Tandemly repeated genes promote RNAi-mediated heterochromatin formation via an antisilencing factor, Epe1, in fission yeast

Abstract

In most eukaryotes, constitutive heterochromatin, defined by histone H3 lysine 9 methylation (H3K9me), is enriched on repetitive DNA, such as pericentromeric repeats and transposons. Furthermore, repetitive transgenes also induce heterochromatin formation in diverse model organisms. However, the mechanisms that promote heterochromatin formation at repetitive DNA elements are still not clear. Here, using fission yeast, we show that tandemly repeated mRNA genes promote RNA interference (RNAi)-mediated heterochromatin formation in cooperation with an antisilencing factor, Epe1. Although the presence of tandemly repeated genes itself does not cause heterochromatin formation, once complementary small RNAs are artificially supplied intrans, the RNAi machinery assembled on the repeated genes starts producing cognate small RNAs incisto autonomously maintain heterochromatin at these sites. This “repeat-induced RNAi” depends on the copy number of repeated genes and Epe1, which is known to remove H3K9me and derepress the transcription of genes underlying heterochromatin. Analogous to repeated genes, the DNA sequence underlying constitutive heterochromatin encodes widespread transcription start sites (TSSs), from which Epe1 activates ncRNA transcription to promote RNAi-mediated heterochromatin formation. Our results suggest that when repetitive transcription units underlie heterochromatin, Epe1 generates sufficient transcripts for the activation of RNAi without disruption of heterochromatin.

Polymeric nature of tandemly repeated genes enhances assembly of constitutive heterochromatin in fission yeast

“…The average degree 𝜎𝜎𝑞𝑞 on of H3K9 methylation and the average production rate of small RNAs also increase dramatically with increasing the number N of genes, consistent with recent experiments, see Fig. 5b and c (Asanuma et al 2022). These results mostly reflect the feature of 𝑞𝑞 on .…”

“…8 a and b . Our recent experiments suggest that the level of H3K9 methylation increases with the depletion of Epe1 (Asanuma et al 2022), implying that these experimental results are not explained only by the role of Epe1 as a transcription activator.…”

“…Epe1 is a putative H3K9 demethylase in fission yeast (Ragunathan et al 2015, Audergon et al 2015). We have experimentally demonstrated that the depletion of Epe1 significantly decreases the production of small RNAs (Asanuma et al 2022). In our theory, the action of Epe1 is implicitly taken into account through the H3K9 demethylation rate k dm .…”

“…We have constructed a theory of the assembly of the constitutive heterochromatin in fission yeast. This theory is motivated by the fact that the repeat sequence and many transcription start sites are the genomic signature of heterochromatin assembly in fission yeast (Asanuma et al 2022). It is analogous to the surface adhesion of polymers (de Gennes 1979, Silberberg 1962), given the fact that small RNAs are produced by RDRC/Dicers at the surfaces of the nuclear membrane (Emmerth et al 2010, Kawakami et al 2012).…”

Polymeric nature of tandemly repeated genes enhances assembly of constitutive heterochromatin in fission yeast

“…Because the H3K9 methylation and small RNA production occur during transcription, one may wonder what will happen if one upregulates the transcription. Indeed, the heterochromatin mark, such as the level of small RNAs, in the centromeric regions is enhanced by the upregulation of transcription (Asanuma et al 2022). Why does the transcription form heterochromatin in centromeric regions, but not in euchromatin regions?…”