TheTARTsequence in this region aligns with the sequences fromHeT-AandTAHREwith no gaps and no misalignment of CCHC residues; however, there are more amino acid differences betweenTARTandHeT-Athan betweenTAHREandHeT-A(Physique S2)

TheTARTsequence in this region aligns with the sequences fromHeT-AandTAHREwith no gaps and no misalignment of CCHC residues; however, there are more amino acid differences betweenTARTandHeT-Athan betweenTAHREandHeT-A(Physique S2).TAHREand the canonicalHeT-Ahave 95% identity in this region but only 50 and 52% identity, respectively withTART.BecauseHeT-AGag interacts efficiently withTARTGag, it appears that these amino acid differences are tolerated. TheD. relative abundance of that element in telomere arrays, suggesting an explanation for the relative rarity ofTAHREelements in telomere arrays and supporting the Tioxolone hypothesis that Gag targeting to telomeres is usually important for the telomere-specific transposition of these elements. DROSOPHILA telomeres are maintained by a remarkable variant of the telomerase mechanism that maintains telomeres in almost all organisms (Pardueand DeBaryshe2003;Melnikovaand Georgiev2005). As in other organisms, Drosophila telomeres are elongated by tandem repeats that are reverse transcribed onto the ends of the chromosomes. What makes Drosophila telomeres unusual is the RNA template that is reverse transcribed to produce these repeats: Drosophila telomere repeats are copied from full-length retrotransposons (HeT-A,TART, andTAHRE), rather than from a short segment of the RNA molecule that makes up part of the telomerase holoenzyme (Physique 1). == Physique1. == The telomere retrotransposons ofD. melanogaster. These three non-LTR retrotransposons are drawn, approximately to size, as the RNA molecules that are reverse transcribed onto the telomere. Thick solid lines, untranslated regions; shaded ovals, Gag and Pol coding sequences; AAAAA, poly(A) 3 tail. Dotted Tioxolone lines enclose regions of significant nucleotide identity betweenTAHREand the other elements. The range of identity in pairwise comparisons ofTAHREwith different copies ofHeT-AorTARTis given for each region. TheTAHRE5-UTR is usually shorter and the 3-UTR is usually longer than the UTRs ofHeT-A.The extra sequences were not included in calculating identity. Although clearly related to other retrotransposons in theDrosophila melanogastergenome, the three retrotransposons that make up telomeres have several characteristics that set them apart from the more typical retrotransposable elements. One of these characteristics is usually their localization to telomere arrays. The euchromatic regions of theD. melanogastergenome have been completely sequenced (Celnikeret al.2002). Analysis of these gene-rich regions reveals no sequence from any of the three telomeric elements (Georgeet al.2006), although these euchromatic regions are littered with other retrotransposons (Kaminkeret al.2002). Conversely, the long arrays of telomeric retrotransposons do not contain their nontelomeric relatives. Thus, the telomeric and nontelomeric elements have distinctly different genomic distributions, except for small transition zones at the proximal ends of telomere arrays where fragments of both kinds of elements are mingled (Georgeet al.2006). The telomere-specific transposition ofHeT-AandTARTappears to depend around the intranuclear targeting of the Gag proteins encoded by each element. These Gags share amino acid sequence motifs with retroviral Gags, proteins known to be important in intracellular transport of viral RNA. The sequence similarities with retroviral Gags suggest that telomeric Gags are important in intracellular transport of the retrotransposon RNA, a suggestion supported by studies of the intracellular localization ofHeT-AandTARTGag proteins. Transient expression of tagged Gag proteins inD. melanogastercells showed that Gags of bothHeT-AandTARTlocalize Tioxolone to nuclei very efficiently. Gags of nontelomeric retrotransposons were also tested in these experiments and found predominantly, if not entirely, in the cytoplasm (Rashkovaet al.2002b). Preventing Gags of nontelomeric retrotransposons from entering the nucleus may be one of the mechanisms cells use to protect their genomes from parasitic invaders. In contrast, the telomeric retrotransposons have an essential role in the nucleus and the cell benefits from facilitating nuclear localization of these Gags. After moving from the cytoplasm into the nucleus,HeT-AGags form aggregates (Het dots) associated with telomeres in interphase nuclei.HeT-AandTARTare intermingled inD. melanogastertelomere arrays so it was surprising thatTARTGags formed loose intranuclear clusters with no obvious telomere associations. However, cotransfection experiments showed that when the two Gags are expressed in the same cells,HeT-AGag dominates the localization and movesTARTGag into telomere-associated Het dots (Rashkovaet Mertk al.2002a). Presumably this localization is necessary for transposition to telomeres. The collaborative localization of the two Gags suggests an explanation for two puzzling observations. The first observation is usually that allD. melanogasterstocks and cell lines have bothHeT-AandTARTin their telomeres, suggesting that both elements are needed by the cell. However, the two elements seem to be distributed randomly in telomere arrays, giving no indication that either one has a special role. The second observation is usually thatHeT-Aelements do not encode reverse transcriptase, whileTARTdoes. Most, if not all, other retrotransposons encode this enzyme. Having the enzyme sequence encoded by the element’s RNA would be expected to allow more.