genome organization, natural genetic engineering, and adaptive mutation. Trends Genet 13:98-104.
19. Hall BG. 1988. Adaptive evolution that requires multiple spontaneous mutations. I. Mutations involving an insertion sequence. Genetics 120: 887-897.
20. Ilves H, Horak R, Kivisaar M. 2001. Involvement of sigma(S) in starvation-induced transposition of Pseudomonas putida transposon Tn4652. J Bacteriol 183:5445-5448.
21. Wessler SR. 1996. Turned on by stress: Plant retrotransposons. Curr Biol 6:959-961.
22. Bregliano JC, Kidwell M. 1983. Hybrid Dysgenesis. In: Shapiro JA, editor. Mobile Genetic Elements. NY: Academic Press; pp. 363-410.
23. O'Neill RJ, O'Neill MJ, Graves JA. 1998. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 393:68-72.
24. Vrana PB, Fossella JA, Matteson PG, O'Neill MJ, Tilghman SM. 2000. Genetic and Epigenetic Incompatibilities Underlie Hybrid Dysgenesis in Peromyscus. Nature Genet 25:120-124.
25. Hama C, Ali Z, Kornberg TB. 1990. Region-specific recombination and expression are directed by portions of the Drosophila engrailed promoter. Genes Dev 4:1079-1093.
26. Kassis JA, Noll E, Vansickle EP, Odenwald WF, Perrimon N. 1992. Altering the insertional specificity of a Drosophila transposable element. Proc Nat Acad Sci USA 89:1919-1923.
27. Fauvarque MO, Dura JM. 1993. Polyhomeotic regulatory sequences induce developmental regulator-dependent variegation and targeted P-element insertions in Drosophila. Genes Dev 7:1508-1520.
28. Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. 1998. Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence. Genome Res 8:464-478.
29. Wu X, Li Y, Crise B, Burgess SM. 2003. Transcription start regions in the human genome are favored targets for MLV integration. Science 300: 1749-1751.
30. Mitchell RS, Beitzel BF, Schroder ARW, Shinn P, Chen H, et al. 2004. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol 2:e234.
31. Kirchner J, Connolly CM, Sandmeyer SB. 1995. Requirement of RNA polymerase III transcription factors for in vitro position-specific integration of a retroviruslike element. Science 267:1488-1491.
32. Xie W, Gai X, Zhu Y, Zappulla DC, Sternglanz R, et al. 2001. Targeting of the yeast TyS retrotransposon to silent chromatin is mediated by interactions between integrase and Sir4p. Molec Cell Biol 21:6606-6614.