Poly-G/poly-C tracts in the genomes of Caenorhabditis

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Zhao, Yang ^a   O'Neil, Nigel J ^a   Rose, Ann M ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN; DOG 1 PROTEIN; POLYCYTIDYLIC ACID; POLYGUANYLIC ACID; UNCLASSIFIED DRUG; DOG 1 PROTEIN, C ELEGANS; DOG-1 PROTEIN, C ELEGANS; HELICASE;

ARTICLE; CAENORHABDITIS; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; CHROMATIN STRUCTURE; CHROMOSOME ANALYSIS; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE IDENTIFICATION; GENE MUTATION; GENETIC CONSERVATION; GENOME ANALYSIS; INTRON; NONHUMAN; ORTHOLOGY; PHENOTYPE; PROTEIN LOCALIZATION; SERIAL ANALYSIS OF GENE EXPRESSION; TRANSCRIPTION REGULATION; ANIMAL; CHROMOSOME; GENE; GENETICS; GENOME;

CAENORHABDITIS; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; CANIS FAMILIARIS;

ANIMALS; CAENORHABDITIS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CHROMOSOMES; DNA HELICASES; GENES, HELMINTH; GENOME, HELMINTH; INTRONS; POLY C; POLY G;

EID: 38349187301     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-403     Document Type: Article

References (47)

