Genome complexity: epigenetics lasting forever (Introduction)

by David Turell , Thursday, January 16, 2020, 20:27 (1558 days ago) @ David Turell

Epigenetic marks may last forever, changing the idea they were temporary:

https://phys.org/news/2020-01-fossil-upend-basic-tenet-evolutionary.html

"...a UC San Francisco-led research team has discovered the first conclusive evidence that selection may also occur at the level of the epigenome—a term that refers to an assortment of chemical "annotations" to the genome that determine whether, when and to what extent genes are activated—and has done so for tens of millions of years. This unprecedented finding subverts the widely accepted notion that over geologic timescales, natural selection acts exclusively on variation in the genome sequence.

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"In a study published Jan. 16, 2020 in the journal Cell, the researchers show that Cryptococcus neoformans—a pathogenic yeast that infects people with weakened immune systems and is responsible for about 20 percent of all HIV/AIDS-related deaths—contains a particular epigenetic "mark" on its DNA sequence, which, based on their lab experiments and statistical models, should have disappeared from the species sometime during the age of the dinosaurs.

"But the study shows that this methylation mark—so named because it's created through a process that attaches a molecular tag called a methyl group to the genome—has managed to stick around for at least 50 million years—maybe as long as 150 million years—past its predicted expiration date. This amazing feat of evolutionary tenacity is made possible by an unusual enzyme and a hefty dose of natural selection.

"What we've seen is that methylation can undergo natural variation and can be selected for over million-year time scales to drive evolution," explained Hiten Madhani, MD, Ph.D., professor of biochemistry and biophysics at UCSF and senior author of the new study. "This is a previously unappreciated mode of evolution that's not based on changes in the organism's DNA sequence."

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"In the new study, Madhani and his collaborators show that hundreds of millions of years ago, the ancestor of C. neoformans had two enzymes that controlled DNA methylation. One was what's known as a "de novo methyltransferase," which was responsible for adding methylation marks to "naked" DNA that had none. The other was a "maintenance methyltransferase" that functioned a bit like a molecular Xerox. This enzyme copied existing methylation marks, which had been put in place by the de novo methyltransferase, onto unmethylated DNA during DNA replication. And like every other species with an epigenome that includes methylation, the ancestor of C. neoformans had both types of methyltransferase.

"But then, sometime during the age of the dinosaurs, the ancestor of C. neoformans lost its de novo enzyme. Its descendants have been living without one since then, making C. neoformans and its closest relatives the only species alive today known to have DNA methylation without a de novo methyltransferase. "We didn't understand how methylation could still be in place since the Cretaceous period without a de novo enzyme," said Madhani.

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"Asked why evolution would select for these particular marks, Madhani explained that "one of methylation's major functions is genome defense. In this case we think it's for silencing transposons."

"Transposons, also known as jumping genes, are stretches of DNA that are able to extract themselves from one part of the genome and insert themselves into another. If a transposon were to insert itself into the middle of a gene needed for survival, that gene may no longer function and the cell would die. Therefore, transposon-silencing methylation provides an obvious survival advantage, which is exactly what's needed to drive evolution."

comment: I don't how this happened, but Lamarck is alive and well. Epigenetics can definitely play a role in progressive evolution