The nomad element

• Main Author: Whalen, James H.
• Format: Others
• Language: English
• Published: 2009
• Online Access: http://hdl.handle.net/2429/10086

The E(var)45-19 mutation of Drosophila melanogaster was isolated in a genetic screen for P-element induced enhancers of the variegating rearrangement, wm4. Remobilization of the P-element in E(var)45-19 resulted in a loss of its ability to enhance position-effect variegation (PEV) of wm4, indicating that the P-element in this mutant resulted in the E(var) phenotype. An allele of E(var)45-19, Su(var)r27, was isolated following mobilization of the P-element. Su(var)r27 was demonstrated to have sex-specific effects on the variegating rearrangements wm4 and bwVDe2. In addition to its effect on PEV, Su(var)r27 was shown to enhance the mutant phenotype associated with the retroelement-induced allele wbl, suggesting that this locus is involved in the regulation of both chromatin structure and retroelement expression. The P-element insert in E(var)45-19 was located in cytogenetic region 63A by in situ hybridization. The P-element was shown to be inserted into the 3'LTR of a novel retrovirus-like transposon, which I named nomad. DNA sequence analysis showed that nomad contained three long ORFs that were similar to the gag, pol and env genes of retroviruses and the copia-like elements of Drososphila melanogaster. The nomad element terminates with 519 base pair long terminal repeats, each of which contains eukaryotic consensus transcription initiation and termination signals, nomad elements are located at approximately 10-15 sites within the euchromatic arms of the genome and at the chromocenter as shown by in situ hybridization. The host DNA sequence TANA was duplicated on each side of the nomad element and appears to be a prefered target site for insertion of nomad elements. Analysis of the zinc finger motif in the pol gene product of retrotransposons known to have target site preference suggests involvement of the integrase subunit in target site selection for retrotransposons that display insert site specificity. A comparison of the predicted amino acid sequence of the pol-like genes of several known retrotransposons was made and the phylogenetic relationship between nomad and other retrovirus-like mobile elements was determined. It was clear from this conceptual protein analysis and from analysis of structural characteristics that retrotransposons of the gypsy class can be generally classified as members of one of two distinct groups. The phylogenetic relationships of these groups are also discussed. The level of nomad transcription in the E(var)45-19 and Su(var)r27 mutations was shown to correlate with their effect on PEV, suggesting that the nomad element may be directly involved in the regulation of chromatin structure. In conclusion, a number of speculative models are presented to explain the effect of mutations in the nomad element on PEV and retroelement expression. [Scientific formulae used in this abstract could not be reproduced.] === Science, Faculty of === Zoology, Department of === Graduate