Swi6/HP1 binding to RNA-DNA hybrids initiates heterochromatin assembly

Abstract

Heterochromatin formation in fission yeast and metazoans involves di/trimethylation of histone H3 at lysine 9 position (me2/me3-K9-H3) by the histone methyltransferase (HMT) Suv39/Clr4, followed by binding of Swi6/HP1 to me2/me3-K9-H3 via its chromodomain1. Subsequent self-association of Swi6/HP1 on adjacent nucleosomes leads to folded heterochromatin structure1-3. An alternate model suggests a concerted participation of Clr4 and Swi6/HP12,3. HP1 binding to RNA has been invoked for heterochromatin silencing in metazoans4,5. Swi6/HP1 also binds and channels RNA to exosome pathway in fission yeast6. Recruitment of Swi6/HP1 to centromere is also dependent on the RNAi pathway7. Here we show that Swi6/HP1 exhibits binding to RNAs, ranging from promiscuous, low-affinity binding to mRNAs, to moderate-affinity binding to the RNAi-generated siRNAs corresponding to the repeats present in heterochromatin regions7, to high affinity binding to the RNA-DNA hybrids cognate to the repeats. Together with sensitivity of Swi6 localization and silencing to RNaseH, our results suggest a dynamic distribution of Swi6/HP1 among the heterochromatin and euchromatic transcripts and binding to RNA-DNA hybrid as an RNAi-dependent and Me2/me3-K9-H3-independent mechanism of recruitment, leading to heterochromatin formation and silencing.