Abundance, distribution, and mutation rates of homopolymeric nucleotide runs in the genome of Caenorhabditis elegans

Journal of Molecular Evolution

Volumn 58, Issue 5, 2004, Pages 584-595

  Denver, Dee R ^a   Morris, Krystalynne ^b   Kewalramani, Avinash ^a   Harris, Katherine E ^c   Chow, Amy ^d   Estes, Suzanne ^e   Lynch, Michael ^a   Thomas, W Kelley ^b  

^a INDIANA UNIVERSITY   (United States)

^b UNIVERSITY OF NEW HAMPSHIRE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d ST LUKE S HOSPITAL   (United States)

^e OREGON STATE UNIVERSITY   (United States)

Author keywords

Caenorhabditis elegans; Genome; Homopolymer; Microsatellite; Mutation

Indexed keywords

NUCLEOTIDE;

ARTICLE; AUTOSOME; CAENORHABDITIS ELEGANS; CHROMOSOME; CONTROLLED STUDY; EMPIRICISM; GENE CLUSTER; GENE LOCATION; GENE MUTATION; GENETIC ANALYSIS; GENOME; MICROSATELLITE MARKER; MITOCHONDRION; MOLECULAR EVOLUTION; MUTAGENESIS; NONHUMAN; POLYMERIZATION; STATISTICAL SIGNIFICANCE; TECHNIQUE;

ANIMALS; BASE SEQUENCE; CAENORHABDITIS ELEGANS; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; GENOME; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; MUTATION; RECOMBINATION, GENETIC;

CAENORHABDITIS; CAENORHABDITIS ELEGANS; EUKARYOTA; INVERTEBRATA; NEMATODA; PROTOZOA;

EID: 1942499339     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-2580-4     Document Type: Article

References (45)

