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The Euchromatic Histone Mark H3k36me3 Preserves Heterochromatin Through Sequestration of an Acetyltransferase Complex in Fission Yeast

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The Euchromatic Histone Mark H3k36me3 Preserves Heterochromatin Through Sequestration of an Acetyltransferase Complex in Fission Yeast bioRxiv preprint doi: https://doi.org/10.1101/738096; this version posted August 16, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The euchromatic histone mark H3K36me3 preserves heterochromatin through sequestration of an acetyltransferase complex in fission yeast Paula R. Georgescu1, Matías Capella1, Sabine Fischer-Burkart1, Sigurd Braun1,* 1Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany *Correspondence: [email protected]. Tel: +49 (89) 2180-77128 Maintaining the identity of chromatin states requires mechanisms that ensure their structural integri- ty through the concerted actions of histone modifiers, readers, and erasers. Histone H3K9me and H3K27me are hallmarks of repressed heterochromatin, whereas H3K4me and H3K36me are associat- ed with actively transcribed euchromatin. Paradoxically, several studies have reported that loss of Set2, the methyltransferase responsible for H3K36me, causes de-repression of heterochromatin. Here we show that unconstrained activity of the acetyltransferase complex Mst2C, which antagoniz- es heterochromatin, is the main cause of the silencing defects observed in Set2-deficient cells. As previously shown, Mst2C is sequestered to actively transcribed chromatin via binding to H3K36me3 that is recognized by the PWWP domain protein Pdp3. We demonstrate that combining deletions of set2+ and pdp3+ results in an epistatic silencing phenotype. In contrast, deleting mst2+, or other members of Mst2C, fully restores silencing in Set2-deficient cells. Suppression of the silencing de- fect in set2∆ cells is specific for pericentromeres and subtelomeres, which are marked by H3K9me, but not seen for loci that lack genuine heterochromatin. Although Mst2 catalyzes acetylation of H3K14, this modification is likely not involved in the Set2-dependent pathway due to redundancy with the HAT Gcn5. Moreover, while Mst2 is required for acetylation of the H2B ubiquitin ligase Brl1 in euchromatin, we find that its role in heterochromatin silencing is not affected by Brl1 acetylation. We propose that it targets another, unknown substrate critical for heterochromatin silencing. Our findings demonstrate that maintenance of chromatin states requires spatial constraint of opposing chromatin activities. Running title: Silencing by Set2 through Mst2 sequestration Keywords: chromatin/heterochromatin/silencing/acetyltransferase/histone modification The stable maintenance of functional chromatin A conserved type of heterochromatin is charac- states is crucial for cellular identity. The nucleus of terized by the presence of methylated Lys-9 of his- eukaryotic cells is organized into topologically dis- tone H3 (H3K9me) (Allshire & Madhani, 2018). This tinct chromatin domains, known as eu- and hetero- repressive mark is recognized by members of the chromatin, which are associated with different nu- Heterochromatin Protein 1 (HP1) family, which bind clear functions. Both types of chromatin are con- to di- and trimethylated H3K9 (H3K9me2/3) via trolled through various post-translational histone their N-terminal chromodomain. HP1 molecules can modifications, nucleosome remodeling and RNA- dimerize through their C-terminal chromo shadow related processes. Euchromatin is associated with domains, which also participate in the recruitment active transcription and hyperacetylated, contrib- of the H3K9 methyltransferase. This has been sug- uting to an open chromatin structure. In contrast, gested to create a positive feedback loop, resulting heterochromatin is associated with gene repression in extensive spreading of H3K9me/HP1 and the and hypoacetylated, often adopting a compact establishment of a recruitment platform for other chromatin structure that restricts transcription and repressive factors. These include histone deacety- prevents genomic rearrangements. Constitutive lases (HDACs), which restrict histone turnover and heterochromatin is present at repeat-rich sequenc- chromatin accessibility through deacetylation of es that are part of specific chromosomal domains, lysine residues at N-terminal histone tails, thereby like centromeres and telomeres, and plays a crucial contributing to the repressive state of heterochro- role in genome integrity and stability. However, so- matin. Those and other chromatin regulating path- called facultative heterochromatin can also form at ways are conserved in the fission yeast