Epigenetic Regulation of Retrotransposons within the Nucleolus of Drosophila

Abstract

R2 retrotransposable elements exclusively insert into a conserved region of the tandemly organized 28S rRNA genes. Despite inactivating a subset of these genes, R2 elements have persisted in the ribosomal DNA (rDNA) loci of insects for hundreds of millions of years. Controlling R2 proliferation was addressed in this study using lines of Drosophila simulans previously shown to have either active or inactive R2 retrotransposition. Lines with active retrotransposition were shown to have high R2 transcript levels, which nuclear run-on transcription experiments revealed were due to increased transcription of R2-inserted genes. Crosses between R2 active and inactive lines indicated that an important component of this transcriptional control is linked to or near the rDNA locus, with the R2 transcription level of the inactive parent being dominant. Pulsed-field gel analysis suggested that the R2 active and inactive states were determined by R2 distribution within the locus. Molecular and cytological analyses further suggested that the entire rDNA locus from the active line can be silenced in favor of the locus from the inactive line. This silencing of entire rDNA loci represents an example of the large-scale epigenetic control of transposable elements and shares features with the nucleolar dominance frequently seen in interspecies hybrids.Eukaryotic genomes have evolved elaborate surveillance and regulatory mechanisms to control the spread of transposable elements (38). The success of a transposable element is thus dependent upon its ability to elude these cellular controls. One ingenious approach used by transposable elements is to target locations within the genome that cannot be completely silenced. The most successful known examples of this approach are the numerous mobile elements that insert specifically into the rRNA genes of animals (10). Eukaryotic genomes encode hundreds to thousands of rRNA genes organized in tandem arrays within one or more chromosomal loci. Transcription of the rRNA gene arrays, also termed nucleolar organizer regions (NORs), is tightly coupled to the growth status of the cell. Significant progress has been made in understanding the transcription of the DNA encoding the rRNA genes (ribosomal DNA [rDNA]) as well as the many subsequent steps involved in ribosome biogenesis (14, 16). The level of regulatory complexity added by the presence of transposable elements is largely unknown.The nonlong terminal repeat (non-LTR) retrotransposable elements, R1 and R2, insert into a conserved central region of the 28S gene (Fig. 1A). R1 and R2 are present in most lineages of arthropods (2), and R2 elements have been found in a number of other divergent animal groups (20, 21). Phylogenetic analyses suggest that R2 elements have been a stable component of genomes throughout the evolution of arthropods (2, 27) and possibly since the origin of multicellular animals (20, 21). As such, they represent the longest known stable relationship of a mobile element and its host. During their long history, R2 elements ...

Y chromosome mediates ribosomal DNA silencing and modulates the chromatin state inDrosophila

“…In F 1 females, which had one X chromosome with a low transcription level and another X chromosome with a high transcription level, the rRNA genes derived from the high-transcription X were silenced. Similar X-X interactions were reported previously as an example of intraspecific nucleolar dominance (16).…”

“…In D. melanogaster, silencing of one X-linked rDNA locus by that of an X chromosome of different origin has been reported in interspecific hybrid females (14,15). Examples in intraspecies crosses of Drosophila simulans females have been reported as well (16). The mechanisms of nucleolar dominance are likely related to chromatin modifications (17), implying a potential role for the rDNA locus in modulating the chromatin state.…”

Nucleolar Dominance of the Y Chromosome in Drosophila melanogaster

“…For example, perhaps the organization of inserted and uninserted units within an array may determine the overall responsiveness of the array, if interactions between neighboring rDNA units affect activation. A similar effect of large-scale array organization has been proposed to account for differences in interspecies nucleolar dominance (Eickbush et al 2008).…”

Ribosomal DNA contributes to global chromatin regulation

“…Others have noted the opposite effectincreased silencing with decreased X-linked rDNA arrays of males (27,28). Whether the X-linked and Y-linked arrays are fundamentally different remains a question, although there are clear differences in sequence and epigenetic regulation of these arrays (20,24). This raises the intriguing possibility that these two arrays may together establish a homeostasis of chromatin while jointly assuring sufficient translational capacity to the cell.…”

“…The rDNA and nucleolus have played a prominent role in evolving theories of aging, metabolism, cell differentiation, cell cycle control, cancer progression, and gene regulation (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). The rDNA is of particular interest in understanding heterochromatin because it is known to be regulated by epigenetic modification (20)(21)(22)(23)(24), is associated with both active and repressive protein modification (25,26), can affect variegation at unlinked genes (27,28), can itself induce variegation (29)(30)(31), and may change its size and regulation through the lifespan of an organism (32,33). Few studies, however, have probed the connection between the rDNA, nucleolus, and heterochromatin formation in the nucleus.…”