TRE5-A retrotransposition profiling reveals putative RNA polymerase III transcription complex binding sites on the Dictyostelium extrachromosomal rDNA element

Abstract

The amoeba Dictyostelium discoideum has a haploid genome in which two thirds of the DNA encodes proteins. Consequently, the space available for selfish mobile elements to expand without excess damage to the host genome is limited. The non-long terminal repeat retrotransposon TRE5-A maintains an active population in the D. discoideum genome and apparently adapted to this gene-dense environment by targeting positions ~47 bp upstream of tRNA genes that are devoid of protein-coding regions. Because only ~24% of tRNA genes are associated with a TRE5-A element in the reference genome, we evaluated whether TRE5-A retrotransposition is limited to this subset of tRNA genes. We determined that a tagged TRE5-A element (TRE5-Absr) integrated at 384 of 405 tRNA genes, suggesting that expansion of the current natural TRE5-A population is not limited by the availability of targets. We further observed that TRE5-Absr targets the ribosomal 5S gene on the multicopy extrachromosomal DNA element that carries the ribosomal RNA genes, indicating that TRE5-A integration may extend to the entire RNA polymerase III (Pol III) transcriptome. We determined that both natural TRE5-A and cloned TRE5-Absr retrotranspose to locations on the extrachromosomal rDNA element that contain tRNA gene-typical A/B box promoter motifs without displaying any other tRNA gene context. Based on previous data suggesting that TRE5-A targets tRNA genes by locating Pol III transcription complexes, we propose that A/B box loci reflect Pol III transcription complex assembly sites that possess a function in the biology of the extrachromosomal rDNA element.

Retrotransposon targeting to RNA polymerase III-transcribed genes

“…However, similar to Ty3 elements, mutations of the box B promoter that interfere with binding of TFIIIC abolish the targeting of TRE5-A to the tRNA target gene [ 133 ]. TRE5-A insertion profiling demonstrated that TRE5-A can also integrate at the Pol III-transcribed ribosomal 5S gene which is located on a multi-copy extrachromosomal DNA element harboring the rRNA genes [ 134 , 135 ]. Unlike TRE5, TRE3 has a broader range of insertion that is 40–150 bp downstream of tRNA genes in the same transcription orientation (Fig.…”

Retrotransposon Domestication and Control in Dictyostelium discoideum

“…Subsequently, cloning and sequencing of de novo integration sites of TRE5-A bsr revealed the authentic positioning around 50 nucleotides upstream of tRNA genes (Beck et al, 2002 ; Siol et al, 2006a ). Additionally, this construct was also instrumental to realize that, in principle, all tRNA genes can be targeted (Spaller et al, 2017 ). Whether integration alters tRNA gene expression cannot be easily investigated due to their high abundance and redundancy in D. discoideum .…”

“…Unexpected TRE5-A bsr integration sites in the extrachromosomal rDNA palindrome of the amoeba (Sucgang et al, 2003 ) were also uncovered, which are characterized by perfect B box sequences (Siol et al, 2011 ). Subsequently, additional integration sites in the vicinity of the RNA polymerase III-transcribed ribosomal 5S gene were characterized (Spaller et al, 2017 ). Taken together, these data strongly point towards a general coupling of TRE5-A integration with active RNA polymerase III transcription.…”