Regulation of heterochromatic RNA decay via heterochromatin protein 1 (HP1)

The central dogma of molecular biology describes the directional flow of biological information from DNA via RNA to protein. Information stored in DNA is copied to an mRNA molecule during the process of transcription. The mRNA is used as a template for translation, in which polypeptides are synthesized. The regulation of this process, which is conserved through all trees of life, has been a central field of study over the last decades.
The discovery that RNA not only serves a simple role as a mere copy, but is much more versatile has created a lot of excitement. For example, RNA molecules themselves can act as enzymes. In the ribosome, rRNAs comprise the catalytic core for peptide bond formation. snRNAs form the core of the splicing machinery. tRNAs are the adaptors and thereby the actual readers of the genetic code. Last but not least, in the RNAi pathway, small RNAs serve as guides to target silencing complexes to complementary RNAs. Altogether, these findings placed RNA at the center of eukaryotic genome regulation.
On the other hand, DNA in eukaryotic cells does not exist as a mere fibre, but is wrapped around the core histone octamer to form a nucleosome. Nucleosomes are the basic building blocks to form higher order chromatin structures. Besides its architectural role in chromosome segregation, genome stability and recombination, chromatin has also been linked to gene expression. In contrast to the rather gene-rich euchromatin, heterochromatin is a highly condensed and repressive structure, serves as a safe storage place for transposable elements and makes up a large fraction of the genome of higher eukaryotes. Repression or activation in different chromatin contexts involves covalent modifications on the histone proteins. The nature and combination of these modifications create different docking sites for various effector proteins that have either activating or repressing function.
Surprisingly, recent studies have suggested that a substantial fraction of the genome, although heterochromatic, is transcribed at least to a certain extent and many of those transcripts do not encode proteins. Moreover, fascinating mechanisms have been discovered, in which the silencing of heterochromatic sequences involves RNA-dependent mechanisms. Altogether this suggests that the regulation of the genomic output in eukaryotes not only occurs at the level of transcription but to a substantial extent via co- or posttranscriptional gene silencing mechanisms (CTGS or PTGS, respectively). The cellular RNA decay machineries therefore have to be equipped with tools to specifically distinguish and degrade certain RNAs.
Generally, RNA decay mechanisms recognize aberrant features that are contained in the RNA molecule itself, for example the presence and length of a poly(A) tail at the 3’end. The RNAi pathway is triggered by the presence of short ssRNA molecules that are complementary to a target RNA and thereby lead to degradation. In some cases degradation induces feedback mechanisms back to chromatin resulting in histone modification and/or transcriptional modulation.
My work has identified a novel mechanism to regulate RNA decay, which is dependent on the chromatin context from which the RNA has been transcribed. This mechanism is independent of the actual RNA sequence/molecule but involves binding to the heterochromatin protein HP1(Swi6). I found that HP1(Swi6) binding to a heterochromatic transcript fulfils a checkpoint function, which mediates repression on at least two levels. First, HP1(Swi6) prevents translation of heterochromatic RNA by inhibiting association with ribosomes. This ensures repression even in the absence of RNA decay. Second HP1(Swi6) mediates elimination by capturing RNA at the site of transcription and escorting it to the degradation machinery. On a molecular level, this is achieved by RNA binding to the HP1(Swi6) hinge region. This renders the chromodomain structurally incompatible with stable H3K9me association leading to heterochromatin eviction and degradation of the RNA.
My data points towards a model in which binding of HP1(Swi6) to a heterochromatic RNA creates a heterochromatin-specific ribonucleoprotein (hsRNP) that is prone to degradation. Importantly, HP1(Swi6) can induce degradation of any RNA of heterochromatic origin, which could be a crucial feature to repress the expression of deleterious sequences and transposons. Last but not least, my work is the first example that demonstrates that RNAs can act as “repellents” for chromatin proteins.