Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. 1998 Aug; 149(4): 1787–1797.
PMCID: PMC1460257

A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation.


In an analysis of 22 of the roughly 100 dispersed 5S rRNA genes in Neurospora crassa, a methylated 5S rRNA pseudogene, Psi63, was identified. We characterized the Psi63 region to better understand the control and function of DNA methylation. The 120-bp 5S rRNA-like region of Psi63 is interrupted by a 1.9-kb insertion that has characteristics of sequences that have been modified by repeat-induced point mutation (RIP). We found sequences related to this insertion in wild-type strains of N. crassa and other Neurospora species. Most showed evidence of RIP; but one, isolated from the N. crassa host of Psi63, showed no evidence of RIP. A deletion from near the center of this sequence apparently rendered it incapable of participating in RIP with the related full-length copies. The Psi63 insertion and the related sequences have features of transposons and are related to the Fot1 class of fungal transposable elements. Apparently Psi63 was generated by insertion of a previously unrecognized Neurospora transposable element into a 5S rRNA gene, followed by RIP. We name the resulting inactivated Neurospora transposon PuntRIP1 and the related sequence showing no evidence of RIP, but harboring a deletion that presumably rendered it defective for transposition, dPunt.

Full Text

The Full Text of this article is available as a PDF (340K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Amado L, Abranches R, Neves N, Viegas W. Development-dependent inheritance of 5-azacytidine-induced epimutations in triticale: analysis of rDNA expression patterns. Chromosome Res. 1997 Nov;5(7):445–450. [PubMed]
  • Buckler ES, 4th, Ippolito A, Holtsford TP. The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics. 1997 Mar;145(3):821–832. [PMC free article] [PubMed]
  • Cambareri EB, Jensen BC, Schabtach E, Selker EU. Repeat-induced G-C to A-T mutations in Neurospora. Science. 1989 Jun 30;244(4912):1571–1575. [PubMed]
  • Cambareri EB, Singer MJ, Selker EU. Recurrence of repeat-induced point mutation (RIP) in Neurospora crassa. Genetics. 1991 Apr;127(4):699–710. [PMC free article] [PubMed]
  • Cambareri EB, Foss HM, Rountree MR, Selker EU, Kinsey JA. Epigenetic control of a transposon-inactivated gene in Neurospora is dependent on DNA methylation. Genetics. 1996 May;143(1):137–146. [PMC free article] [PubMed]
  • Cogoni C, Irelan JT, Schumacher M, Schmidhauser TJ, Selker EU, Macino G. Transgene silencing of the al-1 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNA-DNA interactions or DNA methylation. EMBO J. 1996 Jun 17;15(12):3153–3163. [PMC free article] [PubMed]
  • Nyyssönen E, Amutan M, Enfield L, Stubbs J, Dunn-Coleman NS. The transposable element Tan1 of Aspergillus niger var. awamori, a new member of the Fot1 family. Mol Gen Genet. 1996 Nov 27;253(1-2):50–56. [PubMed]
  • Panaccione DG, Pitkin JW, Walton JD, Annis SL. Transposon-like sequences at the TOX2 locus of the plant-pathogenic fungus Cochliobolus carbonum. Gene. 1996 Oct 17;176(1-2):103–109. [PubMed]
  • Enkerli J, Bhatt G, Covert SF. Nht1, a transposable element cloned from a dispensable chromosome in Nectria haematococca. Mol Plant Microbe Interact. 1997 Aug;10(6):742–749. [PubMed]
  • Perkins DD, Metzenberg RL, Raju NB, Selker EU, Barry EG. 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. [PMC free article] [PubMed]
  • Farman ML, Taura S, Leong SA. The Magnaporthe grisea DNA fingerprinting probe MGR586 contains the 3' end of an inverted repeat transposon. Mol Gen Genet. 1996 Jul 26;251(6):675–681. [PubMed]
  • Fedoroff N, Schläppi M, Raina R. Epigenetic regulation of the maize Spm transposon. Bioessays. 1995 Apr;17(4):291–297. [PubMed]
  • Rountree MR, Selker EU. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev. 1997 Sep 15;11(18):2383–2395. [PMC free article] [PubMed]
  • Foss HM, Roberts CJ, Claeys KM, Selker EU. Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation. Science. 1993 Dec 10;262(5140):1737–1741. [PubMed]
  • Geever RF, Huiet L, Baum JA, Tyler BM, Patel VB, Rutledge BJ, Case ME, Giles NH. DNA sequence, organization and regulation of the qa gene cluster of Neurospora crassa. J Mol Biol. 1989 May 5;207(1):15–34. [PubMed]
  • Glass NL, Grotelueschen J, Metzenberg RL. Neurospora crassa A mating-type region. Proc Natl Acad Sci U S A. 1990 Jul;87(13):4912–4916. [PMC free article] [PubMed]
  • Schechtman MG. Characterization of telomere DNA from Neurospora crassa. Gene. 1990 Apr 16;88(2):159–165. [PubMed]
  • Goyon C, Rossignol JL, Faugeron G. Native DNA repeats and methylation in Ascobolus. Nucleic Acids Res. 1996 Sep 1;24(17):3348–3356. [PMC free article] [PubMed]
