Genome size and chromatin condensation in vertebrates

Chromosoma

Volumn 113, Issue 7, 2005, Pages 362-369

  Vinogradov, Alexander E ^a  

^a INSTITUTE OF CYTOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AMPHIBIA; ANALYSIS OF VARIANCE; ANIMAL CELL; ARTICLE; CELL MEMBRANE; CHROMATIN CONDENSATION; CONTROLLED STUDY; CORRELATION ANALYSIS; CYCLOSTOME; DNA PACKAGING; EPIGENETICS; ERYTHROCYTE; EXTRACELLULAR SPACE; FLOW CYTOMETRY; GENOME SIZE; NONHUMAN; REPTILE; SALINITY; SARCOPTES; SPECIES DIFFERENCE; SPECIES DIVERSITY; VERTEBRATE;

ANIMALS; BASE COMPOSITION; CELL MEMBRANE; CHROMATIN; DNA; ERYTHROCYTES; FLOW CYTOMETRY; GENOME; HUMANS; SOLVENTS; SPECIES SPECIFICITY; VERTEBRATES;

EID: 13844276612     PISSN: 00095915     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00412-004-0323-3     Document Type: Article

References (74)

1. Allison DC, Ridolpho PF, Rasch EM, Rasch RW, Johnson TS (1981) Increased accuracy of absorption cytophotometric DNA values by control of stain intensity. J Histochem Cytochem 29:1219-1228 1:CAS:528:DyaL3MXmtVSjtL4%3D
2. Anatskaya OV, Vinogradov AE (2004) Heart and liver as developmental bottlenecks of mammal design: Evidence from cell polyploidization. Biol J Linn Soc 83:175-186 10.1111/j.1095-8312.2004.00377.x
3. Bachmann K (1970) Feulgen slope determinations of urodele nuclear DNA amounts. Histochemistry 22:289-293 1:STN:280:CS%2BB2M7itV0%3D
4. Beaton MJ, Cavalier-Smith T (1999) Eukaryotic non-coding DNA is functional: Evidence from the differential scaling of cryptomonad genomes. Proc R Soc Lond B 266:2053-2059 10.1098/rspb.1999.0886
5. Bennett MD (1971) The duration of meiosis. Proc R Soc Lond B 178:277-299 1:CAS:528:DyaE3MXkvVGisbw%3D
6. Bennett MD (1987) Variation in genomic form in plants and its ecological implications. New Phytol 106(Suppl):177-200
7. Bennett MD (1998) Plant genome values: How much do we know? Proc Natl Acad Sci U S A 95:2011-2016
8. Bennett MD, Leitch IJ (2003) Plant DNA C-values database (release 2.0). Available at http://www.rbgkew.org.uk/cval/homepage.html
9. Bird AP (1995) Gene number, noise reduction and biological complexity. Trends Genet 11:94-100 10.1016/S0168-9525(00)89009-5
10. VY Brodsky IV Uryvaeva 1985 Genome multiplication in growth and development Cambridge University Press Cambridge
11. Byers TJ (1986) Molecular biology of DNA in Acanthamoeba, Amoeba, Entamoeba, and Naegleria. Int Rev Cytol 99:311-341 1:CAS:528:DyaL28XkvFajur8%3D
12. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA (2002) Selection for short introns in highly expressed genes. Nat Genet 31:415-418
13. Cavalier-Smith T (1978) Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox. J Cell Sci 34:247--278 1:CAS:528:DyaE1MXot1GrtA%3D%3D
14. T Cavalier-Smith 1985 Cell volume and the evolution of eukaryote genome size T Cavalier-Smith The evolution of genome size. Wiley Chichester 105-184
15. Cavalier-Smith T, Beaton MJ (1999) The skeletal function of non-genic nuclear DNA: New evidence from ancient cell chimaeras. Genetica 106:3-13 10.1023/A:1003701925110
16. Comeron JM (2001) What controls the length of noncoding DNA? Curr Opin Genet Dev 11:652-659 10.1016/S0959-437X(00)00249-5
17. Eisenberg E, Levanon EY (2003) Human housekeeping genes are compact. Trends Genet 19:362-365 10.1016/S0168-9525(03)00140-9
18. Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1-15 10.1086/284325
19. Gregory TR (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev Camb Philos Soc 76:65-101 10.1017/S1464793100005595
20. Gregory TR (2002a) A bird's-eye view of the C-value enigma: Genome size, cell size, and metabolic rate in the class Aves. Evolution 56:121-130 1:CAS:528:DC%2BD38Xit1ynsrg%3D
21. Gregory TR (2002b) Genome size and developmental complexity. Genetica 115:131-146 10.1023/A:1016032400147
22. Grime JP, Mowforth MA (1982) Variation in genome size-an ecological interpretation. Nature 299:151-153 10.1038/299151a0
