Final Report Summary - RIBOGENES (The role of noncoding RNA in sense and antisense or orientation in epigenetic control of rRNA genes)
RNA plays a major, but still largely unexplored role in the regulation of gene expression. Non-coding RNAs (ncRNAs) have been shown to be directly involved in regulating transcription by guiding chromatin modifying enzymes to specific genomic loci and to modulate gene expression by altering their epigenetic signature and chromatin structure. In several cases we have gone beyond the state of the art, which enabled us to decipher novel mechanisms of ncRNA-mediated regulation of gene expression. The main findings of the ERC-funded project are:
• Noncoding RNAs have the potential to directly associate with DNA, forming a DNA:RNA triplex structure at specific regulatory sequences. Such triplexes are specifically recognized by the DNA methyltransferase DNMT3b, which mediates DNA methylation and transcriptional silencing. This is an important result with great impact, implying that DNA:RNA triplex-mediated recruitment or displacement of chromatin modifying enzymes and transcription regulator have the potential to target modifying enzymes to distinct gene sequences, thereby establishing a specific epigenetic landscape that either facilitates or prevents gene expression.
• Down-regulation of transcription in response to environmental or developmental cues correlates with increased levels of distinct long ncRNAs (lncRNA). These quiescence-induced lncRNAs interact with the histone methyltransferase Suv4-20h2. In accord with an lncRNA serving as an address label to recruit Suv4-20h2 and throttle transcription in quiescent cells, elevated levels of lncRNA in growth-arrested cells lead to increased chromatin occupancy of Suv4-20h2, global up-regulation of the repressive histone mark (H4K20me3) and chromatin compaction, thus creating a chromatin environment that impairs transcription. The results link growth-dependent transcriptional regulation to H4K20 trimethylation, suggesting a compelling mechanism of gene regulation that leads to changes of chromatin structure in response to external challenges.
• Noncoding RNAs have the potential to directly associate with DNA, forming a DNA:RNA triplex structure at specific regulatory sequences. Such triplexes are specifically recognized by the DNA methyltransferase DNMT3b, which mediates DNA methylation and transcriptional silencing. This is an important result with great impact, implying that DNA:RNA triplex-mediated recruitment or displacement of chromatin modifying enzymes and transcription regulator have the potential to target modifying enzymes to distinct gene sequences, thereby establishing a specific epigenetic landscape that either facilitates or prevents gene expression.
• Down-regulation of transcription in response to environmental or developmental cues correlates with increased levels of distinct long ncRNAs (lncRNA). These quiescence-induced lncRNAs interact with the histone methyltransferase Suv4-20h2. In accord with an lncRNA serving as an address label to recruit Suv4-20h2 and throttle transcription in quiescent cells, elevated levels of lncRNA in growth-arrested cells lead to increased chromatin occupancy of Suv4-20h2, global up-regulation of the repressive histone mark (H4K20me3) and chromatin compaction, thus creating a chromatin environment that impairs transcription. The results link growth-dependent transcriptional regulation to H4K20 trimethylation, suggesting a compelling mechanism of gene regulation that leads to changes of chromatin structure in response to external challenges.