An H3-K9-me-independent binding of Swi6/HP1 to siRNA-DNA hybrids initiates heterochromatin assembly at cognate dg-dh repeats in Fission Yeast

Abstract

Canonically, 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 chromodomain. Subsequent self-association of Swi6/HP1 on adjacent nucleosomes leads to folded heterochromatin structure. An alternate model suggests a cooperative interaction between Clr4 and Swi6/HP1 in heterochromatin assembly. HP1 binding to RNA has also been invoked for heterochromatin silencing in metazoans. Recruitment of Swi6/HP1 to centromere has been shown to be dependent on the RNAi pathway in fission yeast. Here we show that Swi6/HP1 exhibits a hierarchy of binding affinity to RNAs, ranging from promiscuous, low-affinity binding to mRNAs, to moderate-affinity binding to the RNAi-generated siRNAs corresponding to the dg-dh repeats present in pericentromeric heterochromatin regions, to high-affinity binding to the RNA-DNA hybrids to the cognate dg-dh repeats. Together with the sensitivity of Swi6 localization and silencing to RNaseH, our results suggest a dynamic control of localization of Swi6/HP1 towards the dg-dh repeats versus euchromatic regions. This is mediated by its binding to RNA-DNA hybrid at the dg-dh repeats, as an RNAi-dependent and Me2/me3-K9-H3-independent mechanism of recruitment, leading to heterochromatin formation and silencing.

Unravelling HP1 functions: post-transcriptional regulation of stem cell fate

“…As Drosophila HP1, also HP1 orthologues in other species display nucleic acid binding activity. In Saccharomyces pombe , Swi6 is able to bind RNAs through its hinge region (Keller et al 2012 ; Kumar et al 2020 ), and, in mammals, HP1α, SUMOylated in the hinge domain, targets pericentromeric heterochromatin by interacting with long nuclear noncoding transcripts corresponding to major satellite repeats (Maison et al 2002 , 2011 ; Muchardt et al 2002 ). Moreover, the unstructured hinge domain, necessary for the targeting of HP1α to constitutive heterochromatin, is also required for the interaction with parallel G-quadruplex structures formed by the TElomericRepeat-containing RNA (TERRA) transcribed from telomeres (Roach et al 2020 ).…”