The SUMO ligase Su(var)2-10 controls eu- and heterochromatic gene expression via establishment of H3K9 trimethylation and negative feedback regulation

Abstract

<jats:title>Abstract</jats:title><jats:p>Chromatin is critical for genome compaction and gene expression. On a coarse scale, the genome is divided into euchromatin, which harbors the majority of genes and is enriched in active chromatin marks, and heterochromatin, which is gene-poor but repeat-rich. The conserved molecular hallmark of heterochromatin is the H3K9me3 modification, which is associated with gene silencing. We found that in <jats:italic>Drosophila</jats:italic> deposition of most of the H3K9me3 mark depends on SUMO and the SUMO-ligase Su(var)2-10, which recruits the histone methyltransferase complex SetDB1/Wde. In addition to repressing repeats, H3K9me3 also influences expression of both hetero- and euchromatic host genes. High H3K9me3 levels in heterochromatin are required to suppress spurious non-canonical transcription and ensure proper gene expression. In euchromatin, a set of conserved genes is repressed by Su(var)2-10/SetDB1-induced H3K9 trimethylation ensuring tissue-specific gene expression. Several components of heterochromatin are themselves repressed by this pathway providing a negative feedback mechanism to ensure chromatin homeostasis.</jats:p><jats:sec><jats:title>Highlights</jats:title><jats:p><jats:list list-type="simple"><jats:list-item><jats:label>-</jats:label><jats:p>Proper expression of host genes residing in heterochromatin requires Su(var)2-10-dependent installation of the H3K9me3 mark to suppress spurious non-canonical transcription.</jats:p></jats:list-item><jats:list-item><jats:label>-</jats:label><jats:p>A set of euchromatic host genes is repressed by transposon-independent installation of H3K9me3 in a process that depends on Su(var)2-10 and SUMO.</jats:p></jats:list-item><jats:list-item><jats:label>-</jats:label><jats:p>Installation of H3K9me3 via Su(var)2-10 ensures tissue-specific gene expression.</jats:p></jats:list-item><jats:list-item><jats:label>-</jats:label><jats:p>H3K9me3-dependent silencing of genes encoding proteins involved in heterochromatin formation provides negative feedback regulation to maintain heterochromatin homeostasis.</jats:p></jats:list-item></jats:list></jats:p></jats:sec>

The control of gene expression and cell identity by H3K9 trimethylation

“…However, H3K9me3 is not always associated with silencing, especially if it is excluded from the transcription start site (TSS). For example, heterochromatin-residing yet active genes in Drosophila are usually enriched in H3K9me3 across their bodies but not around the TSS (Ninova et al, 2019b;Riddle et al, 2011). Studies in flies have shown that some active genes that reside in constitutive heterochromatin require this environment for their proper expression, as they become silent if translocated to euchromatin (Wakimoto et al, 1990;Yasuhara and Wakimoto, 2006).…”

“…Studies in flies have shown that some active genes that reside in constitutive heterochromatin require this environment for their proper expression, as they become silent if translocated to euchromatin (Wakimoto et al, 1990;Yasuhara and Wakimoto, 2006). Loss of H3K9me3 results in transcriptional downregulation of a significant fraction of genes residing in constitutive heterochromatin and the H3K9me3-rich chromosome 4 in various tissues, as well as of genomic loci encoding piRNA precursors in the germline (Ninova et al, 2019b;Rangan et al, 2011;Tzeng et al, 2007). These findings suggest that, despite its common silencing function, H3K9me3 enrichment over gene bodies outside of the TSS is not only compatible with transcription but is even required for proper expression of heterochromatic genes.…”

“…As piRNA/Piwi are maternally loaded into the egg (but not zygotically expressed outside of the gonads), an attractive model is that maternal piRNA/Piwi complexes guide initial heterochromatin establishment in the early embryo, which is later maintained piRNA independently. There are also some H3K9me3-marked genes in regions that do not have local TEs and cannot be targeted by piRNA, pointing to the existence of piRNA-independent targeting mechanisms (Ninova et al, 2019b). DNA-binding proteins that recruit SetDB1 analogous to the vertebrate-specific KRAB-ZFP family have not been identified.…”

“…As in mammalian systems, epigenetic silencing of TEs affects the host transcriptome of Drosophila germ cells. For example, H3K9me3 loss is associated with activation of cryptic promoters within TE sequences, the appearance of chimeric or truncated transcripts and mis-regulation of canonical gene isoforms (Ninova et al, 2019b). Finally, even though the piRNA pathway is the only known mode of H3K9me3 deposition in Drosophila ovaries, a recent ChIP-seq study revealed a number of discrete H3K9me3 peaks at euchromatic genes that are conserved, show no evidence of TE insertions or targeting by piRNAs, and do not lose H3K9me3 upon Piwi depletion, i.e.…”

“…Finally, even though the piRNA pathway is the only known mode of H3K9me3 deposition in Drosophila ovaries, a recent ChIP-seq study revealed a number of discrete H3K9me3 peaks at euchromatic genes that are conserved, show no evidence of TE insertions or targeting by piRNAs, and do not lose H3K9me3 upon Piwi depletion, i.e. are likely piRNA-independent (Ninova et al, 2019b). About 20% of these H3K9me3-marked genes become upregulated upon knockdown of the SUMO ligase Su(var)2-10, suggesting that they are regulated in a SUMOdependent manner and possibly through SetDB1.…”