Transposons Move the Case for Design Ahead

Transposable elements, once thought to be a class of junk DNA, show signs of function and, consequently, design based on new research.

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We live in a mobile society. People move around from city to city and state to state. Often, new career opportunities or the wish to live in a particularly desirable part of the country prompt the moves.

Within genomes, mobile pieces of DNA, called transposons, move around from place to place, too. Retrotransposons are the most common type; they include LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), and LTRs (long terminal repeats).

iStock_000002040220XLargeEvolutionary biologists believe these various sequence elements originate from a class of junk DNA called endogenous retroviruses (ENVs). Many scientists imagine ENVs are remnants of a retroviral infection, in which biochemical processes incorporate the viral DNA into the genome. Once part of the genome, the retroviral sequences suffer mutations, becoming inactive and leading to the formation of ENVs. These sequences, in turn, spawn LINEs, SINEs, and LTRs.

Retrotransposons not only move around the genome, they also duplicate themselves. However, unlike a person carefully planning a move across country, retrotransposons seem to proliferate and insert randomly throughout the genome. Evolutionary biologists have long thought that these mobile pieces of DNA served no useful function in the genome. In fact, they have argued that retrotransposons persist in the genome as parasitic pieces of DNA that infest genomes. (Just like the proverbial ne’er-do-well relative who moves across the country to live with you.)

Retrotransposons comprise roughly half the human genome. And for many evolutionary biologists, the mere presence of LINEs, SINEs, and LTRs indicates that much of the human genome consists of nonfunctional junk DNA.

Yet a number of studies demonstrate that retrotransposons play a role in gene expression. To read about a few of these discoveries, check out the following links:

Recently, scientists from Canada published one of the first attempts to quantify the extent to which transposable elements play a role in gene regulation.1 These researchers used ENCODE Project data to identify accessible regions of the genome. (Presumably, these accessible regions reflect active regions.)

The researchers then determined how many transposable elements mapped to these regions. They discovered that transposons made up 44 percent of the accessible regions (which amounts to about 730,000 sequence elements). It turns out transcription factor binding sites enrich these regions. (Transcription factors are proteins that bind to specific sequences, thus impacting gene expression.) In other words, transposable elements seem to play a comprehensive role in regulating gene expression in the human genome.

Evolutionary biologists argue that evolutionary processes will co-opt a percentage of junk DNA sequences to develop new capabilities—such as binding transcription factors and turning genes on and off—thus accounting for the function of transposons. This explanation appeared reasonable when only a few examples of transposon function had been reported. However, the scientists from Canada have uncovered in the human genome a recognized pervasiveness of transposon function that makes it hard to argue that transposons’ functional distribution is due to neofunctionalization. Instead, transposons’ widespread functional properties are best explained as the deliberate work of a Creator.

This new work also has implications for the debate over the ENCODE Project. Published in September 2012, ENCODE’s phase two results indicated that at least 80 percent of the human genome consists of functional DNA. A number of scientists have challenged the ENCODE conclusion for various reasons, including transposons’ extensive presence in the human genome. In a previous article I responded to this objection by stating that when it comes to transposable elements and pseudogenes in the human genome, it is highly likely that the 80 percent of the human genome that possesses functional elements overlaps the 50 percent comprised of transposable elements and pseudogenes. Based on the latest insight into the global occurrence of functional transposons, it looks like my assessment was correct.

References:

  1. Pierre-Étienne Jacques,
Justin Jeyakani, and
Guillaume Bourque, “The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements,” PLoS Genetics 9 (May 9, 2013): e1003504, doi:10.1371/journal.pgen.1003504.t001.
  2. The ENCODE Project Consortium, “An Integrated Encyclopedia of DNA Elements in the Human Genome,” Nature 489 (September 6, 2012): 57–74.
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