Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target.
Nature. 2009 Dec 10; 462(7274):799-802
This paper reports an unexpected finding that cold-treated plants induce long, non-coding antisense transcripts of the Arabidopsis floral repressor FLC, which silence the expression of their sense counterparts.
FLC is the central floral repressor that transcriptionally down-regulates several genes required for flowering. It is well known that exposure of plants to prolonged cold (i.e. vernalization) attenuates this FLC-dependent floral repression through the Polycomb-mediated epigenetic silencing of the FLC locus. The authors discovered that, in addition to this well-characterized mechanism, cold treatment induces production of long antisense transcripts designated COOLAIR that overlap the entire FLC coding region. The cold-induced upregulation of COOLAIR coincides with reduction of FLC mRNA, suggesting that such non-coding antisense transcripts play an indispensable role in the FLC transcriptional silencing. More importantly, it was shown that incorporation of the putative COOLAIR promoter sequence, which corresponds to the 3' region of FLC, downstream of the green fluorescent protein (GFP) reporter gene is sufficient to repress the reporter expression in a cold-responsive manner. To our knowledge, this is the first description of long antisense transcripts involved in transcriptional silencing in plants. In the future, it would be interesting to see what fraction of the plant genome is subject to regulation by such long antisense transcript-mediated gene silencing.
Citovsky V and Magori S: F1000Prime Recommendation of [Swiezewski S et al., Nature 2009, 462(7274):799-802]. In F1000Prime, 18 Jan 2010; DOI: 10.3410/f.1491956.974055. F1000Prime.com/1491956#eval974055
F1000Prime Recommendations, Dissents and Comments for [Swiezewski S et al., Nature 2009, 462(7274):799-802]. In F1000Prime, 18 Dec 2013; F1000Prime.com/1491956
Nat Genet. 2004 Feb; 36(2):167-71
PLoS ONE. 2011; 6(3):e17444
Transcription in eukaryotic genomes generates an extensive array of non-protein-coding RNA, the functional significance of which is mostly unknown. 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 vernalization. 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 markers 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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