Arabidopsis PAI Gene Arrangements, Cytosine Methylation and Expression

Corresponding author: Judith Bender, Department of Biochemistry, Johns Hopkins University School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205., jbender{at}welchlink.welch.jhu.edu (E-mail)

Communicating editor: J. A. BIRCHLER

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.

This article has been cited by other articles:

				L. Mull, M. L. Ebbs, and J. Bender A Histone Methylation-Dependent DNA Methylation Pathway Is Uniquely Impaired by Deficiency in Arabidopsis S-Adenosylhomocysteine Hydrolase Genetics, November 1, 2006; 174(3): 1161 - 1171. [Abstract] [Full Text] [PDF]

				M. L. Ebbs and J. Bender Locus-Specific Control of DNA Methylation by the Arabidopsis SUVH5 Histone Methyltransferase PLANT CELL, May 1, 2006; 18(5): 1166 - 1176. [Abstract] [Full Text] [PDF]

				M. L. Ebbs, L. Bartee, and J. Bender H3 Lysine 9 Methylation Is Maintained on a Transcribed Inverted Repeat by Combined Action of SUVH6 and SUVH4 Methyltransferases Mol. Cell. Biol., December 1, 2005; 25(23): 10507 - 10515. [Abstract] [Full Text] [PDF]

				O. Mathieu and J. Bender RNA-directed DNA methylation J. Cell Sci., October 1, 2004; 117(21): 4881 - 4888. [Abstract] [Full Text] [PDF]

				S. Melquist and J. Bender An Internal Rearrangement in an Arabidopsis Inverted Repeat Locus Impairs DNA Methylation Triggered by the Locus Genetics, January 1, 2004; 166(1): 437 - 448. [Abstract] [Full Text] [PDF]

				S. Melquist and J. Bender Transcription from an upstream promoter controls methylation signaling from an inverted repeat of endogenous genes in Arabidopsis Genes & Dev., August 15, 2003; 17(16): 2036 - 2047. [Abstract] [Full Text] [PDF]

				J. A. Quiel and J. Bender Glucose Conjugation of Anthranilate by the Arabidopsis UGT74F2 Glucosyltransferase Is Required for Tryptophan Mutant Blue Fluorescence J. Biol. Chem., February 14, 2003; 278(8): 6275 - 6281. [Abstract] [Full Text] [PDF]

				T. Kakutani Epi-Alleles in Plants: Inheritance of Epigenetic Information over Generations Plant Cell Physiol., October 15, 2002; 43(10): 1106 - 1111. [Abstract] [Full Text] [PDF]

				G. A. Smolen, L. Pawlowski, S. E. Wilensky, and J. Bender Dominant Alleles of the Basic Helix-Loop-Helix Transcription Factor ATR2 Activate Stress-Responsive Genes in Arabidopsis Genetics, July 1, 2002; 161(3): 1235 - 1246. [Abstract] [Full Text] [PDF]

				T. L. Stokes, B. N. Kunkel, and E. J. Richards Epigenetic variation in Arabidopsis disease resistance Genes & Dev., January 15, 2002; 16(2): 171 - 182. [Abstract] [Full Text] [PDF]

				G. Smolen and J. Bender Arabidopsis Cytochrome P450 cyp83B1 Mutations Activate the Tryptophan Biosynthetic Pathway Genetics, January 1, 2002; 160(1): 323 - 332. [Abstract] [Full Text] [PDF]

				R. A. Martienssen and V. Colot DNA Methylation and Epigenetic Inheritance in Plants and Filamentous Fungi Science, August 10, 2001; 293(5532): 1070 - 1074. [Abstract] [Full Text] [PDF]

				L. Bartee, F. Malagnac, and J. Bender Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene Genes & Dev., July 15, 2001; 15(14): 1753 - 1758. [Abstract] [Full Text] [PDF]

				L. Bartee and J. Bender Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family Nucleic Acids Res., May 15, 2001; 29(10): 2127 - 2134. [Abstract] [Full Text] [PDF]

				C. D. Day, E. Lee, J. Kobayashi, L. D. Holappa, H. Albert, and D. W. Ow Transgene integration into the same chromosome location can produce alleles that express at a predictable level, or alleles that are differentially silenced Genes & Dev., November 15, 2000; 14(22): 2869 - 2880. [Abstract] [Full Text]