Distribution of the DNA transposon family, Pokey in the Daphnia pulex species complex

Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing

Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes.

Sleeping Beauty Transposon Insertions into Nucleolar DNA by an Engineered Transposase Localized in the Nucleolus

Transposons are nature's gene delivery vehicles that can be harnessed for experimental and therapeutic purposes. The Sleeping Beauty (SB) transposon shows efficient transposition and long-term transgene expression in human cells, and is currently under clinical development for gene therapy. SB transposition occurs into the human genome in a random manner, which carries a risk of potential genotoxic effects associated with transposon integration. Here, we evaluated an experimental strategy to manipulate SB's target site distribution by preferentially compartmentalizing the SB transposase to the nucleolus, which contains repetitive ribosomal RNA (rRNA) genes. We generated a fusion protein composed of the nucleolar protein nucleophosmin (B23) and the SB100X transposase, which was found to retain almost full transposition activity as compared to unfused transposase and to be predominantly localized to nucleoli in transfected human cells. Analysis of transposon integration sites generated by B23-SB100X revealed a significant enrichment into the p-arms of chromosomes containing nucleolus organizing regions (NORs), with preferential integration into the p13 and p11.2 cytobands directly neighboring the NORs. This bias in the integration pattern was accompanied by an enrichment of insertions into nucleolus-associated chromatin domains (NADs) at the periphery of nucleolar DNA and into lamina-associated domains (LADs). Finally, sub-nuclear targeting of the transposase resulted in preferential integration into chromosomal domains associated with the Upstream Binding Transcription Factor (UBTF) that plays a critical role in the transcription of 47S rDNA gene repeats of the NORs by RNA Pol I. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.

The Wide Distribution and Change of Target Specificity of R2 Non-LTR Retrotransposons in Animals

Transposons, or transposable elements, are the major components of genomes in most eukaryotes. Some groups of transposons have developed target specificity that limits the integration sites to a specific nonessential sequence or a genomic region to avoid gene disruption caused by insertion into an essential gene. R2 is one of the most intensively investigated groups of sequence-specific non-LTR retrotransposons and is inserted at a specific site inside of 28S ribosomal RNA (rRNA) genes. R2 is known to be distributed among at least six animal phyla even though its occurrence is reported to be patchy. Here, in order to obtain a more detailed picture of the distribution of R2, we surveyed R2 using both in silico screening and degenerate PCR, particularly focusing on actinopterygian fish. We found two families of the R2C lineage from vertebrates, although it has previously only been found in platyhelminthes. We also revealed the apparent movement of insertion sites of a lineage of actinopterygian R2, which was likely concurrent with the acquisition of a 28S rRNA-derived sequence in their 3' UTR. Outside of actinopterygian fish, we revealed the maintenance of a single R2 lineage in birds; the co-existence of four lineages of R2 in the leafcutter bee Megachile rotundata; the first examples of R2 in Ctenophora, Mollusca, and Hemichordata; and two families of R2 showing no target specificity. These findings indicate that R2 is relatively stable and universal, while differences in the distribution and maintenance of R2 lineages probably reflect characteristics of some combination of both R2 lineages and host organisms.