Abstract
Repeat-induced point mutation (RIP) is a process that efficiently detects DNA duplications prior to meiosis in Neurospora crassa and peppers them with G:C to A:T mutations. Cytosine methylation is typically associated with sequences affected by RIP, and methylated cytosines are not limited to CpG dinucleotides. We generated and characterized a collection of methylated and unmethylated amRIP alleles to investigate the connection(s) between DNA methylation and mutations by RIP. Alleles of am harboring 84 to 158 mutations in the 2.6-kb region that was duplicated were heavily methylated and triggered de novo methylation when reintroduced into vegetative N. crassa cells. Alleles containing 45 and 56 mutations were methylated in the strains originally isolated but did not become methylated when reintroduced into vegetative cells. This provides the first evidence for de novo methylation in the sexual cycle and for a maintenance methylation system in Neurospora cells. No methylation was detected in am alleles containing 8 and 21 mutations. All mutations in the eight primary alleles studied were either G to A or C to T, with respect to the coding strand of the am gene, suggesting that RIP results in only one type of mutation. We consider possibilities for how DNA methylation is triggered by some sequences altered by RIP.
Full Text
The Full Text of this article is available as a PDF (1.1 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Antequera F., Bird A. CpG islands. EXS. 1993;64:169–185. doi: 10.1007/978-3-0348-9118-9_8. [DOI] [PubMed] [Google Scholar]
- Behe M., Zimmerman S., Felsenfeld G. Changes in the helical repeat of poly(dG-m5dC) . poly(dG-m5dC) and poly(dG-dC) . poly(dG-dC) associated with the B-Z transition. Nature. 1981 Sep 17;293(5829):233–235. doi: 10.1038/293233a0. [DOI] [PubMed] [Google Scholar]
- Bestor T. H., Gundersen G., Kolstø A. B., Prydz H. CpG islands in mammalian gene promoters are inherently resistant to de novo methylation. Genet Anal Tech Appl. 1992 Apr;9(2):48–53. doi: 10.1016/1050-3862(92)90030-9. [DOI] [PubMed] [Google Scholar]
- Bird A. P. Genomic imprinting: imprints on islands. Curr Biol. 1993 May 1;3(5):275–277. doi: 10.1016/0960-9822(93)90177-p. [DOI] [PubMed] [Google Scholar]
- Brandeis M., Frank D., Keshet I., Siegfried Z., Mendelsohn M., Nemes A., Temper V., Razin A., Cedar H. Sp1 elements protect a CpG island from de novo methylation. Nature. 1994 Sep 29;371(6496):435–438. doi: 10.1038/371435a0. [DOI] [PubMed] [Google Scholar]
- Burge C., Campbell A. M., Karlin S. Over- and under-representation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1358–1362. doi: 10.1073/pnas.89.4.1358. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cambareri E. B., Jensen B. C., Schabtach E., Selker E. U. Repeat-induced G-C to A-T mutations in Neurospora. Science. 1989 Jun 30;244(4912):1571–1575. doi: 10.1126/science.2544994. [DOI] [PubMed] [Google Scholar]
- Cambareri E. B., Singer M. J., Selker E. U. Recurrence of repeat-induced point mutation (RIP) in Neurospora crassa. Genetics. 1991 Apr;127(4):699–710. doi: 10.1093/genetics/127.4.699. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Evans B. E., Mitchell G. N., Wolfenden R. The action of bacterial cytidine deaminase on 5,6-dihydrocytidine. Biochemistry. 1975 Feb 11;14(3):621–624. doi: 10.1021/bi00674a024. [DOI] [PubMed] [Google Scholar]