  • Selker EU. Control of DNA methylation in fungi. EXS. 1993;64:212–217. [PubMed]
  • Grayburn WS, Selker EU. A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication. Mol Cell Biol. 1989 Oct;9(10):4416–4421. [PMC free article] [PubMed]
  • Selker EU. Epigenetic phenomena in filamentous fungi: useful paradigms or repeat-induced confusion? Trends Genet. 1997 Aug;13(8):296–301. [PubMed]
  • Irelan JT, Selker EU. Cytosine methylation associated with repeat-induced point mutation causes epigenetic gene silencing in Neurospora crassa. Genetics. 1997 Jun;146(2):509–523. [PMC free article] [PubMed]
  • Selker EU, Garrett PW. DNA sequence duplications trigger gene inactivation in Neurospora crassa. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6870–6874. [PMC free article] [PubMed]
  • Kachroo P, Leong SA, Chattoo BB. Pot2, an inverted repeat transposon from the rice blast fungus Magnaporthe grisea. Mol Gen Genet. 1994 Nov 1;245(3):339–348. [PubMed]
  • Selker EU, Stevens JN. DNA methylation at asymmetric sites is associated with numerous transition mutations. Proc Natl Acad Sci U S A. 1985 Dec;82(23):8114–8118. [PMC free article] [PubMed]
  • Kinnaird JH, Fincham JR. The complete nucleotide sequence of the Neurospora crassa am (NADP-specific glutamate dehydrogenase) gene. Gene. 1983 Dec;26(2-3):253–260. [PubMed]
  • Selker EU, Stevens JN. Signal for DNA methylation associated with tandem duplication in Neurospora crassa. Mol Cell Biol. 1987 Mar;7(3):1032–1038. [PMC free article] [PubMed]
  • Kinsey JA, Helber J. Isolation of a transposable element from Neurospora crassa. Proc Natl Acad Sci U S A. 1989 Mar;86(6):1929–1933. [PMC free article] [PubMed]
  • Selker EU, Yanofsky C, Driftmier K, Metzenberg RL, Alzner-DeWeerd B, RajBhandary UL. Dispersed 5S RNA genes in N. crassa: structure, expression and evolution. Cell. 1981 Jun;24(3):819–828. [PubMed]
  • Kinsey JA, Garrett-Engele PW, Cambareri EB, Selker EU. The Neurospora transposon Tad is sensitive to repeat-induced point mutation (RIP). Genetics. 1994 Nov;138(3):657–664. [PMC free article] [PubMed]
  • Selker EU, Yanofsky C, Driftmier K, Metzenberg RL, Alzner-DeWeerd B, RajBhandary UL. Dispersed 5S RNA genes in N. crassa: structure, expression and evolution. Cell. 1981 Jun;24(3):819–828. [PubMed]
  • Kinsey JA, Garrett-Engele PW, Cambareri EB, Selker EU. The Neurospora transposon Tad is sensitive to repeat-induced point mutation (RIP). Genetics. 1994 Nov;138(3):657–664. [PMC free article] [PubMed]
  • Kochanek S, Hosokawa K, Schiedner G, Renz D, Doerfler W. DNA methylation in the promoter of ribosomal RNA genes in human cells as determined by genomic sequencing. FEBS Lett. 1996 Jun 17;388(2-3):192–194. [PubMed]
  • Selker EU, Cambareri EB, Jensen BC, Haack KR. Rearrangement of duplicated DNA in specialized cells of Neurospora. Cell. 1987 Dec 4;51(5):741–752. [PubMed]
  • Levis C, Fortini D, Brygoo Y. Flipper, a mobile Fot1-like transposable element in Botrytis cinerea. Mol Gen Genet. 1997 May;254(6):674–680. [PubMed]
  • Selker EU, Jensen BC, Richardson GA. A portable signal causing faithful DNA methylation de novo in Neurospora crassa. Science. 1987 Oct 2;238(4823):48–53. [PubMed]
  • Metzenberg RL, Stevens JN, Selker EU, Morzycka-Wroblewska E. Identification and chromosomal distribution of 5S rRNA genes in Neurospora crassa. Proc Natl Acad Sci U S A. 1985 Apr;82(7):2067–2071. [PMC free article] [PubMed]
  • Selker EU, Richardson GA, Garrett-Engele PW, Singer MJ, 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. [PubMed]
  • Miao VP, Singer MJ, Rountree MR, Selker EU. A targeted-replacement system for identification of signals for de novo methylation in Neurospora crassa. Mol Cell Biol. 1994 Nov;14(11):7059–7067. [PMC free article] [PubMed]
  • Villa VD, Storck R. Nucleotide composition of nuclear and mitochondrial deoxyribonucleic acid of fungi. J Bacteriol. 1968 Jul;96(1):184–190. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • Yoder JA, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997 Aug;13(8):335–340. [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America


Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • MedGen
    Related information in MedGen
  • Nucleotide
    Primary database (GenBank) nucleotide records reported in the current articles as well as Reference Sequences (RefSeqs) that include the articles as references.
  • PubMed
    PubMed citations for these articles
  • Taxonomy
    Taxonomy records associated with the current articles through taxonomic information on related molecular database records (Nucleotide, Protein, Gene, SNP, Structure).
  • Taxonomy Tree
    Taxonomy Tree

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...