Humans may have benefited from mobile genetic element insertions

Humans may have benefited from mobile genetic element insertions
Standard genome-wide DNA arrays often miss LINE-1 retrotransposons. Credit: Tomasz Wyszołmirski/iStock/Thinkstock

Mobile pieces of DNA can jump around in the human genome and exert powerful regulatory effects on neighboring genes at new insertion sites. The most common mobile genetic elements are known as LINE-1 retrotransposons and comprise almost 20 per cent of all our DNA. Yet most genome-wide studies have underestimated the full impact of these important genetic regulators.

To correct this, a team led by William Burkholder at the A*STAR Institute of Molecular and Cell Biology in Singapore took a fresh look at the effects of LINE-1 retrotransposons on gene function and disease susceptibility. When they did this, the researchers found evidence that a subset of LINE-1 elements seems to have exerted a beneficial effect on recent human evolution.

Alexandre Kuhn from the Burkholder laboratory and other colleagues performed a comprehensive survey of LINE-1 retrotransposons in the genomes of 20 individuals of Asian descent. The research team, which included scientists from Singapore and the United States, found that, on average, an individual has more than 800 LINE-1 retrotransposons. Despite their high prevalence, these important have not been adequately accounted for in standard arrays designed for genome-wide analyses of human disease or natural variation.

The researchers showed that this oversight, rather than originating from a technical error, was due to a limitation of the most commonly used methodologies. Specifically, they found that the DNA letter differences, known as single-nucleotide polymorphisms (SNPs), measured on the arrays are not closely linked to nearby LINE-1 elements, and hence the standard arrays failed to 'tag' them.

In order to tag LINE-1 retrotransposons to neighboring SNPs, Burkholder's team integrated LINE-1 information with whole-genome sequencing data collected by the 1000 Genomes Project—a massive international effort to create a detailed map of . They found that most LINE-1 elements could indeed be tightly associated with SNPs. According to Kuhn, this means "that genome-wide association studies of their phenotypic effects could be conducted based on SNP genotyping in large populations."

To prove the point, the researchers ran the new analysis and then studied the genetic sequences surrounding the mobile genetic elements. In this way, they found evidence for recent positive selection, meaning that some of the LINE-1 retrotransposons conferred an evolutionary advantage when they jumped into new spots in the genome. This could be seen in the unusually long blocks of DNA surrounding several LINE-1 —an indication that the genetic elements and their flanking sequences had swept through the population.


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More information: Kuhn, A., Ong, Y. M., Cheng, C.-Y., Wong, T. Y., Quake, S. R. & Burkholder, W. F. Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome. Proceedings of the National Academy of Sciences USA 111, 8131–8136 (2014). dx.doi.org/10.1073/pnas.1401532111
Citation: Humans may have benefited from mobile genetic element insertions (2014, September 10) retrieved 20 July 2019 from https://medicalxpress.com/news/2014-09-humans-benefited-mobile-genetic-element.html
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Sep 11, 2014
Interesting that rather than there being a particular code for evolution, the entirety of the system is composed harmoniously as Leibniz stated.

JVK
Sep 11, 2014
It would be more interesting if they placed the evidence for recent positive selection into the context of nutrient-dependent amino acid substitutions that differentiate the cell types of species from microbes to man via their pheromone-controlled reproduction.

The nutrient-dependent RNA-mediated events link the epigenetic landscape to the physical landscape of DNA in organized genomes, which links ecological variation to ecological adaptations via conserved molecular mechanisms. Theories about mutations, natural selection and the evolution of biodiversity that fail to include details of any evolutionary event are replaced by RNA-mediated events, which have been detailed in experimental evidence across species that links ecological variation to ecological adaptations in exactly the same way predicted by serious scientists for more than 50 yrs.

Sep 11, 2014
It would be more interesting if they placed the evidence for recent positive selection into the context of nutrient-dependent amino acid substitutions that differentiate the cell types of species from microbes to man via their pheromone-controlled reproduction.

The nutrient-dependent RNA-mediated events link the epigenetic landscape to the physical landscape of DNA in organized genomes, which links ecological variation to ecological adaptations via conserved molecular mechanisms. Theories about mutations, natural selection and the evolution of biodiversity that fail to include details of any evolutionary event are replaced by RNA-mediated events, which have been detailed in experimental evidence across species that links ecological variation to ecological adaptations in exactly the same way predicted by serious scientists for more than 50 yrs.


GKY

JVK
Sep 11, 2014
Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems http://stm.scienc...abstract

The differences in the gut microbes are linked from nutrient-dependent amino acid substitutions to differences in immune system function as is predicted in the context of RNA-mediated cell type differentiation in all cells of all individuals of all species via the conserved molecular mechanisms of transgenerational epigenetic inheritance manifested in the morphological and behavioral phenotypes of insects and worms, which are model organisms for the development of morphological and behavioral phenotypes in humans.

In insects and worms the role of mobile genetic elements is well described, but no evolutionary events have been described that would lead from mutations to natural selection and the evolution of biodiversity. See instead: http://www.cell.c...)00806-X "Starvation-Induced Transgenerational..

Sep 13, 2014
Mobile pieces of DNA can jump around in the human genome and exert powerful regulatory effects on neighboring genes at new insertion sites.

(The first sentence)

A control group is at hand. Reinsert the same removed piece of DNA at the same removal site.
Is the simple removal and reinsertion exerting a powerful regulatory effects on neighboring genes?
Of course the assumption you are checking is that no new powerful regulatory effects are expected to occur. If new effects do occur the search for a control group becomes critical.

JVK
Sep 13, 2014
Does anyone understand the concept of RNA-mediated events, or must we continue to focus on the pseudoscientific nonsense of evolutionary events that have never been described as study after study is meaningfully interpreted in the context of meaningless results that link mutations and natural selection to DNA and the evolution of biodiversity without RNA-mediated events that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms?

That was a rhetorical question. If others understood the concept of RNA-mediated events, they would not be so focused on DNA as to ignore everything known about the molecular epigenetics of cell type differentiation in all cells of all individuals of all species.

See: My comment on RNA and dynamic nuclear organization http://comments.s....1252966 and evolution http://comments.s....1247472

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