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Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

Abstract

Transcription in eukaryotic genomes generates an extensive array of non-protein-coding RNA, the functional significance of which is mostly unknown1. We are investigating the link between non-coding RNA and chromatin regulation through analysis of FLC — a regulator of flowering time in Arabidopsis and a target of several chromatin pathways. Here we use an unbiased strategy to characterize non-coding transcripts of FLC and show that sense/antisense transcript levels correlate in a range of mutants and treatments, but change independently in cold-treated plants. Prolonged cold epigenetically silences FLC in a Polycomb-mediated process called vernalization2. Our data indicate that upregulation of long non-coding antisense transcripts covering the entire FLC locus may be part of the cold-sensing mechanism. Induction of these antisense transcripts occurs earlier than, and is independent of, other vernalization markers3 and coincides with a reduction in sense transcription. We show that addition of the FLC antisense promoter sequences to a reporter gene is sufficient to confer cold-induced silencing of the reporter. Our data indicate that cold-induced FLC antisense transcripts have an early role in the epigenetic silencing of FLC, acting to silence FLC transcription transiently. Recruitment of the Polycomb machinery then confers the epigenetic memory. Antisense transcription events originating from 3′ ends of genes might be a general mechanism to regulate the corresponding sense transcription in a condition/stage-dependent manner.

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Figure 1: FLC is associated with extensive antisense transcription.
Figure 2: FLC antisense transcripts are strongly induced by cold.
Figure 3: Vernalization-induced transcriptional repression of FLC.
Figure 4: FLC antisense promoter region is sufficient to confer cold-dependent silencing of sense transcription.

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Acknowledgements

We thank all members of the Dean laboratory for discussions, J. Ecker and B. Gregory (Salk Institute) for help with the RiboMinus technique, C. Lister for help with cloning steps, M. Lenhard and H. Breuninger for seeds of LUC control plants. This research was supported by the BBSRC Core Strategic Grant to the John Innes Centre and BBSRC BB/D010799/1, NERC NE/C507629 and EU SIROCCO LSHG-CT-2006-037900 grants to C.D.

Author Contributions C.D. and S.S. designed the study. S.S. performed most experiments. S.S. and F.L. performed the array experiment. A.M. and S.S. analysed microarray data. C.D. and S.S. wrote the manuscript.

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Correspondence to Caroline Dean.

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Swiezewski, S., Liu, F., Magusin, A. et al. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462, 799–802 (2009). https://doi.org/10.1038/nature08618

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