Transcriptional interference mediated by retrotransposons within the genome of their host: lessons from alleles of the white gene from Drosophila melanogaster

Silencing of Euchromatic Transposable Elements as a Consequence of Nuclear Lamina Dysfunction

Transposable elements (TEs) are mobile genomic sequences that are normally repressed to avoid proliferation and genome instability. Gene silencing mechanisms repress TEs by RNA degradation or heterochromatin formation. Heterochromatin maintenance is therefore important to keep TEs silent. Loss of heterochromatic domains has been linked to lamin mutations, which have also been associated with derepression of TEs. In fact, lamins are structural components of the nuclear lamina (NL), which is considered a pivotal structure in the maintenance of heterochromatin domains at the nuclear periphery in a silent state. Here, we show that a lethal phenotype associated with Lamin loss-of-function mutations is influenced by Drosophila gypsy retrotransposons located in euchromatic regions, suggesting that NL dysfunction has also effects on active TEs located in euchromatic loci. In fact, expression analysis of different long terminal repeat (LTR) retrotransposons and of one non-LTR retrotransposon located near active genes shows that Lamin inactivation determines the silencing of euchromatic TEs. Furthermore, we show that the silencing effect on euchromatic TEs spreads to the neighboring genomic regions, with a repressive effect on nearby genes. We propose that NL dysfunction may have opposed regulatory effects on TEs that depend on their localization in active or repressed regions of the genome.

Unravelling the world of cis-regulatory elements

Genome-wide comparisons indicate that only studying the coding regions will not be enough for explaining the biological complexity of an organism, while the genetic variants and the epigenetic differences of cis-regulatory elements are crucial to elucidate many complicated biological phenomena. Their various regulatory functions also play indispensable roles in forming organismal polymorphism. Recent studies showed that the cis-regulatory elements can regulate gene expression as nuclear organizers, and involve in functional noncoding transcription and produce regulatory noncoding RNA molecules. Novel high-throughput strategies and in silico analysis make a great amount data of cis-regulatory elements available. Particularly, the computational methods could help to combine reductionist studies with network biomedical investigations, and begin the era to understand organismal regulatory events at systems biology level.

A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes

A family of at least eleven genes called Mar related to long terminal repeat retrotransposons from the Ty3/gypsy group, including two genes previously identified as such, is present in human and mouse genomes. Single orthologous copies were identified for most Mar genes in different mammals. All of them have lost essential structural features necessary for autonomous retrotransposition before divergence between mouse and human. Three Mar genes also have introns at identical positions in human and mouse. Hence, Mar genes do not correspond to functional retrotransposons. Mar genes evolved under purifying selection, strongly suggesting that they are not pseudogenic relics but rather neofunctionalized retrotransposon genes. All putative Mar proteins display sequence similarity to the capsid-like domain of the Gag protein of Tf1/Sushi retrotransposons. In addition, three Mar proteins have conserved the Gag CCHC zinc finger motif, suggesting a role in nucleic acid binding. Some Mar genes have also retained from their retrotransposon origin a -1 ribosomal frameshifting between the gag-related open reading frame and a region encoding a putative aspartyl protease domain. EST analysis revealed that the majority of Mar genes are expressed in brain as well as in other tissues and organs. Some Mar proteins might function as transcription factors or be involved in the control of cell proliferation and apoptosis. Strikingly, as many as eight Mar genes are located on the X chromosome in human, mouse and other mammals, and at least two of the autosomal genes are subject to imprinting. We suggest that retrotransposons might be a source for epigenetically regulated genes. Epigenetic regulation of these neogenes might be derived from the cellular defense mechanisms having controlled their retrotransposon ancestor.