Genome complexity: transposons drive adaptation (Introduction)

by David Turell , Friday, January 21, 2022, 15:31 (1037 days ago) @ David Turell

A review as junk DNA disappears:

https://www.the-scientist.com/features/adapting-with-a-little-help-from-jumping-genes-6...

"The notion that TEs are vital to genomes, and not parasites or trash, harks back to the 1950s and Barbara McClintock, who won a Nobel Prize in 1983 for the discovery of transposons in maize: she proposed that TEs play an important role in gene expression in the very first paper on them. But the idea that genetic elements could be mobile clashed with the prevailing view of an organism’s genome as fixed. It would be decades before transposons were described from other organisms and their near-universal presence in genomes became clear. By then, researchers had figured out that these bits of DNA coopt a cell’s machinery, and the parasite framing emerged. Further, research showing that TEs don’t code for essential cellular proteins meant that, at best, they got lumped in with other kinds of noncoding DNA as genetic junk.

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"But with long-read sequencing methods enabling scientists to document the transposon content—the “mobilome”—of individual organisms, TEs are entering the spotlight. And, it turns out, they can and do regulate genes. McClintock was right.

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"There are numerous ways that mobile genetic elements can affect evolution. For example, many transposable elements (TEs), often called transposons, contain genes that code for their jumping or copying machinery, and over time these may be “domesticated” through mutation and selection, becoming integral parts of the organisms’ genome. The RAG1 and RAG2 enzymes that mix up DNA segments in immune proteins (antibodies and T cell receptors) are a notable example. “Wild” TEs can also have adaptive potential, creating genetic diversity as they leap. If TEs land inside a gene, they can directly alter coding regions, mRNA splice sites, or expression-related motifs (left). And because transposons often contain transcription factor binding sites and other regulatory sequences, they can alter a gene’s expression even if they land nearby (right). The transposable elements can also alter the genome in other ways—such as by picking up huge chunks of DNA as they jump (not pictured)—that scientists suspect are similarly altering the course of evolution.

"Arguably the most immediate and dramatic impacts TEs have on genomes occur when they insert into active genes. They can jump into coding regions, altering protein sequences, or they can insert into noncoding regions and alter gene splicing or expression. This is what happened in peppered moths, when a 22-kb TE inserted into the cortex gene and led to overproduction of melanin, turning dark the normally lightly bespeckled moths and improving their survival in polluted environments.

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"In addition to a growing body of evidence that transposons can generate diversity in host genomes to drive change over millions of years, Mirouze says TEs are likely major drivers of rapid evolution—changes measured in terms of generations rather than millennia.

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"Chuong, who says his group’s unpublished work in cattle has suggested that TEs can be activated by immune responses after eons of being silenced, says it’s plausible that TEs are a “major source of variation . . . that could be selected upon” during times of extreme stress, especially when that stress is novel and sudden, such as infection with a deadly pathogen. In such cases, he says, “I think transposons and their activity are much more likely to provide an outsized source of variation compared to littler mutations.'”

Comment: Perhaps transposons are God's dabble mechanism. Enormous article worth reading.