Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2004 Dec 1;18(23):2873-8.
doi: 10.1101/gad.1217304. Epub 2004 Nov 15.

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

Jun Liu  1 , Yuehui He, Richard Amasino, Xuemei Chen
Affiliations

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

Jun Liu et al. Genes Dev. .

Abstract

Allelic variation in FLOWERING LOCUS C (FLC), a central repressor of flowering, contributes to natural differences in flowering behavior among Arabidopsis accessions. The weak nature of the FLC allele in the Ler accession is due to low levels of FLC RNA resulting, through an unknown mechanism, from a transposable element inserted in an intron of FLC. Here we show that the transposable element renders FLC-Ler subject to repressive chromatin modifications mediated by short interfering RNAs generated from homologous transposable elements in the genome. Our studies have general implications for the role of transposable elements in eukaryotic gene expression and evolution.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Flowering time of various genotypes under long-day (LD) conditions. (a) One-month-old Ler and hen1-1 plants. (b) A 50-d hen1-1 plant. (c) A 30-d hen1-1 flc-3 plant. (d) A 50-d hen1-1 FRI-SF2 plant. (e,f) Flowering time (total leaf number and/or days to bolting) of the indicated genotypes. n = 90 (e) or 20-30 (f).
Figure 2.
Figure 2.
Analysis of FLC expression. (a,b) FLC RNA filter hybridization with probe A (d). The numbers in a indicate the abundance of the RNAs relative to FLC mRNA in Ler. An image of a stained RNA gel in b indicates the amount of RNAs in each lane. (c) A diagram of FLC-Ler genomic region, with white boxes representing exons, lines representing introns, and the TE represented by the striped box. The thick, black line represents the intron 1 sequence downstream of the TE. (d) FLC mRNA. (e) Two FLCTE RNAs that differ in intron 1 sequences 3′ to the TE. The sequence at the junction of exon 1 and the TE was not determined, but RT-PCR experiments indicate the presence of exon 1 and the lack of intron 1 sequence 5′ to the TE. A-C indicate probes for RNA filter hybridization.
Figure 3.
Figure 3.
Transposon siRNA accumulation and DNA methylation in various genotypes. Sense (a,c) or antisense (b) probes both detected siRNATEs. (d) Detection of siRNAs corresponding to AtSN1 in various genotypes. The 5S rRNA served as an internal control. rdr6sgs2-1, sgs3-1, and hen1-4 are in the Col accession; sde4-1 is in the C24 accession; and all other genotypes are in the Ler accession. The size of the siRNATEs was estimated with a 10-nt RNA ladder (Ambion) and by probing the same blot to visualize miR173 of known size (22 nt). (e) Determination of DNA methylation status at FLC-Ler in Ler (L), hen1-1 (h), ago4-1 (a), and cmt3-7 (c). A diagram of FLC-Ler genomic region is shown on top with the positions of restriction sites as indicated: (Hh) HhaI; (Hi) HindIII; (C) ClaI; (A) AciI; (Hh) HhaI. The probe corresponds to sequences flanking the TE (black box). The fragments that can hybridize to the probe in various digests are diagramed. The size of the fragments is indicated by numbers (in kilobases) underneath the fragments.
Figure 4.
Figure 4.
Chromatin immunoprecipitation (ChIP) to detect histone H3-K9 dimethylation at the FLC-Ler locus. (a) Schematic structure of the genomic FLC-Ler region. I-VI represent the regions for which H3-K9 dimethylation states were examined by ChIP. The translation initiation point is +1. The filled boxes represent exons, and open boxes represent introns. (b) ChIP analyses of the H3-K9 dimethylation state of various genomic FLC regions. The input is Ler chromatin before immunoprecipitation. “No AB” refers to the control sample lacking antibody. ACTIN served as an internal control. (c) ChIP analyses of the H3-K9 dimethylation state of FLC chromatin in Ler, hen1-1, and cmt3-7. (d) The fold reduction of dimethylated H3-K9 of FLC chromatin in hen1-1 compared to Ler at the indicated regions. The fold reduction of hen1-1 compared to Ler was calculated as follows: FLC in Ler was first normalized to ACTIN; the normalized FLC in Ler was then divided by the normalized FLC in hen1-1 to obtain the fold reduction in the mutant. The error bars represent standard deviations of three independent immunoprecipitations.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Bartee L., Malagnac, F., and Bender, J. 2001. Arabidopsis cmt3 chromo-methylase mutations block non-CG methylation and silencing of an endogenous gene. Genes & Dev. 15 1753-1758. - PMC - PubMed
    1. Bartel D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116 281-297. - PubMed
    1. Boss P.K., Bastow, R.M., Mylne, J.S., and Dean, C. 2004. Multiple pathways in the decision to flower: Enabling, promoting, and resetting. Plant Cell 16 Suppl: S18-S31. - PMC - PubMed
    1. Boutet S., Vazquez, F., Liu, J., Beclin, C., Fagard, M., Gratias, A., Morel, J.B., Crete, P., Chen, X., and Vaucheret, H. 2003. Arabidopsis HEN1. A genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr. Biol. 13 843-848. - PMC - PubMed
    1. Chen X., Liu, J., Cheng, Y., and Jia, D. 2002. HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development 129 1085-1094. - PMC - PubMed

Publication types