- Faugeron G., Rhounim L., Rossignol J. L. How does the cell count the number of ectopic copies of a gene in the premeiotic inactivation process acting in Ascobolus immersus? Genetics. 1990 Mar;124(3):585–591. doi: 10.1093/genetics/124.3.585. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fincham J. R. Generation of new functional mutant alleles by premeiotic disruption of the Neurospora crassa am gene. Curr Genet. 1990 Dec;18(5):441–445. doi: 10.1007/BF00309914. [DOI] [PubMed] [Google Scholar]
- Foss H. M., Roberts C. J., Claeys K. M., Selker E. U. Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation. Science. 1993 Dec 10;262(5140):1737–1741. doi: 10.1126/science.7505062. [DOI] [PubMed] [Google Scholar]
- Giles N. H., Case M. E., Baum J., Geever R., Huiet L., Patel V., Tyler B. Gene organization and regulation in the qa (quinic acid) gene cluster of Neurospora crassa. Microbiol Rev. 1985 Sep;49(3):338–358. doi: 10.1128/mr.49.3.338-358.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Grayburn W. S., Selker E. U. A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication. Mol Cell Biol. 1989 Oct;9(10):4416–4421. doi: 10.1128/mcb.9.10.4416. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hagerman P. J. Sequence-directed curvature of DNA. Annu Rev Biochem. 1990;59:755–781. doi: 10.1146/annurev.bi.59.070190.003543. [DOI] [PubMed] [Google Scholar]
- Harland R. M. Inheritance of DNA methylation in microinjected eggs of Xenopus laevis. Proc Natl Acad Sci U S A. 1982 Apr;79(7):2323–2327. doi: 10.1073/pnas.79.7.2323. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Holliday R., Pugh J. E. DNA modification mechanisms and gene activity during development. Science. 1975 Jan 24;187(4173):226–232. [PubMed] [Google Scholar]
- Jarai G., Marzluf G. A. Generation of new mutants of nmr, the negative-acting nitrogen regulatory gene of Neurospora crassa, by repeat induced mutation. Curr Genet. 1991 Sep;20(4):283–288. doi: 10.1007/BF00318516. [DOI] [PubMed] [Google Scholar]
- Kinnaird J. H., Fincham J. R. The complete nucleotide sequence of the Neurospora crassa am (NADP-specific glutamate dehydrogenase) gene. Gene. 1983 Dec;26(2-3):253–260. doi: 10.1016/0378-1119(83)90195-6. [DOI] [PubMed] [Google Scholar]
- Li E., Bestor T. H., Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 1992 Jun 12;69(6):915–926. doi: 10.1016/0092-8674(92)90611-f. [DOI] [PubMed] [Google Scholar]
- Macleod D., Charlton J., Mullins J., Bird A. P. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 1994 Oct 1;8(19):2282–2292. doi: 10.1101/gad.8.19.2282. [DOI] [PubMed] [Google Scholar]
- Miao V. P., Singer M. J., Rountree M. R., Selker E. U. A targeted-replacement system for identification of signals for de novo methylation in Neurospora crassa. Mol Cell Biol. 1994 Nov;14(11):7059–7067. doi: 10.1128/mcb.14.11.7059. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Miller C. A., Kowalski D. cis-acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae. Mol Cell Biol. 1993 Sep;13(9):5360–5369. doi: 10.1128/mcb.13.9.5360. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Monk M., Boubelik M., Lehnert S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development. 1987 Mar;99(3):371–382. doi: 10.1242/dev.99.3.371. [DOI] [PubMed] [Google Scholar]
- Nelson M., Raschke E., McClelland M. Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res. 1993 Jul 1;21(13):3139–3154. doi: 10.1093/nar/21.13.3139. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Perkins D. D., Barry E. G. The cytogenetics of Neurospora. Adv Genet. 1977;19:133–285. doi: 10.1016/s0065-2660(08)60246-1. [DOI] [PubMed] [Google Scholar]
