title: Small RNA-directed epigenetic natural variation in Arabidopsis thaliana.
abstract: Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations. Nevertheless, little is known about the role of epigenetics in evolution. This is due in part to scant data on epigenetic variation among natural populations. In plants, small interfering RNA (siRNA) is involved in both the initiation and maintenance of gene silencing by directing DNA methylation and/or histone methylation. Here, we report that, in the model plant Arabidopsis thaliana, a cluster of approximately 24 nt siRNAs found at high levels in the ecotype Landsberg erecta (Ler) could direct DNA methylation and heterochromatinization at a hAT element adjacent to the promoter of FLOWERING LOCUS C (FLC), a major repressor of flowering, whereas the same hAT element in ecotype Columbia (Col) with almost identical DNA sequence, generates a set of low abundance siRNAs that do not direct these activities. We have called this hAT element MPF for Methylated region near Promoter of FLC, although de novo methylation triggered by an inverted repeat transgene at this region in Col does not alter its FLC expression. DNA methylation of the Ler allele MPF is dependent on genes in known silencing pathways, and such methylation is transmissible to Col by genetic crosses, although with varying degrees of penetrance. A genome-wide comparison of Ler and Col small RNAs identified at least 68 loci matched by a significant level of approximately 24 nt siRNAs present specifically in Ler but not Col, where nearly half of the loci are related to repeat or TE sequences. Methylation analysis revealed that 88% of the examined loci (37 out of 42) were specifically methylated in Ler but not Col, suggesting that small RNA can direct epigenetic differences between two closely related Arabidopsis ecotypes.
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jixian
authors.initials: J
authors.lastname: Zhai
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Pingchuan
authors.initials: P
authors.lastname: Li
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.forename: Xuemei
authors.initials: X
authors.lastname: Chen
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Cao
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics; D001483:Base Sequence; D003433:Crosses, Genetic; D019175:DNA Methylation; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D044127:Epigenesis, Genetic; D035264:Flowers / Q000254:growth & development; D014644:Genetic Variation; D018745:Genome, Plant; D026161:MADS Domain Proteins / Q000235:genetics; D030821:Plants, Genetically Modified; D011401:Promoter Regions, Genetic; D034622:RNA Interference; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D017931:DNA Primers; D018744:DNA, Plant; C418902:At5g10140 protein, Arabidopsis; D026161:MADS Domain Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering