title: Identification of RNA-dependent DNA-methylation regulated promoters in Arabidopsis.
abstract: RNA-dependent DNA methylation (RdDM) is an important regulatory event involved in repressive epigenetic modifications that can trigger transcriptional gene silencing (TGS). The criteria we used to pick out promoter sequences targeted by RdDM in Arabidopsis thaliana were the main RdDM hallmark properties: 24nt siRNAs as inducers of DNA methylation and transposable elements (TE) as one of the major targets of RdDM. Those genes whose promoters comprised overlapping sites for 24nt siRNA hits, TE and DNA methylation (siRNA/TE/Methylation overlapping regions), were defined as candidates that might be silenced by RdDM. On this basis two gene sets were created which include abiotic and biotic stress-responsive genes whose promoters may be silenced by RdDM. The DNA methylation status of the At3g50770 (CML41) promoter - one of the selected candidates, was experimentally assayed, and it showed dependence on the RdDM-associated Polymerase IV and Polymerase V. A publicly available 24nt siRNA-centered database called starPRO was developed that allows users easily to discover whether a particular promoter sequence is related to RdDM-associated features such as 24nt siRNA-target sites, TE, tandem repeats and DNA methylation.
authors.affiliation: Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria.
authors.forename: Vesselin
authors.initials: V
authors.lastname: Baev
authors.forename: Mladen
authors.initials: M
authors.lastname: Naydenov
authors.forename: Elena
authors.initials: E
authors.lastname: Apostolova
authors.forename: Desislava
authors.initials: D
authors.lastname: Ivanova
authors.forename: Slaveya
authors.initials: S
authors.lastname: Doncheva
authors.forename: Ivan
authors.initials: I
authors.lastname: Minkov
authors.forename: Galina
authors.initials: G
authors.lastname: Yahubyan
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics; D019175:DNA Methylation; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000378:metabolism*; D004259:DNA-Directed DNA Polymerase; D016208:Databases, Factual; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D017343:Genes, Plant; D011401:Promoter Regions, Genetic; D034741:RNA, Small Interfering / Q000378:metabolism*; D013312:Stress, Physiological / Q000235:genetics; D020080:Tandem Repeat Sequences
chemical_list: D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements; D018744:DNA, Plant; D034741:RNA, Small Interfering; D004259:DNA-Directed DNA Polymerase