Schizosac- gene-rich regions, e.g. during cellular differentiation charomyces pombe (S. pombe), which makes it a and adaptation to environmental changes. Re- powerful model system to study the molecular sponding to these changes and maintaining the mechanisms of heterochromatin establishment and structural integrity of heterochromatin domains maintenance (Allshire & Ekwall, 2015). Distinct once established requires the concerted actions of heterochromatin domains are present at the sub- histone modifiers, readers, and erasers (Cavalli & telomeres downstream of the telomeric repeats, the Heard, 2019; Allshire & Madhani, 2018; Grewal & silent mating type locus, and the pericentromeric dg Jia, 2007). and dh sequences of the outer repeats (otr). Georgescu et al. Silencing by Set2 through Mst2 sequestration Page 1 of 10 bioRxiv preprint doi: https://doi.org/10.1101/738096; this version posted August 16, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. H3K9me is deposited by a sole histone methyl- teins and competes with SHREC for HP1 binding, transferase, Clr4, which is present in a complex thereby facilitating access of RNAP II to chromatin known as CLRC and catalyzes all three steps of (Zofall & Grewal, 2006; Shimada et al, 2009; Bar- methylation (mono-, di -and trimethylation) (Naka- rales et al, 2016). Conversely, the association of yama et al, 2001; Allshire & Ekwall, 2015; Iglesias Epe1 with heterochromatin is restricted on one et al, 2018). The repressive H3K9me mark is rec- hand through HP1 phosphorylation, which favors ognized by chromodomain-containing proteins, SHREC recruitment (Shimada et al, 2009), and on such as Clr4 itself (Zhang et al, 2008) and the HP1 the other hand through ubiquitin-dependent degra- homologs Swi6 and Chp2 that interact with various dation, which confines Epe1 to the heterochromatin chromatin factors including the repressor complex boundaries (Braun et al, 2011). Heterochromatin is SHREC (Motamedi et al, 2008; Fischer et al, 2009). further antagonized by the RNA polymerase II- This complex comprises a Snf2-like nucleosome associated factor 1 complex (Paf1C), which is in- remodeler (Mit1) and an HDAC (Clr3) subunit, volved in multiple steps in transcription. Mutants of analogous to the mammalian NuRD complex, and Paf1C are susceptible to siRNA-mediated stochas- restricts access of RNA polymerase II (RNAP II) to tic heterochromatin initiation at ectopic sites, possi- heterochromatin (Sugiyama et al, 2007; Job et al, bly due to altered kinetics in the processing and 2016; Leopold et al, 2019). Clr3 specifically termination of nascent transcripts (Kowalik et al, deacetylates histone H3 at lysine K14 (H3K14ac), 2015; Yu et al, 2018; Shimada et al, 2016). Besides whereas other HDACs, such as Sir2 and Clr6, initiation, Paf1C affects heterochromatin mainte- show a preference for H3K9ac (Wiren et al, 2005). nance. The Paf1C subunit Leo1 prevents spreading Similar to Clr3, Clr6 is part of a multimeric complex at heterochromatin boundaries and promotes his- and associates with Swi6 (Fischer et al, 2009). tone turnover (Verrier et al, 2015; Sadeghi et al, Both Clr3 and Clr6 are not restricted to hetero- 2015). Paf1C also seems to be important to over- chromatin but have global functions in histone come the repressive activity of H3K9me3, which deacetylation (Nicolas et al, 2007; Wiren et al, has been linked to its elongation promoting function 2005). by which it may help RNAP II to more easily disrupt Heterochromatin assembly is guided by several nucleosomes (Duempelmann et al, 2019). targeting mechanisms among which the RNA inter- Histone acetyltransferases (HATs) also counter- ference machinery plays a prominent role in S. act heterochromatin, either directly by altering the pombe (Verdel et al, 2004; Martienssen & Moazed, nucleosomes’ charge and structure, or indirectly 2015). Small interfering RNAs (siRNAs) produced through the recruitment of factors to acetylated from heterochromatic DNA repeats are loaded onto histones. HATs can similarly modify the structure the Argonaute-containing RNA-induced transcrip- and activity of non-histone targets. The HAT Mst2 tional silencing (RITS) complex, which targets mediates acetylation of H3K14 redundantly with the complementary nascent transcripts (Verdel et al, SAGA complex subunit Gcn5 (Wang et al, 2012). 2004). RITS further interacts with the RNA- Loss of Mst2 enhances silencing at subtelomeres dependent RNA polymerase complex (RDRC), (Gómez et al, 2005) and bypasses the need for leading to the generation of dsRNAs that are pro- RNAi in centromeric heterochromatin maintenance cessed by Dicer into siRNAs and fed into the ampli- (Reddy et al, 2011). The absence of Mst2 aggra-
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