Intrinsic Characteristics of Neighboring DNA Modulate Transposable Element Activity in Drosophila melanogaster

Abstract

Identifying factors influencing transposable element activity is essential for understanding how these elements impact genomes and their evolution as well as for fully exploiting them as functional genomics tools and gene-therapy vectors. Using a genetics-based approach, the influence of genomic position on piggyBac mobility in Drosophila melanogaster was assessed while controlling for element structure, genetic background, and transposase concentration. The mobility of piggyBac elements varied over more than two orders of magnitude solely as a result of their locations within the genome. The influence of genomic position on element activities was independent of factors resulting in position-dependent transgene expression (''position effects''). Elements could be relocated to new genomic locations without altering their activity if $500 bp of genomic DNA originally flanking the element was also relocated. Local intrinsic factors within the neighboring DNA that determined the activity of piggyBac elements were portable not only within the genome but also when elements were moved to plasmids. The predicted bendability of the first 50 bp flanking the 59 and 39 termini of piggyBac elements could account for 60% of the variance in position-dependent activity observed among elements. These results are significant because positional influences on transposable element activities will impact patterns of accumulation of elements within genomes. Manipulating and controlling the local sequence context of piggyBac elements could be a powerful, novel way of optimizing gene vector activity.

Post-Integration Silencing of piggyBac Transposable Elements in Aedes aegypti

“…Esnault et al (2011) found that local chromosomal DNA sequences immediately flanking integrated piggyBac elements in D. melanogaster account for almost all of the variance in element mobility observed among identical piggyBac elements integrated in different positions and exposed to a fixed source of piggyBac transposase [27]. Esnault et al (2011) could remove integrated piggyBac elements along with varying amounts of flanking DNA and re-integrate the elements and flanking DNA using site specific recombination into new positions within the genome of D. melanogaster [27].…”

“…P{ry+t7.2 = hsp70-flp}1, y1 w*; M{3xP3-RFP.attP}ZH-86Fb; M{vas-int.B}ZH-102D with an integrated copy of the plasmid PB{RB} [21], [27].…”

“…Two transgenic lines of D. melanogaster were created essentially as described by Esnault et al (2011) [27]. Preblastoderm embryos of P{ry+t7.2 = hsp70-flp}1, y1 w*; M{3×P3-RFP.attP}ZH-86 Fb; M{vas-int.B}ZH-102D [32] were injected with pCL1w + and p40Dw + at 0.25 mg/ml and individual adults arising from these embryos were out-crossed to w 1118 flies of the opposite sex.…”

“…While integrated piggyBac elements in the genome of D. melanogaster remobilize frequently enough for them to be valuable genomics tools in this species, piggyBac remobilization activity is highly variable among integrated elements and dependent, in part, upon the elements’ positions within the genome [27]. Esnault et al (2011) saw a range of somatic and germ-line remobilization frequencies spanning two or three orders of magnitude for identical piggyBac elements and most of the observed variance could be attributed to the positions of the elements within the genome.…”

“…Esnault et al (2011) saw a range of somatic and germ-line remobilization frequencies spanning two or three orders of magnitude for identical piggyBac elements and most of the observed variance could be attributed to the positions of the elements within the genome. They also showed, by moving elements with variable amounts of flanking chromosomal DNA to new genomic locations and measuring again the elements’ mobility, that less than a kilobase of flanking chromosomal DNA was responsible for determining the remobilization activity of an element [27]. Elements could be moved to different locations within the genome and retain their original remobilzation activities as long as approximately one kilobase of the original integration sites were included.…”