siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis

Jun Liu, Xuemei Chen

Waksman Institute, Rutgers University

Allelic variation in FLOWERING LOCUS C (FLC), a major repressor of flowering, contributes to natural differences in flowering behavior among Arabidopsis accessions. While the late-flowering accessions have dominant, functional FLC alleles, some early accessions have recessive flc alleles that do not have mutations in the coding region of the gene. The weakness of the FLC allele in Ler, a commonly used laboratory strain, is due to low levels of FLC RNA resulting, through an unknown mechanism, from a transposable element inserted in the first intron of FLC. Here we show that the transposable element renders flc-Ler subject to posttranscriptional gene silencing (PTGS) mediated by short interfering RNAs generated from homologous transposable elements elsewhere in the genome. Relieving the PTGS results in increased FLC mRNA level and renders the flc-Ler allele active in causing late flowering. Eukaryotic genomes contain numerous transposable elements or repeat sequences, many of which are found in introns or recruited as exons of genes during evolution. Since small RNA-based regulatory mechanisms are conserved in plants and animals, our study may have uncovered a general mechanism of eukaryotic gene expression modulated by transposable elements or repeat sequences.