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Abstract
Involvement of long non-coding RNAs (lncRNAs) in the regulation of gene expression in cis has been well studied in eukaryotes but relatively little is known whether and how lncRNAs affect gene expression in tans. In Arabidopsis thaliana, COLDAIR, a previously reported lncRNA, is produced from the first intron of FLOWERING LOCUS C (FLC), which encodes a repressor of flowering time. Our results indicated that the exogenously overexpressed COLDAIR enhances the expression of FLC in trans, resulting in a late-flowering phenotype. In 35S-COLDAIR lines, the enhanced expression of FLC is correlated with the down-regulation of the repressive histone mark H3K27me3 and with the up-regulation of the active histone mark H3K4me3 at the FLC chromatin. Furthermore, we demonstrated that overexpression of intronic lncRNAs from several other H3K27me3-enriched MADS-box genes also activates the expression of their host genes. This study suggests that the involvement of overexpressed intronic lncRNAs in gene activation may be conserved in H3K27me3-enriched genes in eukaryotes.
Highlights
Involvement of long non-coding RNAs in the regulation of gene expression in cis has been well studied in eukaryotes but relatively little is known whether and how lncRNAs affect gene expression in tans
The results showed that 25% (5/20) of randomly selected 35S-COLDAIR lines displayed late flowering, which is accompanied by the increased expression of FLOWERING LOCUS C (FLC) (Fig. 1C,D)
In Arabidopsis, the endogenous COLDAIR was previously shown to associate with the major H3K27 methyltransferase CURLY LEAF (CLF) and thereby enhance H3K27me[3] at the late stage of vernalization[12]
Summary
Involvement of long non-coding RNAs (lncRNAs) in the regulation of gene expression in cis has been well studied in eukaryotes but relatively little is known whether and how lncRNAs affect gene expression in tans. We demonstrated that overexpression of intronic lncRNAs from several other H3K27me3-enriched MADS-box genes activates the expression of their host genes. COLDAIR, an intronic lncRNA from the first intron of FLC, cooperates with the FLC promoter-derived lncRNA COLDWRAP to facilitate the establishment of H3K27me[3] and to thereby repress FLC expression during the late stage of vernalization[12,28]. Considering that COLDAIR is a functional lncRNA generated from the intron of FLC, we wonder how COLDAIR regulates FLC and whether there other intronic RNAs involved in regulating the expression of their corresponding host genes. Intronic lncRNAs have been extensively identified and demonstrated to be functional in regulating the expression of their corresponding host genes in eukaryotes[30]. The function of intronic RNAs in the regulation of transcription has been extensively studied, it remains largely unknown how these intronic RNAs regulate transcription through affecting chromatin modification
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