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.
Highlights
Regulation of ribosomal DNA transcription is a fine-tuned mechanism that defines the global level of protein synthesis and controls cell growth and differentiation [1,2]
The Selective factor 1 (SL1)-like complex is thought to be pivotal for the ribosomal DNA (rDNA) transcription, which mediates the expression of transposable elements (TEs) incorporated into pre-rRNA, we surprisingly found that germline knockdowns of TAF1B, TAF1C-like and Udd led to 40- to 70-fold upregulation of R2 and to a lesser extent of R1 elements (Figure 3A)
Our observations suggest that the reduction of the H3K9me3 level in rRNA genes in the udd mutant ovaries can be caused by their transcriptional activation, and vice versa repressive chromatin marks can normally be recruited to rDNA units as a consequence of their transcriptional silencing
Summary
Regulation of ribosomal DNA (rDNA) transcription is a fine-tuned mechanism that defines the global level of protein synthesis and controls cell growth and differentiation [1,2]. Each gene expresses a pre-rRNA transcript harboring an external transcribed spacer (ETS) followed by the sequences of 18S, 5.8S and 28S rRNAs, which are interspaced by internal transcribed spacers (ITSs). Both ETS and ITSs are eliminated during nuclease processing steps, leading to formation of mature rRNAs. Numerous genetic, microscopic and biochemical studies have demonstrated that only a part of rDNA units is transcriptionally active at any time, while the rest, or even the majority of rDNA repeats, are in a repressed state [6,7,8,9,10,11,12,13,14]. This phenomenon can be useful to maintain an optimal level of ribosome production regardless of the rDNA copy
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