23. Grime JP, Shacklock JML, Band SR (1985) Nuclear DNA contents, shoot phenology and species co-existence in a limestone grassland community. New Phytol 100:435-445 1:CAS:528:DyaL2MXlt1Sgsrc%3D
24. Hartl DL (2000) Molecular melodies in high and low C. Nat Rev Genet 1:145-149
25. Hoffman J, Katz U (1997) Salt and water balance in the toad Bufo viridis during recovery from two different osmotically stressful conditions. Comp Biochem Physiol A 117:147-154 10.1016/S0300-9629(96)00360-X
26. Hurst LD (1995) Evolutionary genetics. The silence of the genes. Curr Biol 5:459-461 10.1016/S0300-9629(96)00360-X
27. James J (1972) DNA constancy and chromatin structure in some cell nuclei of Amphiuma. Histochem J 4:181-192 1:STN:280:CS2B2MfotlU%3D
28. Kalney VS, Kudryavtsev BN, Kudryavtseva MV (1974) Relation between radiosensitivity and DNA content in nuclei of various Amoeba proteus strains. Acta Protozool 12:111-116
29. Kato H, Harada M, Tsuchiya K, Moriwaki K (1980) Absence of correlation between DNA repair in ultraviolet irradiated mammalian cells and life span of the donor species. Jpn J Genet 55:99-108
30. Kim C, Rubin CM, Schmid CW (2001) Genome-wide chromatin remodeling modulates the Alu heat shock response. Gene 276:127-133 10.1016/S0378-1119(01)00639-4
31. Kinsman EA, Lewis C, Davies MS, Young JE, Francis D, Vilhar B, Ougham HJ (1997) Elevated CO2 stimulates cells to divide in grass meristems: A differential effect in two natural populations of Dactylis glomerata. Plant Cell Environ 20:1309-1316 10.1046/j.1365-3040.1997.d01-21.x
32. Kozlowski J, Konarzewski M, Gawelczyk AT (2003) Cell size as a link between noncoding DNA and metabolic rate scaling. Proc Natl Acad Sci U S A 100:14080-14085
33. Li TH, Kim C, Rubin CM, Schmid CW (2000) K562 cells implicate increased chromatin accessibility in Alu transcriptional activation. Nucleic Acids Res 28:3031-3039 10.1093/nar/28.16.3031
34. Licht LE, Lowcock LA (1991) Genome size and metabolic rate in salamanders. Comp Biochem Physiol B 100:83-92 10.1016/0305-0491(91)90089-V
35. Loborg H, Rundquist I (1997) DNA binding fluorochromes as probes for histone H1-chromatin interactions in situ. Cytometry 28:212-219 10.1002/(SICI)1097-0320(19970701)28:3<212::AID-CYTO5>3.0.CO;2-F
36. Lynch M, Conery JS (2003) The origins of genome complexity. Science 302:1401-1404 10.1126/science.1089370
37. Macgillivray CW, Grime JP (1995) Genome size predicts frost resistance in British herbaceous plants: Implications for rates of vegetation response to global warming. Funct Ecol 9:320-325
38. Martins EP (2001) COMPARE, v. 4.4. Computer programs for the statistical analysis of comparative data. Available at: http://compare.bio.indiana.edu/. Department of Biology, Indiana University, Bloomington, Ind
39. McAdams HH, Arkin A (1999) It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet 15:65-69 10.1016/S0168-9525(98)01659-X
40. Mommsen TP (2001) Paradigms of growth in fish. Comp Biochem Physiol B Biochem Mol Biol 129:207-219 10.1016/S1096-4959(01)00312-8
41. Moore PD (1985) Nuclear DNA content as a guide to plant growth rate. Nature 318:412-413
42. Ohno S (1999) Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999. Semin Cell Dev Biol 10:517-522 1:CAS:528:DyaK1MXnvFOmsb4%3D
43. Olmo E (1983) Nucleotype and cell size in vertebrates: A review. Basic Appl Histochem 27:227-254 1:STN:280:BiuD2sblvF0%3D
44. Olmo E (2003) Reptiles: A group of transition in the evolution of genome size and of the nucleo0typic effect. Cytogenet Genome Res 101:166-171 10.1159/000074174
45. Pedersen RA (1971) DNA content, ribosomal gene multiplicity, and cell size in fish. J Exp Zool 177:65-79 1:CAS:528:DyaE3MXktlWqsb4%3D
46. Petrov DA (2001) Evolution of genome size: New approaches to an old problem. Trends Genet 17:23-28 10.1016/S0168-9525(00)02157-0
47. Petrov DA (2002) Mutational equilibrium model of genome size evolution. Theor Popul Biol 61:531-544 10.1006/tpbi.2002.1605
