The Y chromosome as a target for acquired and amplified genetic material in evolution

BioEssays

Volumn 27, Issue 12, 2005, Pages 1256-1262

  Gvozdev, Vladimir A ^a   Kogan, Galina L ^a   Usakin, Lev A ^a  

^a INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

COMPARATIVE STUDY; DROSOPHILA; DROSOPHILA MELANOGASTER; EVOLUTION; GENE; GENE AMPLIFICATION; GENE SILENCING; GENE TARGETING; HUMAN; MAMMAL; NONHUMAN; REVIEW; TRANSPOSON; X CHROMOSOME; Y CHROMOSOME;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE AMPLIFICATION; GENOME; HUMANS; X CHROMOSOME; Y CHROMOSOME;

DROSOPHILA MELANOGASTER; MAMMALIA;

EID: 30444442109     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20321     Document Type: Review

References (70)

1. Charlesworth B. 1996. The evolution of chromosomal sex determination and dosage compensation. Curr Biol 6:149-162.
2. Rice WR. 1987. Genetic hitch-hiking and the evolution of reduced genetic activity of the Y sex chromosome. Genetics 116:161-167.
3. Skaletsky H, Kugoda-Kawaguchl T, Minx PJ, Cordum HS, Hillier L, et al. 2003. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423:825-837.
4. Charlesworth B, Chrlesworth D. 2000. The degeneration of Y chromosomes. Phil Trans Roy Soc Lond B 355:1563-1572.
5. Orr HA, Kim Y. 1998. An adaptive hypothesis for the evolution of the Y chromosome. Genetics 150:1693-1698.
6. Lahn BT, Pearson NM, Jegalian K. 2001. The human Y chromosome in the light of evolution. Nat Rev Genet 2:207-216.
7. Charlesworth D, Charlesworth B, Martin G. 2005. Steps in the evolution of heteromorphic sex chromosomes. Heredity 95:118-128.
8. Carvalho AB, Dobo BA, Vibranovski MD, Clark AG. 2001. Identification of five new genes on the Y chromosome of Drosophila melanogaster. Proc Natl Acad Sci USA 98:13225-13230.
9. Charlesworth B, Sniegowski P, Stephan W. 1994. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215-220.
10. Britten RY, Davidson EH. 1969. Gene regulation for higher cells: a theory. Science 165:349-357.
11. Allen TA, von Kaenel S, Goudrich JA, Kugek JF. 2004. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Biol 11:816-821.
12. Espinoza CA, Allen TA, Hieb A, Kugel JF, Goorich JA. 2004. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Molec Biol 11:822-829.
13. Mattick JS. 2003. Challenging the dogva: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25:930-939.
14. Eissenberg JC, Hilliker AJ. 2000. Versality of conviction: heterochromatin as both repressor and an activator of transcription. Genetica 109:19-24.
15. Biggs WH, Zavitz KH, Dickson B, Van Der Strafen A, Brunner D, Hafen E, Zipursky SL. 1994. The Drosophila rolled locus encodes a MAP kinase required in the sevenless signal transduction pathway. EMBO J 13:1628-1635.
16. Tulin A, Spradling A. 2003. Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Science 299:528-529.
17. Dimitri P, Corradini N, Rossi F, Verni F. 2004. The paradox of functional heterochromatin. BioEssays 27:29-41.
18. Allshire R. Molecular biology. 2002. RNAi and heterochromatin-a hushed-up affair. Science 297:1818-1819.
19. Schramke V, Allshire R. 2004. These interfering little RNAs! Silencing and eliminating chromatin. Curr Opin Genet Dev 14:174-180.
20. Rice WR. 1994. Degeneration of a nonrecombining chromosome. Science 263:230-232.
21. Graves JAM. 2002. The rice and fall of SRY. Trends Genet 18:259-264.
22. Hackstein JHP, Hochstenbach R, Hauschteck-Jugen E, Beukeboom LW. 1996. Is the Y chromosome of Drosophila an evolved supernumerary chromosome? BioEssays 18:317-323.
23. Saxena R, Brown LG, Hawkins T, Alagapan RK, Skaletsky E, et al. 1996. The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned. Nat Genet 14:292-299.
24. Kogan GL, Epstein VN, Aravin AA, Gvozdev VA. 2000. Molecular evolution of two paralogous tandemly repeated heterochromatic gene clusters linked to the X and Y chromosomes of Drosophila melanogaster. Mol Biol Evol 17:697-702.