1. Barnes T, Kohara M, Coulson Y, Hekimi S (1995) Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics 141:159-179
2. Brahmachari SK, Sarkar PS, Raghavan S, Narayan M, Maiti AK (1997) Polypurine/polypyrimidine sequences as cis-acting transcriptional regulators. Gene 190:17-26
3. Brohede J, Ellegren H (1999) Microsatellite evolution: Polarity of substitutions within repeats and neutrality of flanking sequences. Proc R Soc Lond B Biol Sci 266:825-833
4. Catasus L, Matias-Guiu X, Machin P, Zannoni GF, Scambia G, Benedetti-Panici P, Prat J (2000) Frameshift mutations at coding mononucleotide repeat microsatellites in endometrial carcinoma with microsatellite instability. Cancer 88:2290-2297
5. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282:2012-2018
6. Chang DK, Metzgar D, Wills C, Boland CR (2001) Microsatellites in the eukaryotic DNA mismatch repair genes as modulators of evolutionary mutation rate. Genome Res 11:1145-1146
7. Coll M, Frederick CA, Wang AH, Rich A (1987) A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc Natl Acad Sci USA 84:8385-8389
8. Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P, Lengieza C, Lew-Smith JE, Tillberg M, Garrels JI (2001) YPD, PombePD and WormPD: Model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res 29:75-79
9. Culigan KM, Meyer-Gauen G, Lyons-Weiler J, Hays JB (2000) Evolutionary origin, diversification and specialization of eukaryotic MutS homolog mismatch repair proteins. Nucleic Acids Res 28:463-471
10. Dechering KJ, Cuelenaere K, Konings RNH, Leunissen JAM (1998) Distinct frequency-distributions of homopolymeric DNA tracts in different genomes. Nucleic Acids Res 26:4056-4062
11. Denver DR, Morris K, Lynch M, Vassilieva LL, Thomas WK (2000) High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science 289:2342-2344
12. Denver DR, Morris K, Thomas WK (2003) Phylogenetics in Caenorhabditis elegans: An analysis of divergence and outcrossing. Mol Biol Evol 20:393-400
13. Duret L, Marais G, Biemont C (2000) Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans. Genetics 156:1661-1669
14. Elkin CJ, Richardson PM, Fourcade HM, Hammon NM, Pollard MJ, Predki PF, Glavina T, Hawkins TL (2001) High-through-put plasmid purification for capillary sequencing. Genome Res 11:1269-1274
15. Frisse LM (1999) Understanding the mechanisms of microsatellite formation and mutation using the model organism Caenorhabditis elegans. PhD dissertation. University of Missouri, Kansas City
16. Gentles AJ, Karlin S (2001) Genome-scale compositional comparisons in eukaryotes. Genome Res 11:540-546
17. Gordenin DA, Resnick MA (1998) Yeast ARMs (DNA at-risk motifs) can reveal sources of genome instability. Mutat Res 400:45-58
18. Gragg H, Harfe BD, Jinks-Robertson S (2002) Base composition of mononucleotide runs affects DNA polymerase slippage and removal of frameshift intermediates by mismatch repair in Saccharomyces cerevisiae. Mol Cell Biol 22:8756-8762
19. Hancock JM (1995) The contribution of slippage-like processes to genome evolution. J Mol Evol 41:1038-1047
20. Harfe BD, Jinks-Robertson S (2000) Sequence composition and context effects on the generation and repair of frameshift intermediates in mononucleotide runs in Saccharomyces cerevisiae. Genetics 156:571-578
21. Hodgkin J, Doniach T (1997) Natural variation and copulatory plug formation in Caenorhabditis elegans. Genetics 146:149-164
22. Iyer V, Struhl K (1995) Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J 14:2570-2579
23. Kashi Y, King D, Soller M (1997) Simple sequence repeats as a source of quantitative genetic variation. Trends Genet 13:74-78
24. Katti MV, Ranjekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161-1167
25. Kroutil LC, Register K, Bebenek K, Kunkel TA (1996) Exonucleolytic proofreading during replication of repetitive DNA. Biochemistry 35:1046-1053
26. Kruglyak S, Durret RT, Schug MD, Aquadro CF (1998) Equilibrium distributions of microsatellite repeat length resulting form a balance between slippage events and point mutations. Proc Natl Acad Sci USA 95:10774-10778
27. Kruglyak S, Durrett R, Schug M, Aquadro CF (2000) Distribution and abundance of microsatellites in the yeast genome can be explained by a balance between slippage events and point mutations. Mol Biol Evol 17:1210-1219
28. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862-864
29. Levy DD, Cebula TA (2001) Fidelity of replication of repetitive DNA in mutS and repair proficient Escherichia coli. Mutat Res 474:1-14
30. Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72-80
31. Nadir E, Margalit H, Gallily T, Ben-Sasson SA (1996) Microsatellite spreading in the human genome: Evolutionary mechanisms and structural implications. Proc Natl Acad Sci USA 93:6470-6475
32. Nelson HCM, Finch JT, Luisi BF, Klug A (1987) The structure of an oligo(dA) oligo(dT) tract and its biological implications. Nature 330:221-226
33. Richard GF, Paques F (2000) Mini- and microsatellite expansions: The recombination connection. EMBO Rep 1:122-126
34. Richetta A, Ottini L, Falchetti M, Innocenzi D, Bottoni U, Faiola R, Mariani-Costantini R, Calvieri S (2001) Instability at sequence repeats in melanocytic tumors. Melanoma Res 11:283-289
35. Sen D, Gilbert W (1988) Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334:364-366
36. Smith GP (1976) Evolution of repeated DNA sequences by unequal crossover. Science 191:528-535
37. Tautz D, Trick M, Dover GA (1986) Cryptic simplicity in DNA is a major source of genetic variation. Nature 322:652-656
38. Templeton AR, Clark AG, Weiss KM, Nickerson DA, Boerwinkle E, Sing CF (2000) Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am J Hum Genet 66:69-83
39. Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Res 10:967-981
40. Tran HT, Keen D, Kricker M, Resnick MA, Gordenin DA (1997) Hypermutability of homonucleotide runs in mismatch repair and DNA polymerase proofreading yeast mutants. Mol Cell Biol 17:2859-2865
41. Vassilieva LL, Lynch M (1999) The rate of spontaneous mutation for life-history traits in Caenorhabditis elegans. Genetics 151:119-129
42. Vassilieva LL, Hook AM, Lynch M (2000) The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evolution 54:1234-1246
43. Wierdl M, Dominska M, Petes TD (1997) Microsatellite instability in yeast: Dependence on the length of the microsatellite. Genetics 146:769-779
44. Wilder J, Hollocher H (2001) Mobile elements and the genesis of microsatellites in dipterans. Mol Biol evol 18:384-392
45. Zhang L, Yu J, Willson JK, Markowitz SD, Kinzler KW, Vogelstein B (2001) Short mononucleotide repeat sequence variability in mismatch repair-deficient cancers. Cancer Res 61:3801-3805