- Perkins D. D., Metzenberg R. L., Raju N. B., Selker E. U., Barry E. G. Reversal of a Neurospora translocation by crossing over involving displaced rDNA, and methylation of the rDNA segments that result from recombination. Genetics. 1986 Nov;114(3):791–817. doi: 10.1093/genetics/114.3.791. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pollack Y., Stein R., Razin A., Cedar H. Methylation of foreign DNA sequences in eukaryotic cells. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6463–6467. doi: 10.1073/pnas.77.11.6463. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Razin A., Riggs A. D. DNA methylation and gene function. Science. 1980 Nov 7;210(4470):604–610. doi: 10.1126/science.6254144. [DOI] [PubMed] [Google Scholar]
- Rhounim L., Rossignol J. L., Faugeron G. Epimutation of repeated genes in Ascobolus immersus. EMBO J. 1992 Dec;11(12):4451–4457. doi: 10.1002/j.1460-2075.1992.tb05546.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Riggs A. D. X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet. 1975;14(1):9–25. doi: 10.1159/000130315. [DOI] [PubMed] [Google Scholar]
- SINSHEIMER R. L. The action of pancreatic deoxyribonuclease. II. Isomeric dinucleotides. J Biol Chem. 1955 Aug;215(2):579–583. [PubMed] [Google Scholar]
- Sasaki H., Allen N. D., Surani M. A. DNA methylation and genomic imprinting in mammals. EXS. 1993;64:469–486. doi: 10.1007/978-3-0348-9118-9_21. [DOI] [PubMed] [Google Scholar]
- Selker E. U., Cambareri E. B., Jensen B. C., Haack K. R. Rearrangement of duplicated DNA in specialized cells of Neurospora. Cell. 1987 Dec 4;51(5):741–752. doi: 10.1016/0092-8674(87)90097-3. [DOI] [PubMed] [Google Scholar]
- Selker E. U. DNA methylation and chromatin structure: a view from below. Trends Biochem Sci. 1990 Mar;15(3):103–107. doi: 10.1016/0968-0004(90)90193-f. [DOI] [PubMed] [Google Scholar]
- Selker E. U., Free S. J., Metzenberg R. L., Yanofsky C. An isolated pseudogene related to the 5S RNA genes in Neurospora crassa. Nature. 1981 Dec 10;294(5841):576–578. doi: 10.1038/294576a0. [DOI] [PubMed] [Google Scholar]
- Selker E. U., Fritz D. Y., Singer M. J. Dense nonsymmetrical DNA methylation resulting from repeat-induced point mutation in Neurospora. Science. 1993 Dec 10;262(5140):1724–1728. doi: 10.1126/science.8259516. [DOI] [PubMed] [Google Scholar]
- Selker E. U., Garrett P. W. DNA sequence duplications trigger gene inactivation in Neurospora crassa. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6870–6874. doi: 10.1073/pnas.85.18.6870. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Selker E. U., Jensen B. C., Richardson G. A. A portable signal causing faithful DNA methylation de novo in Neurospora crassa. Science. 1987 Oct 2;238(4823):48–53. doi: 10.1126/science.2958937. [DOI] [PubMed] [Google Scholar]
- Selker E. U. Premeiotic instability of repeated sequences in Neurospora crassa. Annu Rev Genet. 1990;24:579–613. doi: 10.1146/annurev.ge.24.120190.003051. [DOI] [PubMed] [Google Scholar]
- Selker E. U., Richardson G. A., Garrett-Engele P. W., Singer M. J., Miao V. Dissection of the signal for DNA methylation in the zeta-eta region of Neurospora. Cold Spring Harb Symp Quant Biol. 1993;58:323–329. doi: 10.1101/sqb.1993.058.01.038. [DOI] [PubMed] [Google Scholar]
