Genome complexity: jumping gene activity (Introduction)

by David Turell @, Monday, November 14, 2016, 18:56 (2692 days ago) @ David Turell

The activity of transposons which can change genetic messages is explored:

http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.117.208101

Abstract: "Transposable elements, or transposons, are DNA sequences that can jump from site to site in the genome during the life cycle of a cell, usually encoding the very enzymes which perform their excision. However, some transposons are parasitic, relying on the enzymes produced by the regular transposons. In this case, we show that a stochastic model, which takes into account the small copy numbers of the active transposons in a cell, predicts noise-induced predator-prey oscillations with a characteristic time scale that is much longer than the cell replication time, indicating that the state of the predator-prey oscillator is stored in the genome and transmitted to successive generations. Our work demonstrates the important role of the number fluctuations in the expression of mobile genetic elements, and shows explicitly how ecological concepts can be applied to the dynamics and fluctuations of living genomes."

Report on the contents of the paper:

http://phys.org/news/2016-11-motion-genes-human-genome.html

"These are genes that are active and are doing genome editing in real time in living cells, and this is a start of trying to really understand them in much more detail than has been done before," said Goldenfeld,

***

"Goldenfeld and Xue embarked on this work because of their interest in transposons, small regions of DNA that can move themselves from one part of the genome to another during the lifetime of a cell—a capability that has earned them the name "jumping genes." Collectively, various types of transposons make up almost half of the human genome. When they move around, they may create mutations in or alter the activity of a functional gene; transposons can therefore create new genetic profiles in a population for natural selection to act on, in either a positive or negative way.

***

"the physical structure of the DNA that makes up the genome acts like an environment, in which two types of transposons, long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), have a competitive relationship with one another. In order to replicate, SINEs steal the molecular machinery that LINEs use to copy themselves, somewhat like a cuckoo bird tricks other birds into raising her chicks for her while abandoning their own.

***

"This method has been successfully applied in ecology to describe predator-prey interactions; Xue and Goldenfeld simulated the movements of transposons within the human genome with the same mathematical method. Their models included a detailed accounting for how Alu elements steal the molecular machinery L1 elements use to copy themselves.

"Xue and Goldenfeld's results predicted that populations of LINE and SINE elements in the genome are expected to oscillate the way those of, for example, wolves and rabbits might.

"'We realized that the transposons' interaction actually was pretty much like the predator-prey interaction in ecology," said Xue. "We came up with the idea, why don't we apply the same idea of predator-prey dynamics . . .we expected to see the oscillations we see in the predator-prey model. So we first did the simulation and we saw the oscillations we expected, and we got really excited."

"In other words, too many SINEs and the LINEs start to suffer, and soon there are not enough for all the SINEs to exploit. SINEs start to suffer, and the LINEs make a come-back. Xue and Goldenfeld's model made the surprising prediction that these oscillations occur over a timescale that is longer than the human lifespan—waves of Alu elements and L1 elements pushing and pulling at each other in slow motion across generations of the human genomes that carry them."

Comment: It is amazing to see different types of transposons struggling with each other, but it certainly adds flexibility to genome changes. This adds to the complexity of the genome. DNA is not a simple code by any measure.


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