Science1 publisher2 min readPublished
Mobile DNA that copies itself through RNA fills nearly half the human genome
A Quanta survey traces jumping genes from Barbara McClintock's speckled corn kernels to the retrovirus-like sequences that make up much of the human genome. It treats host and transposon as long-term coevolutionary partners.
The Scientist · Science desk
What happened
- Barbara McClintock found the first evidence of mobile genetic elements more than 80 years ago at Cold Spring Harbor Laboratory in New York, while trying to explain colour variation in corn kernels.
- Three decades later, in 1983, she was awarded a Nobel Prize for a discovery that showed genes are not fixed in place.
- Researchers have since found transposons in organisms across the tree of life and described a taxonomy of subtypes that clusters into two main groups.
- Nearly half of the human genome is retrotransposon sequence, a share built up over time by elements that multiply by copying themselves.
- Quanta's survey reports that transposons are increasingly treated as a feature of many genetic tool kits, with links to the evolution of moths and wombs and to the switching of genes on and off.
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Why it matters
- constraint If about half the genome is sequence held in many similar copies, then any method that needs a unique location for a read is effectively working on the other half, and the repetitive half has to be handled deliberately.
- contradiction The two figures Quanta gives, nearly half the genome mobile and repetitive and nearly half retrotransposon, almost entirely overlap, so the class McClintock discovered contributes very little of the human genome's bulk.
- precedent With the order of retrovirus and retrotransposon still argued over, describing a human sequence as viral in origin is a claim about ancestry the field has not closed, and papers that treat the label as settled are ahead of the evidence.
The two classes move by different means, and the difference decides how much of a genome each can occupy. A DNA transposon is spliced out by enzymes called transposases and pasted back in elsewhere by the cell's own repair machinery, so it ends up in a different location [8]. A retrotransposon never has to leave: the sequence is copied into RNA, and that RNA copy is reverse-transcribed into DNA at a different location [9]. Each round of copying adds sequence, and Quanta's account says this is how retrotransposons come to flood a genome with many iterations of themselves [10].
Quanta also puts the total mobile and repetitive fraction of the human genome at nearly half [1]. Set that beside the figure for retrotransposons alone and the two nearly coincide, which leaves the cut-and-paste class, the one McClintock actually found in corn, with a small share of the bulk [18].
Her evidence ran in both directions. Eighty years later, that is what makes the corn work hold up. The strain she used produced kernels that were usually solid purple, and some that were speckled, purple pigment spattered over a yellow base [4]. An element landing inside a pigment gene interfered with it and the cell came out speckled; when the element jumped out again, the pigment gene was restored and the cell was purple [5]. An ordinary mutation could explain a one-way loss of pigment, but not the restoration of the same gene. The reversion points to an element that had physically left.
Many retrotransposons are related to viruses. Biologists still debate which came first, according to Quanta [12]. Retroviruses insert a DNA copy of their RNA sequence into the host cell's genome; HIV does this to infection-fighting white blood cells [13]. When the virus does not kill its host, that inserted genetic legacy can remain, and the remnants accumulate over millions of years [14].
Quanta describes the host-transposon relationship as a deep coevolutionary entanglement [16]. The cases it assembles establish that a transposon insertion can become something a host uses. How often that happens is not quantified in the piece [20], and I would want that fraction before treating an unannotated repeat in a newly sequenced genome as a candidate for function.
What to watch
- A published count of human adaptations traceable to specific transposon insertions, which would test the tool-kit framing against a rate.
- Evidence that settles whether retroviruses descend from retrotransposons or the reverse.
- Annotation work that reports what share of the repetitive half of the human genome is DNA transposon versus retrotransposon.