1. Bird CP Stranger BE Dermitzakis ET Functional variation and evolution of non-coding DNA Curr Opin Genet Dev 2006, 16(6):559-564. 10.1016/ j.gde.2006.10.003 17055246
2. Maizels N Dynamic roles for G4 DNA in the biology of eukaryotic cells Nat Struct Mol Biol 2006, 13(12):1055-1059. 10.1038/nsmb1171 17146462
3. Gellert M Lipsett MN Davies DR Helix formation by guanylic acid Proc Natl Acad Sci U S A 1962, 48:2013-2018. 221115 13947099 10.1073/ pnas.48.12.2013
4. Dempsey LA Sun H Hanakahi LA Maizels N G4 DNA binding by LR1 and its subunits, nucleolin and hnRNP D, A role for G-G pairing in immunoglobulin switch recombination J Biol Chem 1999, 274(2):1066-1071. 10.1074/jbc.274.2.1066 9873052
5. Zhang QS Manche L Xu RM Krainer AR hnRNP A1 associates with telomere ends and stimulates telomerase activity Rna 2006, 12(6):1116-1128. 1464852 16603717 10.1261/rna.58806
6. Hanakahi LA Sun H Maizels N High affinity interactions of nucleolin with G-G-paired rDNA J Biol Chem 1999, 274(22):15908-15912. 10.1074/ jbc.274.22.15908 10336496
7. Siddiqui-Jain A Grand CL Bearss DJ Hurley LH Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription Proc Natl Acad Sci U S A 2002, 99(18):11593-11598. 129314 12195017 10.1073/pnas.182256799
8. Sen D Gilbert W Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis Nature 1988, 334(6180):364-366. 10.1038/334364a0 3393228
9. Liu Z Lee A Gilbert W Gene disruption of a G4-DNA-dependent nuclease in yeast leads to cellular senescence and telomere shortening Proc Natl Acad Sci U S A 1995, 92(13):6002-6006. 41630 7597069 10.1073/ pnas.92.13.6002
10. Sun H Bennett RJ Maizels N The Saccharomyces cerevisiae Sgs1 helicase efficiently unwinds G-G paired DNAs Nucleic Acids Res 1999, 27(9):1978-1984. 148410 10198430 10.1093/nar/27.9.1978
11. Ghosal G Muniyappa K Saccharomyces cerevisiae Mre11 is a high-affinity G4 DNA-binding protein and a G-rich DNA-specific endonuclease: implications for replication of telomeric DNA Nucleic Acids Res 2005, 33(15):4692-4703. 1188515 16116037 10.1093/nar/gki777
12. Muniyappa K Anuradha S Byers B Yeast meiosis-specific protein Hop1 binds to G4 DNA and promotes its formation Mol Cell Biol 2000, 20(4):1361-1369. 85284 10648621 10.1128/MCB.20.4.1361-1369.2000
13. Anuradha S Muniyappa K Meiosis-specific yeast Hop1 protein promotes synapsis of double-stranded DNA helices via the formation of guanine quartets Nucleic Acids Res 2004, 32(8):2378-2385. 419448 15115800 10.1093/nar/gkh559
14. Anuradha S Tripathi P Mahajan K Muniyappa K Meiosis-specific yeast Hop1 protein promotes pairing of double-stranded DNA helices via G/C isochores Biochem Biophys Res Commun 2005M 336(3):934-941. 10.1016/ j.bbrc.2005.08.196 16154534
15. Duquette ML Handa P Vincent JA Taylor AF Maizels N Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA Genes Dev 2004, 18 (13):1618-1629. 443523 15231739 10.1101/gad.1200804
16. CelegansSequencingConsortium Genome sequence of the nematode C. elegans: a platform for investigating biology Science 1998, 282(5396):2012-2018. 10.1126/science.282.5396.2012 9851916
17. Denver DR Morris K Kewalramani A Harris KE Chow A Estes S Lynch M Thomas WK Abundance, distribution, and mutation rates of homopolymeric nucleotide runs in the genome of Caenorhabditis elegans J Mol Evol 2004, 58(5):584-595. 10.1007/s00239-004-2580-4 15170261
18. Cheung I Schertzer M Rose A Lansdorp PM Disruption of dog-1 in Caenorhabditis elegans triggers deletions upstream of guanine-rich DNA Nat Genet 2002, 31(4):405-409. 12101400
19. Youds JL O'Neil NJ Rose AM Homologous recombination is required for genome stability in the absence of DOG-1 in Caenorhabditis elegans Genetics 2006, 173(2):697-708. 1526509 16547095 10.1534/ genetics.106.056879
20. Maydan JS Flibotte S Edgley ML Lau J Selzer RR Richmond TA Pofahl NJ Thomas JH Moerman DG Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization Genome Res 2007, 17(3):337-347. 1800925 17267812 10.1101/gr.5690307
21. Swan KA Curtis DE McKusick KB Voinov AV Mapa FA Cancilla MR High-throughput gene mapping in Caenorhabditis elegans Genome Res 2002, 12(7):1100-1105. 186621 12097347
22. Stein LD Bao Z Blasiar D Blumenthal T Brent MR Chen N Chinwalla A Clarke L Clee C Coghlan A Coulson A D'Eustachio P Fitch DH Fulton LA Fulton RE Griffiths-Jones S Harris TW Hillier LW Kamath R Kuwabara PE Mardis ER Marra MA Miner TL Minx P Mullikin JC Plumb RW Rogers J Schein JE Sohrmann M Spieth J Stajich JE Wei C Willey D Wilson RK Durbin R Waterston RH The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics PLoS Biol 2003, 1(2):E45. 261899 14624247 10.1371/journal.pbio.0000045
23. Wormbase http://www.wormbase.org/
24. Barnes TM Kohara Y Coulson A Hekimi S Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans Genetics 1995, 141(1):159-179. 1206715 8536965
