The complete Tirant transposable element in Drososphila melanogaster shows a structural relationship with retrovirus-like retrotransposons

Abstract We have determined the structure and organization of Tirant, a retrotransposon of Drosophila melanogaster reported in literature to be responsible for four independent mutations. Tirant is a long terminal repeat (LTR) retrotransposon 8527 bp long. It possesses three open reading frames (ORF ) encoding Gag, Pol and Env proteins with a strong similarity with ZAM, a recently identified member of the gypsy class of retrovirus-like mobile elements. Molecular analysis of the Tirant genomic copies present in four D. melanogaster strains revealed that most of them are defective, non-autonomous elements that differ in the position and extension of the conserved internal portion. Defective elements lacking the Gag ORF but retaining the Env ORF are abundant in heterochromatin. Four discrete Tirant transcripts are observed during embryogenesis in the strain Oregon-R, the smaller of which, 1.8 kb in size, originates from the splicing of a primary transcript and leads to a subgenomic RNA coding for the Env product

Mosquitoes LTR Retrotransposons: A Deeper View into the Genomic Sequence of Culex quinquefasciatus

A set of 67 novel LTR-retrotransposon has been identified by in silico analyses of the Culex quinquefasciatus genome using the LTR_STRUC program. The phylogenetic analysis shows that 29 novel and putatively functional LTR-retrotransposons detected belong to the Ty3/gypsy group. Our results demonstrate that, by considering only families containing potentially autonomous LTR-retrotransposons, they account for about 1% of the genome of C. quinquefasciatus. In previous studies it has been estimated that 29% of the genome of C. quinquefasciatus is occupied by mobile genetic elements

The green valley of Drosophila melanogaster constitutive heterochromatin: protein-coding genes involved in cell division control

Constitutive heterochromatin represents a significant fraction of eukaryotic genomes (10% in Arabidopsis, 20% in humans, 30% in D. melanogaster, and up to 85% in certain nematodes) and shares similar genetic and molecular properties in animal and plant species. Studies conducted over the last few years on D. melanogaster and other organisms led to the discovery of several functions associated with constitutive heterochromatin. This made it possible to revise the concept that this ubiquitous genomic territory is incompatible with gene expression. The aim of this review is to focus the attention on a group of protein-coding genes resident in D. melanogaster constitutive of heterochromatin, which are implicated in different steps of cell division

Epigenetic Silencing of P-Element Reporter Genes Induced by Transcriptionally Active Domains of Constitutive Heterochromatin in <i>Drosophila melanogaster</i>

Reporter genes inserted via P-element integration into different locations of the Drosophila melanogaster genome have been routinely used to monitor the functional state of chromatin domains. It is commonly thought that P-element-derived reporter genes are subjected to position effect variegation (PEV) when transposed into constitutive heterochromatin because they acquire heterochromatin-like epigenetic modifications that promote silencing. However, sequencing and annotation of the D. melanogaster genome have shown that constitutive heterochromatin is a genetically and molecularly heterogeneous compartment. In fact, in addition to repetitive DNAs, it harbors hundreds of functional genes, together accounting for a significant fraction of its entire genomic territory. Notably, most of these genes are actively transcribed in different developmental stages and tissues, irrespective of their location in heterochromatin. An open question in the genetic and molecular studies on PEV in D. melanogaster is whether functional heterochromatin domains, i.e., heterochromatin harboring active genes, are able to silence reporter genes therein transposed or, on the contrary, can drive their expression. In this work, we provide experimental evidence showing that strong silencing of the Pw+ reporters is induced even when they are integrated within or near actively transcribed loci in the pericentric regions of chromosome 2. Interestingly, some Pw+ reporters were found insensitive to the action of a known PEV suppressor. Two of them are inserted within Yeti, a gene expressed in the deep heterochromatin of chromosome 2 which carries active chromatin marks. The difference sensitivity to suppressors-exhibited Pw+ reporters supports the view that different epigenetic regulators or mechanisms control different regions of heterochromatin. Together, our results suggest that there may be more complexity regarding the molecular mechanisms underlying PEV

Schematic representation showing the syntenic chromosomal regions of <i>D</i>. <i>virilis</i> and <i>D</i>. <i>pseudoobscura</i> containing the <i>D</i>. <i>melanogaster</i> heterochromatic gene orthologs.

<p>Black boxes correspond to heterochromatin regions; black oval shape indicates the centromere.</p

Phylogenetic relationships among syntenic chromosomes of the analysed <i>Drosophila</i> species.

<p>The scheme shows the phylogenetic relationships between <i>D</i>. <i>melanogaster</i>, <i>D</i>. <i>pseudoobscura</i>, its sibling species <i>D</i>. <i>persimilis</i> and <i>D</i>. <i>virilis</i>, as defined by Muller [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006212#pgen.1006212.ref045" target="_blank">45</a>]. The syntenic Muller elements (right) are shown by the number of their corresponding chromosomes.</p

Immunolocalization of HP1a on polytene chromosomes.

<p>HP1a distribution is shown on polytene chromosomes of <i>D</i>. <i>virilis</i> (upper panels) and <i>D</i>. <i>pseudoobscura</i> (lower panels). The HP1a fluorescence signals clearly marks Dvir_42F-43A, Dvir_47C and Dvir_55D and to Dpse_63A, Dpse_83A, Dpse_82AB and Dpse_93. Three additional strongly stained regions are present in <i>D</i>. <i>pseudoobscura</i>.</p

Features of the non-autonomous LTR retrotransposons identified in this paper.

<p>For each non-autonomous element is reported the supercontig in which a representative element can be found, the overall length, the LTR size, the tRNA complementary to the PBS. It is also indicated the position, the period and the copies of the repeated DNA contained in the elements listed. The entropy value gives an estimation of the complexity of the repeats (see main text). The portion occupied by repeats in terms of % of the total size of the element is also indicated (column %).</p

List of <i>D</i>. <i>pseudoobscura</i> genes at Dpse_78B orthologous to genes of <i>D</i>. <i>virilis</i> and <i>D</i>. <i>melanogaster</i>.

<p>List of <i>D</i>. <i>pseudoobscura</i> genes at Dpse_78B orthologous to genes of <i>D</i>. <i>virilis</i> and <i>D</i>. <i>melanogaster</i>.</p

Evolutionary relationships of <i>C. quinquefasciatus</i> LTR-retrotransposons.

<p>Phylogenetic relationships of the LTR retrotransposons based on the amino acids alignment of the conserved RT, RNase H and INT domains. The clades in which fall retrotransposons detected in this paper are indicated with different colors, along with the most common tRNA complementary to the PBS is indicated for each homogeneous group. Elements from this study are indicated as “cpgypsy_” followed by a number. AAGYPSY# elements are LTR retrotransposons identified in previous analyses <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030770#pone.0030770-Minervini1" target="_blank">[17]</a>. The N-J bootstrap values supporting the internal branches are indicated at the nodes. Only bootstrap values greater than 50% are reported. Bel-like elements were used as outgroup. Note that, for families composed of two or more copies (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030770#pone-0030770-t001" target="_blank">table 1</a>), representative elements (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030770#pone.0030770.s001" target="_blank">file S1</a>) were used for the phylogenetic analyses.</p