• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Sep 1999; 153(1): 401–413.
PMCID: PMC1460723

Arabidopsis PAI gene arrangements, cytosine methylation and expression.


Previous analysis of the PAI tryptophan biosynthetic gene family in Arabidopsis thaliana revealed that the Wassilewskija (WS) ecotype has four PAI genes at three unlinked sites: a tail-to-tail inverted repeat at one locus (PAI1-PAI4) plus singlet genes at two other loci (PAI2 and PAI3). The four WS PAI genes are densely cytosine methylated over their regions of DNA identity. In contrast, the Columbia (Col) ecotype has three singlet PAI genes at the analogous loci (PAI1, PAI2, and PAI3) and no cytosine methylation. To understand the mechanism of PAI gene duplication at the polymorphic PAI1 locus, and to investigate the relationship between PAI gene arrangement and PAI gene methylation, we analyzed 39 additional ecotypes of Arabidopsis. Six ecotypes had PAI arrangements similar to WS, with an inverted repeat and dense PAI methylation. All other ecotypes had PAI arrangements similar to Col, with no PAI methylation. The novel PAI-methylated ecotypes provide insights into the mechanisms underlying PAI gene duplication and methylation, as well as the relationship between methylation and gene expression.

Full Text

The Full Text of this article is available as a PDF (320K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bollmann J, Carpenter R, Coen ES. Allelic interactions at the nivea locus of Antirrhinum. Plant Cell. 1991 Dec;3(12):1327–1336. [PMC free article] [PubMed]
  • Bonham-Smith PC, Moloney MM. Nucleotide and protein sequences of a cytoplasmic ribosomal protein S15a gene from Arabidopsis thaliana. Plant Physiol. 1994 Sep;106(1):401–402. [PMC free article] [PubMed]
  • Church GM, Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. [PMC free article] [PubMed]
  • Elledge SJ, Mulligan JT, Ramer SW, Spottswood M, Davis RW. Lambda YES: a multifunctional cDNA expression vector for the isolation of genes by complementation of yeast and Escherichia coli mutations. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):1731–1735. [PMC free article] [PubMed]
  • Gibson S, Arondel V, Iba K, Somerville C. Cloning of a temperature-regulated gene encoding a chloroplast omega-3 desaturase from Arabidopsis thaliana. Plant Physiol. 1994 Dec;106(4):1615–1621. [PMC free article] [PubMed]
  • Hanfstingl U, Berry A, Kellogg EA, Costa JT, 3rd, Rüdiger W, Ausubel FM. Haplotypic divergence coupled with lack of diversity at the Arabidopsis thaliana alcohol dehydrogenase locus: roles for both balancing and directional selection? Genetics. 1994 Nov;138(3):811–828. [PMC free article] [PubMed]
  • Henderson ST, Petes TD. Instability of a plasmid-borne inverted repeat in Saccharomyces cerevisiae. Genetics. 1993 May;134(1):57–62. [PMC free article] [PubMed]
  • Innan H, Terauchi R, Miyashita NT. Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics. 1997 Aug;146(4):1441–1452. [PMC free article] [PubMed]
  • Jeddeloh JA, Bender J, Richards EJ. The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 1998 Jun 1;12(11):1714–1725. [PMC free article] [PubMed]
  • Kass SU, Pruss D, Wolffe AP. How does DNA methylation repress transcription? Trends Genet. 1997 Nov;13(11):444–449. [PubMed]
  • Kunkel TA, Roberts JD, Zakour RA. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 1987;154:367–382. [PubMed]
  • Last RL, Bissinger PH, Mahoney DJ, Radwanski ER, Fink GR. Tryptophan mutants in Arabidopsis: the consequences of duplicated tryptophan synthase beta genes. Plant Cell. 1991 Apr;3(4):345–358. [PMC free article] [PubMed]
  • Li J, Zhao J, Rose AB, Schmidt R, Last RL. Arabidopsis phosphoribosylanthranilate isomerase: molecular genetic analysis of triplicate tryptophan pathway genes. Plant Cell. 1995 Apr;7(4):447–461. [PMC free article] [PubMed]
  • Luff B, Pawlowski L, Bender J. An inverted repeat triggers cytosine methylation of identical sequences in Arabidopsis. Mol Cell. 1999 Apr;3(4):505–511. [PubMed]
  • Maloisel L, Rossignol JL. Suppression of crossing-over by DNA methylation in Ascobolus. Genes Dev. 1998 May 1;12(9):1381–1389. [PMC free article] [PubMed]
  • Mette MF, van der Winden J, Matzke MA, Matzke AJ. Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. EMBO J. 1999 Jan 4;18(1):241–248. [PMC free article] [PubMed]
  • Minet M, Dufour ME, Lacroute F. Complementation of Saccharomyces cerevisiae auxotrophic mutants by Arabidopsis thaliana cDNAs. Plant J. 1992 May;2(3):417–422. [PubMed]
  • Montgomery MK, Fire A. Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet. 1998 Jul;14(7):255–258. [PubMed]
  • Niyogi KK, Fink GR. Two anthranilate synthase genes in Arabidopsis: defense-related regulation of the tryptophan pathway. Plant Cell. 1992 Jun;4(6):721–733. [PMC free article] [PubMed]
  • Niyogi KK, Last RL, Fink GR, Keith B. Suppressors of trp1 fluorescence identify a new arabidopsis gene, TRP4, encoding the anthranilate synthase beta subunit. Plant Cell. 1993 Sep;5(9):1011–1027. [PMC free article] [PubMed]
  • Bender J. Cytosine methylation of repeated sequences in eukaryotes: the role of DNA pairing. Trends Biochem Sci. 1998 Jul;23(7):252–256. [PubMed]
  • Ruskin B, Fink GR. Mutations in POL1 increase the mitotic instability of tandem inverted repeats in Saccharomyces cerevisiae. Genetics. 1993 May;134(1):43–56. [PMC free article] [PubMed]
  • Sato S, Kotani H, Nakamura Y, Kaneko T, Asamizu E, Fukami M, Miyajima N, Tabata S. Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones. DNA Res. 1997 Jun 30;4(3):215–230. [PubMed]
  • Bhatt AM, Lister C, Crawford N, Dean C. The transposition frequency of Tag1 elements is increased in transgenic Arabidopsis lines. Plant Cell. 1998 Mar;10(3):427–434. [PMC free article] [PubMed]
  • Stinard PS, Robertson DS, Schnable PS. Genetic Isolation, Cloning, and Analysis of a Mutator-Induced, Dominant Antimorph of the Maize amylose extender1 Locus. Plant Cell. 1993 Nov;5(11):1555–1566. [PMC free article] [PubMed]

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


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...