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

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 ТAF1c-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. Udd ChIP libraries were sequenced on Illumina HiSeq 4000. rRNA-depleted RNA-seq in udd mutant ovaries.cDNA libraries were sequenced on MGISEQ-2000

真核基因组携带有数百个核糖体RNA（rRNA）基因，其中多数处于转录沉默状态。然而，目前针对单个核糖体DNA（rDNA）单体的选择性调控机制仍知之甚少。在黑腹果蝇（Drosophila melanogaster）中，部分rDNA重复序列存在R2反转录转座子的插入片段，该元件仅能作为前体rRNA分子的一部分进行转录。携带R2插入片段的rDNA单体通常会被沉默，但当细胞内rDNA拷贝数降低时，R2的表达可能对细胞有益。本研究发现，携带R2插入片段的rDNA单体富集HP1a与H3K9me3这类抑制性组蛋白修饰标记；而异染色质组分的功能受损仅会轻度影响其在卵巢生殖细胞中的沉默状态。令人意外的是，我们在缺失Udd（未发育基因，Under-developed）或SL1样复合物其他亚基（TAF1b与TAF1c类似蛋白）的卵巢中，观察到携带R2插入片段的rRNA基因出现显著上调；该SL1样复合物与哺乳动物中参与rDNA转录起始的选择性因子1（Selective factor 1, SL1）同源。携带R2插入片段的rRNA基因的去抑制现象，伴随有H3K9me3与HP1a富集水平的降低。我们推测，SL1样复合物的功能受损会干扰完整rDNA单体的选择性激活机制，而该机制与异染色质形成存在竞争关系。此外我们提出，R2基因的去抑制或许是对受损rRNA合成的一种适应性应答。Udd染色质免疫共沉淀（ChIP, chromatin immunoprecipitation）文库在Illumina HiSeq 4000测序平台上完成测序。对udd突变体卵巢开展的rRNA去除型RNA测序（RNA-seq）实验中，其cDNA文库在MGISEQ-2000测序平台上完成测序。