25. Carvalho AB, Lazzaro BP, Clark AG. 2000. Y chromosomal fertility factors kl-2 and kl-3 of Drosophila melanogaster encode dynein heavy chain polypeptides. Proc Natl Acad Sci USA 24:13239-13244.
26. Aravin AA, Naumova NM, Tulin AV, Rosovsky YM, Gvozdev VA. 2001. Double stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in Drosophila melanogaster germline. Current Biology 11:1017-1027.
27. Carvalho AB, Clark AG. 2005. Y chromosome of D. pseudoobscura is not homologous to the ancestral Drosophila Y. Science 307:108-110.
28. Balakirev ES, Ayala FJ. 2003. Pseudogenes: are they "junk" or functional DNA? Annu Rev Genet 37:123-151.
29. Lee JT. 2003. Complicity of gene and pseudogene. Nature 423:26-28.
30. Kuff EL, Fewell JE, Lueders KK, DiPaolo JA, Amsbaugh SC, Popescu C. 1986. Chromosome distribution of intracisternal A-particle sequences in the Syrian hamster and mouse. Chromosoma 93:213-219.
31. Wichman HA, Van Den Bussche RA, Hamilton JJ, Baker RJ. 1992. Transposable elements and the evolution of genome organization in mammals. Genetica 86:287-294.
32. Steinemann M, Steinemann S. 1990. Evolutionary changes in the organization of the major LCP gene cluster during sex chromosomal differentiation in the sibling species Drosophila persimilis, Drosophila pseudoobscura and Drosophila miranda. Chromosoma 99:424-431.
33. Steinemann M, Steinemann S. 1997. The enigma of Y chromosome degeneration: TRAM, a novel retrotransposon is preferentially located on the neo-Y chromosome of Drosophila miranda. Genetics 145:261-266.
34. Bachtrog D. 2003. Accomulation of spack and werf, two novel non-LTR retrotransposons on the neo-Y chromosome of Drosophila miranda. Mol Biol Evol 20:173-181.
35. Steinemann S, Steinemann M. 2001. Biased distribution of repetitive elements: a landmark for neo-Y chromosome evolution in Drosophila miranda. Cytogenet Cell Genet 93:228-233.
36. Bachtrog D. 2003. Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila. Nat Genet 34:215-219.
37. Krzywinsky J, Nusskern DR, Kern MK, Besansky NJ. 2004. Isolation and characterization of Y chromosome sequences from the African malaria mosquito Anopheles gambiae. Genetics 166:1291-1302.
38. Pimpinelli S, Berloco M, Fanti L, Dimitri P, Bonaccorsi S, et al. 1995. Transposable elements are stable structural components of Drosophila melanogaster heterochromatin. Proc Natl Acad Sci USA 92:3804-3808.
39. Pardue ML, Danilevskaya ON, Lowenhaupt K, Slot F, Traverse KL. 1996. Drosophila telomeres: new views on chromosome evolution. Trends Genet 12:48-52.
40. Junakovic N, Fortunati D, Berloco M, Fanti L, Pimpinelli S. 2003. The subset of the elements of the 1731 retrotransposon family are preferentially located in regions of the Y chromosome that are polytenized in larval salivary glands of Drosophila melanogaster. Genetica 117:303-310.
41. Kalmykova AI, Kwon DA, Rozovsky YM, Hueber N, Capy P. 2004. Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes. Mol Biol Evol 21:2281-2289.
42. Yasuhara JC, Decrease CH, Wakimoto BT. 2005. Evolution of heterochromatic genes of Drosophila. Proc Natl Acad Sci 102:10958-10963.
43. Lahn BT, Page DC. 1997. Functional coherence of the human Y chromosome. Science 278:675-679.
44. Reijo R, Lee TY, Sako P. 1995. Diverse spermatogenic defects in humans caused by Y chromosome deletions encompassing a novel RNA binding gene. Nat Genet 10:383-395.
45. Kalmykova AI, Shevelyov YY, Dobritsa AA, Gvozdev VA. 1997. Acquisition and amplification of a testis-expressed autosomal gene, SSL. by the Drosophila Y chromosome. Proc Natl Acad Sci USA 94:6927-6302.
46. Lahn BT, Page DC. 1999. Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome. Nature Genet 21:429-433.
47. Matsunaga S, Isono E, Kejnovsky E, Vyskot B, Dolezel J, et al. 2003. Duplicative transfer of a MADS box gene to a plant Y chromosome. Mol Biol Evol 20:1062-1069.
48. Betran E, Thornton K, Long M. 2002. Retroposed new genes out of the X in Drosophila. Genome Research 12:1854-1859.
