Analysis of hypermethylation in the RPS element suggests a signal function for short inverted repeats in de novo methylation

• Published in: Plant molecular biology Vol. 48; no. 4; pp. 383 - 399
• Main Authors: Müller, Andreas, Marins, Mozart, Kamisugi, Yasuko, Meyer, Peter
• Format: Journal Article
• Language: English
• Published: Netherlands Springer Nature B.V 01.03.2002
• Subjects: Animals; Arabidopsis; Arabidopsis thaliana; Base Sequence; Binding Sites; Blotting, Southern; chromosomes; Deoxyribonucleases, Type II Site-Specific; Deoxyribonucleases, Type II Site-Specific - metabolism; Deoxyribonucleic acid; DNA; DNA - genetics; DNA - metabolism; DNA conformation; DNA Methylation; DNA, Plant; DNA, Plant - genetics; DNA, Plant - metabolism; Evolution, Molecular; Gene Expression Regulation, Plant; Genes; genetic transformation; Genetic Variation; genetics; Genome, Plant; Heterochromatin; Heterochromatin - genetics; Humans; In Situ Hybridization, Fluorescence; metabolism; methylation; Models, Genetic; Molecular Sequence Data; Nicotiana - genetics; nucleic acid hybridization; Petunia hybrida; Plants; Plants - genetics; protein secondary structure; repetitive sequences; Repetitive Sequences, Nucleic Acid; Repetitive Sequences, Nucleic Acid - genetics; Solanaceae; Solanaceae - genetics; Species Specificity; Tobacco; transgenic plants
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1023/A:1014091131490

A repetitive DNA sequence (RPS) from Petunia hybrida had previously been shown to enhance expression variegation in petunia and tobacco and to carry a hot spot for de novo DNA methylation. Here we show that a strong de novo hypermethylation site is located within a palindromic segment of the RPS and present indirect evidence, based on sequence homologies to other repeat units within the RPS, for the formation of secondary structures at the methylation site in vivo. We demonstrate that the palindromic RPS element, which is moderately to highly repetitive in petunia, does not predominantly localise to constitutive heterochromatin. To test whether the RPS is subject to de novo methylation due to its repetitive nature or to intrinsic signals within the RPS, we integrated the RPS into the genome of Arabidopsis thaliana, a plant lacking homology to the RPS. Our data indicate that the palindromic element also acts as a de novo hypermethylation site in the non-repetitive genomic background of Arabidopsis, strongly suggesting a signal function of the palindromic RPS element.