The highly dynamic heterochromatin protein Swi6 mediates degradation of heterochromatic transcripts

The aim of my thesis was to investigate the mechanism of heterochromatin repression mediated by heterochromatin protein Swi6 in S. pombe.
Research over the years challenged the view of heterochromatin as a static and transcriptionally inert structure. Especially in fission yeast it has become clear that heterochromatin silencing requires not only the action of chromatin modifying factors, but also transcriptional activity and RNA degradation processes. Moreover, heterochromatin protein Swi6 was shown to be highly dynamic, unlike what was expected for a protein that is perceived as a major structural component of heterochromatin. Yet, the prevailing model of heterochromatin establishment and spreading is thought to occur by iterative HP1 binding to methylated H3K9 and recruitment of histone methylation activity.
Driven by recent findings in our lab that described a new role for Swi6 in repression and provided a possible explanation for its dynamic behavior, I set out to investigate the mechanism in vivo by studying Swi6 dynamics. Therefore, a major focus of my PhD was to establish a suitable, robust microscopy-based method that allowed me to follow rapid dynamics and produce reliable data. The work I have done challenged the role of Swi6 in heterochromatin maintenance and spreading, but coincides with a clear involvement in sustaining tight repression. While H3K9me levels remained high in the absence of Swi6 and even spread into neighboring regions, heterochromatic transcript levels increased. These observations revealed unanticipated functions for Swi6 and made us reconsider the mechanism of Swi6-mediated silencing. As previously proposed, Swi6 could function as a co-transcriptional checkpoint that mediates RNA degradation (Keller et al., 2012). In this model RNA binds to Swi6 and gets primed for destruction as it is handed over to the RNA decay machinery, involving Cid14 and the exosome or the RNAi machinery. The target specificity depends on the epigenetic make-up of the locus, meaning the recognition of H3K9me by the CD of Swi6, while RNA binding occurs in a sequence independent manner (Keller et al., 2012). Therefore, additional processes that confer specificity, like siRNAs, are needed to ensure correct targeting of H3K9me marks to trigger Swi6-mediated turnover of unwanted RNA transcripts and not of any other random region in the genome.