49. Long M, Betran E, Thornton K, Wang W. 2003. The origin of new genes: glimpses from the young and old. Nature Rev Genet 4:865-875.
50. Rozen S, Skaletsky H, Marszalek JD, Minx PJ, Cordum HS. 2003. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423:873-876.
51. Balakireva MD, Shevelev YY, Nurminsky DI, Livak KJ, Gvozdev VA. 1992. Structural organization and diversification of Y-linked sequences comprising Su(Ste) gene in Drosophila melanogaster. Nucleic Acids Res 20:3731-3736.
52. Carvalho AB. 2002. Origin and evolution of the Drosophila Y chromosome. Curr Opin Gen Devel 12:664-668.
53. Reugels AM, Kurek R, Lammermann U, Bunemann H. 2000. Mega-introns in the dynein gene DhDhc7(Y) on the heterochromatic Y chromosome give rise to the giant Threads loops in primary spermatocytes of Drosophila hydei. Genetics 154:759-769.
54. Carvalho AB, Vicoso B, Russo CAM, Sceurman B, Clark AG. 2003. Birth of a new gene on the Y chromosome of Drosophila melanogaster. Abstract book. Sixth international conference on Drosophila heterochromatin. Ravello, Italy.
55. Hardy RW, Lindsley DL, Livak KJ, Lewis B, Silverstein AL, et al. 1984. Cytogenetic analysis of a segment of the Y chromosome of the Drosophila melanogaster. Genetics 107:591-610.
56. Livak KJ. 1984. Organization and mapping of a sequence of Drosophila melanogaster X and Y chromosomes that is transcribed during spermatogenesis. Genetics 107:611-634.
57. Livak KJ. 1990. Detailed structure of the Drosophila melanogaster Stellate genes and their transcripts. Genetics 124:303-316.
58. Bozzetti M, Massari S, Finelli P, Meggio F, Pinna LA, et al. 1995. The Ste locus, a component of the parasitic cry-Ste system of Drosophila melanogaster, encodes a protein that forms crystals in primary spermatocytes and mimics properties of the β subunit of casein kinase 2. Proc Natl Acad Sci USA 92:6067-6071.
59. Kalmykova AI, Dobritsa AA, Gvozdev VA. 1998. Su(Ste) diverged tandem repeats in a Y chromosome of Drosophila melanogaster are transcribed and variously processed. Genetics 148:243-249.
60. McKee B, Satter MT. 1996. Structure of the Y chromosomal Su(Ste) locus in Drosophila melanogaster and evidence for localized recombination among repeats. Genetics 142:149-161.
61. Kalmykova AI, Shevelyov YY, Polesskaya OO, Dobritsa AA, Evstafieva AG, et al. 2002. CK2βtes gene encodes a testis-specific isoform of the regulatory subunit of casein kinase 2 in Drosophila melanogaster. Eur J Biochem 269:1418-1427.
62. Usakin LA, Kogan GL, Kalmykova AI, Gvozdev VA. 2005. An alien promoter capture as a primary step of the evolution of testes expressed repeats in Drosophila melanogaster genome. Mol Biol Evol 22:1555-1560.
63. Schmidt A, Palumbo G, Bozzetti MP, Tritto P, Pimpinelli S, Shafer U. 1999. Genetic and Molecular characterization of sting, a gene involved in crystal formation and meiotic drive in the male germ line of Drosophila melanogaster. Genetics 151:749-760.
64. Aravin AA, Klenov MS, Vagin W, Bantignies F, Cavalli G, Gvozdev A. 2004. Dissection of a natural RNA silencing process in the Drosophila melanogaster germ line. Mol Cell Biol 24:6742-6750.
65. Gvozdev VA, Aravin AA, Abramov YA, Klenov MS, Kogan GL, et al. 2003. Stellate repeats: targets of silencing and modules of repeat induced cis-inactivation and trans-activation. Genetica 117:239-245.
66. Kidwell MG, Lisch DR. 2001. Perspective: transposable elements, parasitic DNA and genome evolution. Evolution 55:1-24.
67. Roth DB, Craig NL. 1998. VDJ recombination: a transposase goes to work. Cell 94:411-414.
68. Zhou L, Mitra B, Atkinson PW, Hickman AB, Dyda A, Craig NL. 2004. Transposition of hAT elements likes transposable elements and V(D)J recombination. Nature 432:995-1001.
69. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, et al. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833-1837.
70. Meister G, Tuschl T. 2004. Mechanisms of gene silencing by double-stranded RNA. Nature 431:343-349.