Structural heterogeneity and genomic distribution of Drosophila melanogaster LTR-retrotransposons

Area de Genética, Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain.
Molecular Biology and Evolution (Impact Factor: 9.11). 04/2003; 20(3):401-9. DOI: 10.1093/molbev/msg047
Source: PubMed


Structural heterogeneity of five long terminal repeat (LTR) retrotransposon families (297, mdg 1, 412, copia, and 1731) was investigated in Drosophila melanogaster. The genomic distribution of canonical and rearranged elements was studied by comparing hybridization patterns of Southern blots on salivary glands from adult females and males with in situ hybridization on polytene chromosomes. The proportion and genomic distribution of noncanonical copies is distinctive to each family and presents constant features in the four different D. melanogaster strains studied. Most elements of families 297 and mdg 1 were noncanonical and presented large interstock and intrastock polymorphism. Noncanonical elements of these two families were mostly located in euchromatin, although not restricted to it. The elements of families 412 and copia were better conserved. The proportion of noncanonical elements was lower. The 1731 family is mainly composed of noncanonical, beta-heterochromatic elements that are highly conserved among stocks. The relation of structural polymorphism to phylogeny, transpositional activity and the role of natural selection in the maintenance of transposable elements are discussed.

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Available from: Ana Domínguez, Jul 09, 2014
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    • "Another non-exclusive hypothesis is that TE accumulation in heterochromatin is not merely the result of passive accumulation, caused by the absence of strong forces tending to eliminate them in such regions, and involves combined effects of specific targeting and positive selection for retention (Dimitri and Junakovic 1999; Biémont 2009). This hypothesis is supported by the fact that TEs often display some selectivity for genomic targets that may be defined by a variety of parameters such as chromatin accessibility, DNA sequence, protein-DNA interactions and bent DNA (Craig 1997) and is also consistent with the observation that some D. melanogaster TE families are preferentially located in heterochromatin while others are mainly euchromatic (Di Franco et al. 1997; Terrinoni et al. 1997; Alonso-González et al. 2003, 2006), being the euchromatic or heterochromatic distribution of recently inserted copies a feature of each family (Mugnier et al. 2008). Transposable elementss have important roles in chromatin formation and centromere function (Glöckner and Heidel 2009; Chueh et al. 2009), the assambly of synaptonemal complexes (van der Heijden and Bortvin 2009) and, thus, cell division. "
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    ABSTRACT: The intragenomic distribution of five retrotransposon families (297, 1731, copia, mdg1 and roo) in the species of the melanogaster complex was studied by comparing results of the Southern blotting technique in males and females with those of in situ hybridization. The degree of structural polymorphism of each family in the different species was also investigated by restriction enzyme analysis. It was found that genomic distribution is a trait that depends on the family and species. The distribution of roo is mainly euchromatic in the four species and 1731 is heterochromatic, but the distribution of families 297, copia and mdg1 is markedly different in the melanogaster and simulans clades. These families were mainly euchromatic in D. melanogaster but heterochromatic in its sibling species. In the simulans clade most copia and mdg1 elements are located on chromosome Y. Differences in genomic distribution are unrelated with structural conservation. The relation of intragenomic distribution to phylogeny, transpositional activity and the role of the host genome are discussed.
    Genetica 12/2009; 138(6):579-86. DOI:10.1007/s10709-009-9430-7 · 1.40 Impact Factor
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    • "Several studies have shown that genomes harbor a mixture of TEs, some of which are still active, whereas others are ancient relics that have degenerated [13-16]. Degraded elements can result from point mutations or from DNA deletion [17]. "
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    ABSTRACT: Several studies have shown that genomes contain a mixture of transposable elements, some of which are still active and others ancient relics that have degenerated. This is true for the non-LTR retrotransposon Helena, of which only degenerate sequences have been shown to be present in some species (Drosophila melanogaster), whereas putatively active sequences are present in others (D. simulans). Combining experimental and population analyses with the sequence analysis of the 12 Drosophila genomes, we have investigated the evolution of Helena, and propose a possible scenario for the evolution of this element. We show that six species of Drosophila have the Helena transposable element at different stages of its evolution. The copy number is highly variable among these species, but most of them are truncated at the 5' ends and also harbor several internal deletions and insertions suggesting that they are inactive in all species, except in D. mojavensis in which quantitative RT-PCR experiments have identified a putative active copy. Our data suggest that Helena was present in the common ancestor of the Drosophila genus, which has been vertically transmitted to the derived lineages, but that it has been lost in some of them. The wide variation in copy number and sequence degeneration in the different species suggest that the evolutionary dynamics of Helena depends on the genomic environment of the host species.
    BMC Evolutionary Biology 08/2009; 9(1):174. DOI:10.1186/1471-2148-9-174 · 3.37 Impact Factor
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    • "It emerged that most families are preferentially distributed on euchromatin. Only the 1731 family was mainly heterochromatic, as previously reported (Montchamp-Moreau et al. 1993; Alonso-Gonzaíez, Domı´nguez & Albornoz, 2003) Lines 201–280 were tested by Southern blot analysis at generation 75. Observed changes in their band patterns are presented in Table 3. "
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    ABSTRACT: Two sets of mutation accumulation lines, one reared at 28 degrees C and the other at 24 degrees C, were compared for their transposition and rearrangement rates of eleven transposable element families. The changes affecting mobile elements were analysed by the Southern technique and in situ hybridization. No differences were found between treated and control lines. The role of the host genotype in transposition control and the significance of structural mutations in transposable element dynamics are discussed.
    Genetica 09/2006; 128(1-3):11-9. DOI:10.1007/s10709-005-2480-6 · 1.40 Impact Factor
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