25. Prachumwat A DeVincentis L Palopoli MF Intron size correlates positively with recombination rate in Caenorhabditis elegans Genetics 2004, 166(3):1585-1590. 1470791 15082572 10.1534/genetics.166.3.1585
26. Chakravarti A A graphical representation of genetic and physical maps: the Marey map Genomics 1991, 11(1):219-222. 10.1016/0888-7543(91)90123-V 1765381
27. Kent WJ Zahler AM Conservation, regulation, synteny, and introns in a large-scale C. briggsae- C. elegans genomic alignment Genome Res 2000, 10(8):1115-1125. 10.1101/gr.10.8.1115 10958630
28. Hillier LW Miller RD Baird SE Chinwalla A Fulton LA Koboldt DC Waterston RH Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny PLoS Biol 2007, 5(7):e167. 1914384 17608563 10.1371/journal.pbio.0050167
29. Tatusov RL Fedorova ND Jackson JD Jacobs AR Kiryutin B Koonin EV Krylov DM Mazumder R Mekhedov SL Nikolskaya AN Rao BS Smirnov S Sverdlov AV Vasudevan S Wolf YI Yin JJ Natale DA The COG database: An updated version includes eukaryotes BMC Bioinformatics 2003, 4:41. 222959 12969510 10.1186/1471-2105-4-41
30. Koonin EV Fedorova ND Jackson JD Jacobs AR Krylov DM Makarova KS Mazumder R Mekhedov SL Nikolskaya AN Rao BS Rogozin IB Smirnov S Sorokin AV Sverdlov AV Vasudevan S Wolf YI Yin JJ Natale DA A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Genome Biol 2004, 5(2):R7. 395751 14759257 10.1186/gb-2004-5-2-r7
31. Eddy J Maizels N Gene function correlates with potential for G4 DNA formation in the human genome Nucleic Acids Res 2006.
32. McKay SJ Johnsen R Khattra J Asano J Baillie DL Chan S Dube N Fang L Goszczynski B Ha E Halfnight E Hollebakken R Huang P Hung K Jensen V Jones SJ Kai H Li D Mah A Marra M McGhee J Newbury R Pouzyrev A Riddle DL Sonnhammer E Tian H Tu D Tyson JR Vatcher G Warner A Wong K Zhao Z Moerman DG Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans Cold Spring Harb Symp Quant Biol 2003, 68:159-169. 10.1101/sqb.2003.68.159 15338614
33. GuhaThakurta D Schriefer LA Waterston RH Stormo GD Novel transcription regulatory elements in Caenorhabditis elegans muscle genes Genome Res 2004, 14(12):2457-2468. 534670 15574824 10.1101/gr.2961104
34. Larson ED Duquette ML Cummings WJ Streiff RJ Maizels N MutSalpha binds to and promotes synapsis of transcriptionally activated immunoglobulin switch regions Curr Biol 2005, 15(5):470-474. 10.1016/j.cub.2004.12.077 15753043
35. Joyce EF McKim KS When specialized sites are important for synapsis and the distribution of crossovers Bioessays 2007, 29(3):217-226. 10.1002/ bies.20531 17295219
36. Rosenbluth RE Baillie DL The genetic analysis of a reciprocal translocation, eT1(III; V), in Caenorhabditis elegans Genetics 1981, 99(3-4):415-428. 1214511 6953041
37. McKim KS Howell AM Rose AM The effects of translocations on recombination frequency in Caenorhabditis elegans Genetics 1988, 120(4):987-1001. 1203590 3224815
38. Phillips CM Dernburg AF A family of zinc-finger proteins is required for chromosome-specific pairing and synapsis during meiosis in C. elegans Dev Cell 2006, 11(6):817-829. 10.1016/j.devcel.2006.09.020 17141157
39. Phillips CM Wong C Bhalla N Carlton PM Weiser P Meneely PM Dernburg AF HIM-8 Binds to the X Chromosome Pairing Center and Mediates Chromosome-Specific Meiotic Synapsis Cell 2005, 123(6):1051-1063. 10.1016/j.cell.2005.09.035 16360035
40. Macqueen AJ Phillips CM Bhalla N Weiser P Villeneuve AM Dernburg AF Chromosome Sites Play Dual Roles to Establish Homologous Synapsis during Meiosis in C. elegans Cell 2005, 123(6):1037-1050. 10.1016/ j.cell.2005.09.034 16360034
41. Rosenbluth RE Johnsen RC Baillie DL Pairing for recombination in LGV of Caenorhabditis elegans: A model based on recombination in deficiency heterozygotes Genetics 1990, 124(3):615-625. 1203955 2311918
42. McKim KS Peters K Rose AM Two types of sites required for meiotic chromosome pairing in Caenorhabditis elegans Genetics 1993, 134(3):749-768. 1205513 8349107
43. Couteau F Nabeshima K Villeneuve A Zetka M A component of C. elegans meiotic chromosome axes at the interface of homolog alignment, synapsis, nuclear reorganization, and recombination Curr Biol 2004, 14(7):585-592. 10.1016/j.cub.2004.03.033 15062099
44. Martinez-Perez E Villeneuve AM HTP-1-dependent constraints coordinate homolog pairing and synapsis and promote chiasma formation during C. elegans meiosis Genes Dev 2005, 19(22):2727-2743. 1283965 16291646 10.1101/gad.1338505
45. Couteau F Zetka M HTP-1 coordinates synaptonemal complex assembly with homolog alignment during meiosis in C. elegans Genes Dev 2005, 19(22):2744-2756. 1283966 16291647 10.1101/gad.1348205
46. GenomeBCCelegansGeneExpressionConsortium http://www.elegans.bcgsc.bc.ca/
47. Brenner S The genetics of Caenorhabditis elegans Genetics 1974, 77(1):71-94. 1213120 4366476