Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon

Abstract

Eukaryotic genomes harbor hundreds of rRNA genes, many of which are transcriptionally silent. However, little is known about selective regulation of individual rDNA units. In Drosophila melanogaster, some rDNA repeats contain insertions of the R2 retrotransposon, which is capable to be transcribed only as part of pre-rRNA molecules. rDNA units with R2 insertions are usually inactivated, although R2 expression may be beneficial in cells with decreased rDNA copy number. Here we found that R2-inserted rDNA units are enriched with HP1a and H3K9me3 repressive mark, whereas disruption of the heterochromatin components slightly affects their silencing in ovarian germ cells. Surprisingly, we observed a dramatic upregulation of R2-inserted rRNA genes in ovaries lacking Udd (Under-developed) or other subunits (TAF1b and TAF1c-like) of the SL1-like complex, which is homologues to mammalian Selective factor 1 (SL1) involved in rDNA transcription initiation. Derepression of rRNA genes with R2 insertions was accompanied by a reduction of H3K9me3 and HP1a enrichment. We suggest that the impairment of the SL1-like complex affects a mechanism of selective activation of intact rDNA units which competes with heterochromatin formation. We also propose that R2 derepression may serve as an adaptive response to compromised rRNA synthesis.

Genomic architecture of 5S rDNA cluster and its variations within and between species

“…Studies in Drosophila show that insertion of a heterologous sequences into rDNA leads to decreased expression [ 53 ]. Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon [ 54 ]. Studies in Arabidopsis reveals that different 5S rDNA units are subjected to differential epigenetic regulation and prone to translocation between strains [ 55 ].…”

A Spontaneous Inversion of the X Chromosome Heterochromatin Provides a Tool for Studying the Structure and Activity of the Nucleolus in Drosophila melanogaster

“…It is well known that only a part of D. melanogaster rDNA repeats is transcriptionally active, while other rDNA units, including those containing insertions of retroelements, are in a silent state [ 49 , 50 , 51 , 52 ]. In preparations of the wild-type salivary gland nucleolus, individual DAPI-stained specks have been shown to correspond to silent rDNA units enriched with repressive chromatin marks, whereas transcriptionally active units were mixed with them and poorly stained by DAPI [ 53 ].…”

“…To identify which part of the nucleolus in the polytene chromosome preparations corresponds to the zone of active DNA transcription, we performed immunostaining to identify Underdeveloped (Udd), a component of the rDNA transcription initiation complex SL1-like [ 46 ]. Udd was shown to be associated with the IGS regions and rDNA promoters of transcriptionally active rDNA units [ 52 ]. In the nucleoli of wild-type salivary glands, Udd aggregates mostly did not co-localize with the DAPI-stained specks ( Figure 7 A).…”

Insulin signaling regulates R2 retrotransposon expression to orchestrate transgenerational rDNA copy number maintenance

“…Interestingly, rDNA magnification is only active when rDNA is reduced at the Y-chromosome locus specifically(Tartof 1973), and it is more active in animals with more severe bobbed defects (Hawley and Marcus 1989), suggesting it is regulated by a combination of locus-specific features and ribosomal deficiency. Conditions that disrupt ribosome biogenesis or rRNA synthesis have been shown to lead to increased R2 expression (He et al 2015; Fefelova et al 2022), suggesting reduced ribosome biogenesis or function may signal cellular rDNA insufficiency. It remains unclear if ribosome biogenesis or function is actually disrupted in the germline of bobbed animals: however, we found over a quarter of genes encoding for ribosomal proteins have reduced expression in GSCs with low rDNA CN (Table S1 , 22.9-fold enrichment, p<10 -15 determined by chi-squared test ) .…”