Genome biology and the evolution of cell-size diversity

Cold Spring Harbor Perspectives in Biology

Volumn 7, Issue 11, 2015, Pages

  Mueller, Rachel Lockridge ^a  

^a Veterinary Dentistry and Oral Surgery   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; CELL SIZE; ENERGY METABOLISM; EVOLUTION; GENETIC SELECTION; GENOME SIZE; SPECIES DIFFERENCE;

BIOLOGICAL EVOLUTION; CELL SIZE; ENERGY METABOLISM; GENOME SIZE; MODELS, GENETIC; SELECTION, GENETIC; SPECIES SPECIFICITY;

EID: 84940847064     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a019125     Document Type: Article

References (73)

1. Arensburger P, Hice RH, Wright JA, Craig NL, Atkinson PW. 2011. The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs. BMC Genomics 12: 606
2. Bennetzen JL, Kellogg EA. 1997. Do plants have a one-way ticket to genomic obesity? Plant Cell 9: 1509
3. Blumenstiel JP. 2011. Evolutionary dynamics of transposable elements in a small RNA world. Trends Genet 27: 23–31
4. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ. 2007. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128: 1089–1103
5. Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ. 2008. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322: 1387
6. Burton DW, Bickham JW, Genoways HH. 1989. Flow-cytometric analyses of nuclear DNA content in four families of neotropical bats. Evolution 43: 756–765
7. Cavalier-Smith T. 1991. Coevolution of vertebrate genome, cell, and nuclear sizes. In Symposium on the evolution of terrestrial vertebrates selected symposia and monographs UZI (ed. Ghiara G, Angelini F, Olmo E, Varano L), pp. 51–86. Mucchi, Modena, Italy
8. Cavalier-Smith T. 2005. Economy, speed and size matter: Evolutionary forces driving nuclear genome miniaturization and expansion. Ann Bot 95: 147–175
9. Charlesworth B, Langley CH. 1986. The evolution of selfregulated transposition of transposable elements. Genetics 112: 359–383
10. Clark JP, Lau NC. 2014. Piwi proteins and piRNAs step onto the systems biology stage. In Systems biology of RNA binding proteins (ed. Yeo GW), pp. 159–197. Springer, New York
11. Cora E, Pandey RR, Xiol J, Taylor J, Sachidanandam R, McCarthy AA, Pillai RS. 2014. The MID-PIWI module of Piwi proteins specifies nucleotide and strand biases of piRNAs. RNA 20: 773–781
12. Cross FR, Buchler NE, Skotheim JM. 2011. Evolution of networks and sequences in eukaryotic cell cycle control. Philos Trans R Soc Lond B Biol Sci 366: 3532–3544
13. De Gobbi M, Viprakasit V, Hughes JR, Fisher C, Buckle VJ, Ayyub H, Gibbons RJ, Vernimmen D, Yoshinaga Y, de Jong PJ, et al. 2006. A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science 26: 1215–1217
14. Dion V, Gasser SM. 2013. Chromatin movement in the maintenance of genome stability. Cell 152: 1355–1364
15. Donachie WD. 1968. Relationship between cell size and time of initiation ofDNA replication. Nature 219: 1077–1079
16. Dumesic PA, Madhani HD. 2014. Recognizing the enemy within: Licensing RNA-guided genome defense. Trends Biochem Sci 39: 25–34
17. Edens LJ, White KH, Jevtic P, Li X, Levy DL. 2013. Nuclear size regulation: From single cells to development and disease. Trends Cell Biol 23: 151–159
18. Edgar BA, Kim KJ. 2009. Sizing up the cell. Science 325: 158–159
19. Fantes PA, Grant WD, Pritchard RH, Sudbery PE, Wheals AE. 1975. The regulation of cell size and the control of mitosis. J Theor Biol 50: 213–244
20. Ferrezuelo F, Colomina N, Palmisano A, Garı´ E, Gallego C, Csikász-Nagy A, Aldea M. 2012. The critical size is set at a single-cell level by growth rate to attain homeostasis and adaptation. Nat Commun 3: 1012
21. Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nat Rev Gen 9: 397–405
22. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531–1545
23. Frahry MB, Sun C, Chong R, Mueller RL. 2015. Lowlevels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders. J Mol Evol 80: 120–129
24. Furano AV, Duvernell DD, Boissinot S. 2004. L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends Genet 20: 9–14
25. Gregory TR. 2001. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev Camb Philos Soc 76: 65–101
26. Gregory TR. 2002. Genome size and developmental complexity. Genetica 115: 131–146
27. Gregory TR. 2005a. The C-value enigma in plants and animals: A review of parallels and an appeal for partnership. Ann Bot 95: 133–146
28. Gregory TR. 2005b. The evolution of the genome. Academic, New York
29. Gunawardane LS, Saito K, Nishika KM, Kawamura Y, Nagami T, Siomi H, Siomi MC. 2007. A slicer-mediated mechanism for repeat-associated siRNA 50 end formation in Drosophila. Science 315: 1587–1590
30. Guzzardo PM, Muerdter F, Hannon GJ. 2013. The piRNA pathway in flies: Highlights and future directions. Curr Opin Genet Dev 23: 44–52
31. Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ. 2001. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293: 1146
32. Hanada K, Shiu S-H, Li W-H. 2007. The nonsynonymous/ synonymous substitution rate ratio versus the radical/ conservative replacement rate ratio in the evolution of mammalian genes. Mol Biol Evol 24: 2235–2241
33. Hoose SA, Rawlings JA, Kelly MM, Leitch MC, Ababneh QO, Robles JP, Taylor D, Hoover EM, Hailu B, McEnery KA. 2012. A systematic analysis of cell cycle regulators in yeast reveals that most factors act independently of cell size to control initiation of division. PLoS Genet 8: e1002590
34. Hughes AL, Hughes MK. 1995. Small genomes for better flyers. Nature 377: 391
35. Jorgensen P, Nishikawa JL, Breitkreutz B, Tyers M. 2002. Systematic identification of pathways that couple cell growth and division in yeast. Science 297: 395–400
36. Kafri R, Levy J, Ginzberg MB, Oh S, Lahav G, Kirschner MW. 2013. Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle. Nature 494: 480–483
37. Kelleher ES, Barbash DA. 2013. Analysis of piRNA-mediated silencing of active TEs in Drosophila melanogaster suggests limits on the evolution of host genome defense. Mol Biol Evol 30: 1816–1829
38. Koivusalo M, Kapus A, Grinstein S. 2009. Sensors, transducers, and effectors that regulate cell size and shape. J Biol Chem 284: 6595–6599
39. Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Gen 11: 204
40. Lee HO, Davidson JM, Duronio RJ. 2009. Endoreplication: Polyploidy with purpose. Genes Dev 23: 2461–2477
41. Lloyd AC. 2013. The regulation of cell size. Cell 154: 1194–1205
42. Luteijn M, Ketting RF. 2013. PIWI-interacting RNAs: From generation to transgenerational epigenetics. Nat Rev Gen 14: 523–534
43. Lynch M. 2007. The origins of genome architecture. Sinauer, Sunderland, MA
44. Malone CD, Hannon GJ. 2009. Small RNAs as guardians of the genome. Cell 136: 656–668
45. Marshall WF, Young KD, Swaffer M, Wood E, Nurse P, Kimura A, Frankel J, Wallingford J, Walbot V, Qu X. 2012. What determines cell size? BMC Biol 10: 101
46. Martin SG, Berthelot-Grosjean M. 2009. Polar gradients of theDYRK-family kinase Pom1 couple cell length with the cell cycle. Nature 459: 852–856
47. Metcalfe CJ, Filee J, Germon I, Joss J, Casane D. 2012. Evolution of the Australian lungfish (Neoceratodus forsteri) genome: A major role for CR1 and L2 LINE elements. Mol Biol Evol 29: 3529–3539
48. Miettinen Teemu P, Pessa Heli KJ, Caldez Matias J, Fuhrer T, Diril MK, Sauer U, Kaldis P, Björklund M. 2014. Identi- fication of transcriptional and metabolic programs related to mammalian cell size. Curr Biol 24: 598–608
