Interactions between epigenetic modifiers and long noncoding RNAs or mRNAs were widely reported and were linked to normal development and to disease. Yet, functional studies to elucidate how, or if, such epigenetic modifiers are regulated by their RNA binding partners are often complicated by promiscuous RNA binding. From the protein side, lack of canonical RNA recognition motifs (RRMs) or sequence homology to other RNA binding proteins often complicates mechanistic studies.
The Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that trimethylates K27 of histone H3 (H3K27me3). PRC2 is essential for the maintenance of the repressed epigenetic state of thousands of genes during development and is dysregulated during cancer. PRC2 binds thousands of transcripts, but despite a decade of extensive study a PRC2-binding motif within its target RNAs was not identified. Furthermore, an RNA-binding domain within PRC2 was not detected and canonical RRMs are not present within any of its protein subunits. Collectively, these complicated mechanistic studies to determine the function of PRC2-RNA interactions.
Through combining biochemical and biophysical approaches with genomics and mass-spectrometry we identified the PRC2-binding motif within RNA and the RNA-binding domain within PRC2. Multiple short tracts of consecutive guanines largely increase the affinity of PRC2 to RNA and significantly associate with PRC2 binding sites on RNA transcripts in cells. DNA sequences coding for PRC2-binding RNA motifs are enriched at PRC2-binding sites on chromatin and H3K27me3-modified nucleosomes, provide means for RNA-mediated regulation of PRC2 in cis. Additional new data will be discussed from our on-going study to understand how the polycomb machinery is regulated.