Sequencing CURLY LEAF-associated RNAs in Arabidopsis revealed prevalent intergenic RNAs from the nuclear mitochondrial sequence

Polycomb Group (PcG) proteins play key roles in development by repressing thousands of targets through histone modifications. How PcG is recruited to specific targets is poorly understood. In Arabidopsis, certain noncoding RNAs are necessary for the recruitment of the Polycomb group (PcG) protein CURLY LEAF (CLF) to its target sites. However, RNAs associated with CLF have not been analyzed at the genomic scale, thus it is unknown whether long noncoding RNA (lncRNA)-mediated PcG recruitment is a widespread mechanism. Here, we systematically searched for CLF-associated RNAs by RNA immunoprecipitation followed by deep sequencing. 1299 genes and 138 intergenic regions were found to produce CLF-associated mRNAs and putative lncRNAs, respectively. The genes that produce CLF-associated RNAs are depleted in PcG targets, carry active chromatin marks, and are highly expressed, suggesting that CLF may possess a promiscuous RNA-binding affinity, similar to what has been observed in animal systems. However, a sizable fraction of the CLF-associated lncRNAs is derived from the nuclear mitochondrial sequence, which is marked extensively by H3K27me3. These RNAs could play a role in establishing the unique epigenetic features of this region, some of which are shared by the mammalian X inactivation center and the Arabidopsis FLC locus.