- Selker E. U., Stevens J. N. DNA methylation at asymmetric sites is associated with numerous transition mutations. Proc Natl Acad Sci U S A. 1985 Dec;82(23):8114–8118. doi: 10.1073/pnas.82.23.8114. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shen J. C., Rideout W. M., 3rd, Jones P. A. High frequency mutagenesis by a DNA methyltransferase. Cell. 1992 Dec 24;71(7):1073–1080. doi: 10.1016/s0092-8674(05)80057-1. [DOI] [PubMed] [Google Scholar]
- Singer-Sam J., Riggs A. D. X chromosome inactivation and DNA methylation. EXS. 1993;64:358–384. doi: 10.1007/978-3-0348-9118-9_16. [DOI] [PubMed] [Google Scholar]
- Smith S. S., Kan J. L., Baker D. J., Kaplan B. E., Dembek P. Recognition of unusual DNA structures by human DNA (cytosine-5)methyltransferase. J Mol Biol. 1991 Jan 5;217(1):39–51. doi: 10.1016/0022-2836(91)90609-a. [DOI] [PubMed] [Google Scholar]
- Stadler D., Macleod H., Dillon D. Spontaneous mutation at the mtr locus of Neurospora: the spectrum of mutant types. Genetics. 1991 Sep;129(1):39–45. doi: 10.1093/genetics/129.1.39. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Szyf M., Schimmer B. P., Seidman J. G. Nucleotide-sequence-specific de novo methylation in a somatic murine cell line. Proc Natl Acad Sci U S A. 1989 Sep;86(18):6853–6857. doi: 10.1073/pnas.86.18.6853. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Toth M., Müller U., Doerfler W. Establishment of de novo DNA methylation patterns. Transcription factor binding and deoxycytidine methylation at CpG and non-CpG sequences in an integrated adenovirus promoter. J Mol Biol. 1990 Aug 5;214(3):673–683. doi: 10.1016/0022-2836(90)90285-T. [DOI] [PubMed] [Google Scholar]
- Turker M. S., Mummaneni P., Bishop P. L. Region- and cell type-specific de novo DNA methylation in cultured mammalian cells. Somat Cell Mol Genet. 1991 Mar;17(2):151–157. doi: 10.1007/BF01232972. [DOI] [PubMed] [Google Scholar]
- Turker M. S., Swisshelm K., Smith A. C., Martin G. M. A partial methylation profile for a CpG site is stably maintained in mammalian tissues and cultured cell lines. J Biol Chem. 1989 Jul 15;264(20):11632–11636. [PubMed] [Google Scholar]
- Ulanovsky L. E., Trifonov E. N. Estimation of wedge components in curved DNA. Nature. 1987 Apr 16;326(6114):720–722. doi: 10.1038/326720a0. [DOI] [PubMed] [Google Scholar]
- VanWye J. D., Bronson E. C., Anderson J. N. Species-specific patterns of DNA bending and sequence. Nucleic Acids Res. 1991 Oct 11;19(19):5253–5261. doi: 10.1093/nar/19.19.5253. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wigler M., Levy D., Perucho M. The somatic replication of DNA methylation. Cell. 1981 Apr;24(1):33–40. doi: 10.1016/0092-8674(81)90498-0. [DOI] [PubMed] [Google Scholar]
- Woodcock D. M., Crowther P. J., Diver W. P. The majority of methylated deoxycytidines in human DNA are not in the CpG dinucleotide. Biochem Biophys Res Commun. 1987 Jun 15;145(2):888–894. doi: 10.1016/0006-291x(87)91048-5. [DOI] [PubMed] [Google Scholar]
- Wu J. C., Santi D. V. Kinetic and catalytic mechanism of HhaI methyltransferase. J Biol Chem. 1987 Apr 5;262(10):4778–4786. [PubMed] [Google Scholar]
- Wyszynski M., Gabbara S., Bhagwat A. S. Cytosine deaminations catalyzed by DNA cytosine methyltransferases are unlikely to be the major cause of mutational hot spots at sites of cytosine methylation in Escherichia coli. Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1574–1578. doi: 10.1073/pnas.91.4.1574. [DOI] [PMC free article] [PubMed] [Google Scholar]