49. Mine-Hattab J, Rothstein R. 2012. Increased chromosome mobility facilitates homology search during recombination. Nat Cell Biol 14: 510–517
50. Montgomery EA, Charlesworth B, Langley CH. 1987. A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster. Genet Res 49: 31–41
51. Moretto F, Sagot I, Daignan-Fornier B, Pinson B. 2013. A pharmaco-epistasis strategy reveals a new cell size controlling pathway in yeast. Mol Syst Biol 9: 707
52. Moseley JB, Mayeux A, Paoletti A, Nurse P. 2009. A spatial gradient coordinates cell size and mitotic entry in fission yeast. Nature 459: 857–860
53. Nuzhdin SV. 1999. Sure facts, speculations, and open questions about the evolution of transposable element copy number. Genetica 107: 129–137
54. Olmo E, Morescalchi A. 1975. Evolution of the genome and cell sizes in salamanders. Experientia 31: 804–806
55. Petrov DA, Aminetzach YT, Davis J, Bensasson D, Hirsch AE. 2003. Size matters: Non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol Biol Evol 20: 880–892
56. Rayburn AL, Dudley JW, Biradar DP. 1994. Selection for early flowering results in simultaneous selection for reduced nuclear DNA content in maize. Plant Breed 112: 318–322
57. Roth G, Rottluff B, Grunwald W, Hanken J, Linke R. 1990. Miniaturization in plethodontid salamanders (Caudata: Plethodontidae) and its consequences for the brain and visual system. Biol J Linn Soc 40: 165–190
58. Roth G, Blanke J, Wake DB. 1994. Cell size predicts morphological complexity in the brains of frogs and salamanders. Proc Natl Acad Sci 91: 4796–4800
59. Roth G, Nishikawa KC, Wake DB. 1997. Genome size, secondary simplification, and the evolution of the brain in salamanders. Brain Behav Evol 50: 50–59
60. Saito K. 2013. The epigenetic regulation of transposable elements by PIWI-interacting RNAs in Drosophila. Genes Genet Syst 88: 9–17
61. Sato K, Siomi MC. 2013. Piwi-interacting RNAs: Biological functions and biogenesis. Essays Biochem 54: 39–52
62. Senti K-A, Brennecke J. 2010. The piRNA pathway: A fly’s perspective on the guardian of the genome. Trends Genet 26: 499–509
63. Siomi MC, Sato K, Pezic D, Aravin AA. 2011. PIWI-interacting smallRNAs: The vanguard of genome defence. Nat Rev Mol Cell Biol 12: 246–258
64. Soria PS, McGary KL, Rokas A. 2014. Functional divergence for every paralog. Mol Biol Evol 31: 984–992
65. Sun C, Shepard DB, Chong RA, Arriaza JL, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL. 2012. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Gen Biol Evol 4: 168–183
66. Szarski H. 1983. Cell size and the concept of wasteful and frugal evolutionary strategies. J Theor Biol 105: 201–209
67. Tian Z, Rizzon C, Du J, Zhu L, Bennetzen JL, Jackson SA, Gaut BS, Ma J. 2009. Do genetic recombination and gene density shape the pattern ofDNA elimination in rice long terminal repeat retrotransposons? Genome Res 19: 2221
68. Turner JJ, Ewald JC, Skotheim JM. 2012. Cell size control in yeast. Curr Biol 22: R350–R359
69. Vourekas A, Zheng Q, Alexiou P, Maragkakis M, Kirino Y, Gregory BD, Mourelatos Z. 2012. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat Struct Mol Biol 19: 773–781
70. Waltari E, Edwards SV. 2002. Evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs. Am Nat 160: 539–552
71. Wang H, Carey LB, Cai Y, Wijnen H, Futcher B. 2009. Recruitment of Cln3 cyclin to promoters controls cell cycle entry via histone deacetylase and other targets. PLoS Biol 7: e1000189
72. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O. 2007. A unified classification system for eukaryotic transposable elements. Nat Rev Gen 8: 973–982
73. Zhang X, Niu D, Carbonell A, Wang A, Lee A, Tun V, Wang Z, Carrington JC, Chang CE, Jin H. 2014. ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis. Nat Commun 5: 5468.