Small Things Considered: Polintons; A Viral Missing Link?

The line between viruses and parasitic elements of the genome is thin and delicate, and probably often crossed. Parasitic elements that acquire the means to escape the host cell become viruses and, conversely, viruses can lose this ability and return to a more limited lifestyle as transposable elements (TEs). This back-and-forth occurs alongside a propensity for gene exchange, with genes acquired horizontally from various hosts, and at various periods of evolution.The result is that, although viruses and other "selfish" elements are obviously related, their relationship cannot be represented by the satisfying, graceful branches seen on phylogenetic trees depicting the evolution of more pedestrian organisms such as primates, for example. Instead, a virus or TE is like a quilt whose patches were added by different quilters, at different times. 

Wrangling Retrotransposons | The Scientist Magazine®

Genomes are hotbeds of evolutionary conflict. Perhaps nothing speaks to this idea better than the war raging between retrotransposons and their host genomes. Retrotransposons, often referred to as jumping genes, are mobile genetic elements that parasitize host machinery to replicate themselves across the genome. Since their emergence more than 100 million years ago, retrotransposons have been enormously successful. Modern mammalian genomes, for example, are riddled with the scars of these copy-and-paste events, with retrotransposon-derived DNA now accounting for nearly 50 percent of the human genome.

Neuron - Increased L1 Retrotransposition in the Neuronal Genome in Schizophrenia

Recent studies indicate that long interspersed nuclear element-1 (L1) are mobilized in the genome of human neural progenitor cells and enhanced in Rett syndrome and ataxia telangiectasia. However, whether aberrant L1 retrotransposition occurs in mental disorders is unknown. Here, we report high L1 copy number in schizophrenia. Increased L1 was demonstrated in neurons from prefrontal cortex of patients and in induced pluripotent stem (iPS) cell-derived neurons containing 22q11 deletions. Whole-genome sequencing revealed brain-specific L1 insertion in patients localized preferentially to synapse- and schizophrenia-related genes. To study the mechanism of L1 transposition, we examined perinatal environmental risk factors for schizophrenia in animal models and observed an increased L1 copy number after immune activation by poly-I:C or epidermal growth factor. These findings suggest that hyperactive retrotransposition of L1 in neurons triggered by environmental and/or genetic risk factors may contribute to the susceptibility and pathophysiology of schizophrenia.

Jumping DNA in the brain may be a cause of schizophrenia

Stretches of DNA called retrotransposons, often dubbed "junk DNA", might play an important role in schizophrenia. In a study published today in the journal Neuron, a Japanese team revealed that LINE-1 retrotransposons are abnormally abundant in the schizophrenia brain, modify the expression of genes related to schizophrenia during brain development, and may be one of the causes of schizophrenia.

Many chronic diseases associated with aging are due to parasitic DNA - Medical News Today

The genomes of organisms from humans to corn are replete with "parasitic" strands of DNA that, when not suppressed, copy themselves and spread throughout the genome, potentially affecting health. Earlier this year Brown University researchers found that these "retrotransposable elements" were increasingly able to break free of the genome's control in cultures of human cells. Now in a new paper in the journal Aging, they show that RTEs are increasingly able to break free and copy themselves in the tissues of mice as the animals aged. In further experiments the biologists showed that this activity was readily apparent in cancerous tumors, but that it also could be reduced by restricting calories.

PLOS Genetics: Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans

The era of whole-genome sequencing has revealed that gene copy-number changes caused by duplication and deletion events have important evolutionary, functional, and phenotypic consequences. Recent studies have therefore focused on revealing the extent of variation in copy-number within natural populations of humans and other species. These studies have found a large number of copy-number variants (CNVs) in humans, many of which have been shown to have clinical or evolutionary importance. For the most part, these studies have failed to detect an important class of gene copy-number polymorphism: gene duplications caused by retrotransposition, which result in a new intron-less copy of the parental gene being inserted into a random location in the genome. Here we describe a computational approach leveraging next-generation sequence data to detect gene copy-number variants caused by retrotransposition (retroCNVs), and we report the first genome-wide analysis of these variants in humans. We find that retroCNVs account for a substantial fraction of gene copy-number differences between any two individuals. Moreover, we show that these variants may often result in expressed chimeric transcripts, underscoring their potential for the evolution of novel gene functions. By locating the insertion sites of these duplicates, we are able to show that retroCNVs have had an important role in recent human adaptation, and we also uncover evidence that positive selection may currently be driving multiple retroCNVs toward fixation. Together these findings imply that retroCNVs are an especially important class of polymorphism, and that future studies of copy-number variation should search for these variants in order to illuminate their potential evolutionary and functional relevance.

Brain Mosaic | The Scientist: Retrotransposons contribute to genetic variability in human brain cells.

Mobile genetic elements may be a source of DNA sequence variation in normal human brain tissue. Geoff Faulkner, now at the University of Queensland, and colleagues showed that retrotransposons, which can copy themselves and integrate into new sites in a cell’s genome, move much more frequently in brain cells compared to germline cells.