Expansion and Evolution of the X-Linked Testis Specific Multigene Families in the melanogaster Species Subgroup

The testis specific X-linked genes whose evolution is traced here in the melanogaster species subgroup are thought to undergo fast rate of diversification. The CK2ßtes and NACβtes gene families encode the diverged regulatory β-subunits of protein kinase CK2 and the homologs of β-subunit of nascent peptide associated complex, respectively. We annotated the CK2βtes-like genes related to CK2ßtes family in the D. simulans and D. sechellia genomes. The ancestor CK2βtes-like genes preserved in D. simulans and D. sechellia are considered to be intermediates in the emergence of the D. melanogaster specific Stellate genes related to the CK2ßtes family. The CK2ßtes-like genes are more similar to the unique autosomal CK2ßtes gene than to Stellates, taking into account their peculiarities of polymorphism. The formation of a variant the CK2ßtes gene Stellate in D. melanogaster as a result of illegitimate recombination between a NACßtes promoter and a distinct polymorphic variant of CK2ßtes-like ancestor copy was traced. We found a close nonrandom proximity between the dispersed defective copies of DINE-1 transposons, the members of Helitron family, and the CK2βtes and NACβtes genes, suggesting an involvement of DINE-1 elements in duplication and amplification of these genes

Distorted Sex Ratios: A Window into RNAi-Mediated Silencing

Some species ofDrosophila have unequal ratios of males to females, and now two genes--one responsible for such sex-ratio distortion and one that suppresses it--have been identified in one of these species

Both piRNA and siRNA Pathways Are Silencing Transcripts of the Suffix Element in the Drosophila melanogaster Germline and Somatic Cells

In the Drosophila melanogaster germline, the piRNA pathway silences retrotransposons as well as other transcribed repetitive elements. Suffix is an unusual short retroelement that was identified both as an actively transcribed repetitive element and also as an element at the 3′ ends of the Drosophila non-LTR F element. The copies of suffix that are F element-independent are far more actively transcribed than their counterparts on the F element. We studied the patterns of small RNAs targeting both strands of suffix in Drosophila ovaries using an RNase protection assay and the analysis of the corresponding RNA sequences from the libraries of total small RNAs. Our results indicate that suffix sense and antisense transcripts are targeted mainly by 23–29 nucleotides in length piRNAs and also by 21 nucleotides in length siRNAs. Suffix sense transcripts actively form longer RNA species, corresponding either to partial digestion products of the RNAi and Piwi pathways or to another RNA silencing mechanism. Both sense and antisense suffix transcripts accumulated in the ovaries of homozygous spn-E, piwi and aub mutants. These results provide evidence that suffix sense and antisense transcripts in the germ line and soma are targeted by both RNAi and Piwi pathways and that a Dicer-independent pathway of biogenesis of siRNAs could exist in Drosophila cells

The cytogenetic architecture of the aphid genome

In recent years aphids, with their well-defined polyphenism, have become favoured as model organisms for the study of epigenetic processes. The availability of the pea aphid (Acyrthosiphon pisum) genome sequence has engendered much research aimed at elucidating the mechanisms by which the phenotypic plasticity of aphids is inherited and controlled. Yet so far this research effort has paid little attention to the cytogenetic processes that play a vital part in the organisation, expression and inheritance of the aphid genome. Aphids have holocentric chromosomes, which have very different properties from the chromosomes with localised centromeres that are found in most other organisms. Here we review the diverse forms of aphid chromosome behaviour that occur during sex determination and male and female meiosis, often in response to environmental changes and mediated by endocrine factors. Remarkable differences occur, even between related species, that could have significant effects on the inheritance of all or parts of the genome. In relation to this, we review the particular features of the distribution of heterochromatin, rDNA genes and other repetitive DNA in aphid chromosomes, and discuss the part that these may play in the epigenetic modification of chromatin structure and function

Multiple alignment of <i>DINE-1</i>copies in syntenic regions of <i>D. melanogaster</i> and <i>D. simulans/D. sechellia</i>.

<p>(<b>A</b>) Alignment of known and novel <i>DINE-1</i> copies with <i>D. melanogaster DINE-1</i> consensus sequence (DINEYang) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Yang2" target="_blank">[26]</a>; consensus regions are designated according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Yang2" target="_blank">[26]</a>; (<b>B</b>) Alignment of the <i>simINE_ben</i> and <i>DNAREP1_DM</i> consensus sequence <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Kapitonov3" target="_blank">[36]</a>.</p

Recombination between the ancestor <i>CK2βtes</i>-<i>like</i> gene (GD15860 or GM17570) and <i>NACβtes</i> promoter region.

<p>Signature sequence of putative <i>CK2βtes</i>-like partner is designated in bold italics. The distances in nucleotides from the start of signature sequence and ORF start are indicated in brackets. Broken line shows the site of fusion of the <i>CK2βtes</i>-like and <i>NACβtes</i> sequences as a result of recombination. The tree represents the similarity of the nucleotide sequences in the selected box measured as the number of base differences <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-S1" target="_blank">[42]</a> and was constructed using the UPGMA method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Sneath1" target="_blank">[43]</a>. The percentage of replicate trees in which the associated sequence clustered together in the bootstrap test (500 iterations) are shown next to the branches. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed.</p

Transcription of the 1.688 Satellite DNA Family Is Under the Control of RNA Interference Machinery in Drosophila melanogaster Ovaries

Here we show that RNA interference (RNAi) machinery operates in Drosophila melanogaster 1.688 satellite transcription. Mutation in the spn-E gene, known to be involved in RNAi in the oocytes, causes an increase of satellite transcript abundance. Transcripts of both strands of 1.688 satellite repeats in germinal tissues were detected. The strength of the effects of the spn-E mutation differs for 1.688 satellite DNA subfamilies and is more pronounced for autosomal pericentromeric satellites compared to the X-linked centromeric ones. The spn-E1 mutation causes an increase of the H3-AcK9 mark and TAF1 (a component of the polymerase II transcriptional complex) occupancy in the chromatin of autosomal pericentromeric repeats. Thus, we revealed that RNAi operates in ovaries to maintain the silenced state of centromeric and pericentromeric 1.688 repeats

Fate of multigene families in the course of the divergence of <i>melanogaster</i> group species.

<p>Fate of multigene families in the course of the divergence of <i>melanogaster</i> group species.</p