48. Rock J, Eldridge M, Champion A, Johnston P, Joss J (1996) Karyotype and nuclear DNA content of the Australian lungfish, Neoceratodus forsteri (Ceratodidae: Dipnoi). Cytogenet Cell Genet 73:187-189 1:STN:280:BymA3c3jtlY%3D
49. Shpun S, Hoffman J, Katz U (1992) Anuran amphibia which are not acclimable to high salt, tolerate high plasma urea. Comp Biochem Physiol A 103:473-477 10.1016/0300-9629(92)90274-T
50. Spear BB, Prescott DM (1980) Nuclear DNA in normal and refed Amoeba proteus. Exp Cell Res 130:387-392 1:CAS:528:DyaL3MXpvFCluw%3D%3D
51. Sternberg R (2002) On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. Ann NY Acad Sci 981: 154-188 12547679
52. Szarski H (1983) Cell size and the concept of wasteful and frugal evolutionary strategies. J Theor Biol 105:201-209 1:STN:280:BiuD1M7mslI%3D
53. Tautvydas KJ (1971) Mass isolated ameba nuclei. I. Isolation procedure and determination of macromolecular composition and RNA polymerase activity. Exp Cell Res 68:299-308 1:CAS:528:DyaE3MXlsVyqtL0%3D
54. Thastrom A, Lowary PT, Widom J (2004) Measurement of histone-DNA interaction free energy in nucleosomes. Methods 33:33-44 10.1016/j.ymeth.2003.10.018
55. Trivers R, Burt A, Palestis BG (2004) B chromosomes and genome size in flowering plants. Genome 47:1-8 10.1139/g03-142
56. Urrutia AO, Hurst LD (2003) The signature of selection mediated by expression on human genes. Genome Res 13:2260-2264
57. Van't Hof J, Sparrow AH (1963) A relationship between DNA content, nuclear volume and minimum mitotic cycle time. Proc Natl Acad Sci U S A 49:897-902 1:STN:280:CC2C1cfgtFw%3D
58. Vervoort A (1980) Tetraploidy in Protopterus (Dipnoi). Experientia 36:294-296
59. Vinogradov AE (1995a) Nucleotypic effect in homeotherms: Body mass-corrected basal metabolic rate of mammals is related to genome size. Evolution 49:1249-1259
60. Vinogradov AE (1995b) Cell membrane-dependent chromatin condensation. Cytometry 19:183-188 1:CAS:528:DyaK2MXksVOnu78%3D
61. Vinogradov AE (1996) Post-fixation method of cell viability assessment with flow cytometry. Acta Histochem Cytochem 29(Suppl):527-528
62. Vinogradov AE (1997) Nucleotypic effect in homeotherms: Body mass-independent resting metabolic rate of passerine birds is related to genome size. Evolution 51:220-225
63. Vinogradov AE (1998a) Buffering: A possible passive-homeostasis role for redundant DNA. J Theor Biol 193:197-199 10.1006/jtbi.1997.0629
64. Vinogradov AE (1998b) Genome size and GC-percent in vertebrates as determined by flow cytometry: The triangular relationship. Cytometry 31:100-109 10.1002/(SICI)1097-0320(19980201)31:2<100::AID-CYTO5>3.0.CO;2-Q
65. Vinogradov AE (2000) Larger genomes for molluskan land pioneers. Genome 43:211-212 10.1139/gen-43-1-211
66. Vinogradov AE (2003) Selfish DNA is maladaptive: Evidence from the plant Red List. Trends Genet 19:609-614 10.1016/j.tig.2003.09.010
67. Vinogradov AE (2004a) Evolution of genome size: Multi-level selection, mutation bias or dynamical chaos? Curr Opin Genet Dev 14:620-626
68. Vinogradov AE (2004b) Genome size and extinction risk in vertebrates. Proc R Soc Lond B 271:1701-1705 10.1098/rspb.2004.2776
69. Vinogradov AE (2004c) Compactness of human housekeeping genes: Selection for economy or genomic design? Trends Genet 20:248-253 10.1016/j.tig.2004.03.006
70. Vinogradov AE, Anatskaya OV (2004) Phenological resonance and quantum life-history. J Theor Biol 228:417-420 10.1016/j.jtbi.2004.02.003
71. Wakamiya I, Newton RJ, Johnston JS, Price HJ (1993) Genome size and environmental factors in the genus Pinus. Am J Bot 80:1235-1241
72. Wakamiya I, Price HJ, Messina MG, Newton RJ (1996) Pine genome size diversity and water relations. Physiol Plantarum 96:13-20 10.1034/j.1399-3054.1996.960103.x
73. Waltari E, Edwards SV (2002) Evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs. Am Nat 160:539-552 10.1086/342079
74. Zuckerkandl E (2002) Why so many noncoding nucleotides? The eukaryote genome as an epigenetic machine. Genetica 115:105-129 10.1023/A:1016080316076