Junk DNA: goodbye!: the importance of heterochromatin (Introduction)

by David Turell , Monday, November 16, 2020, 18:47 (1469 days ago) @ David Turell
edited by David Turell, Monday, November 16, 2020, 19:02

How new genes appear when necessary:

https://www.sciencenews.org/article/essential-genes-fast-evolution-junk-dna-heterochrom...

"A new study in fruit flies may help solve that puzzle. It shows that some new genes quickly become crucial because they regulate a type of DNA called heterochromatin. Once considered “junk DNA,” heterochromatin actually performs many important jobs, including acting like a tightly guarded prison: It locks up “bad actor” genes, preventing them from turning on and doing damage.

"Heterochromatin is also one of the fastest-changing bits of DNA in the body, so the genes that regulate it have to adapt quickly just to keep up, evolutionary biologist Harmit Malik at the Fred Hutchinson Cancer Research Center in Seattle and his colleagues report.

“'The work is a milestone,” said Manyuan Long, an evolutionary biologist at the University of Chicago who was not involved in the research. “It is really amazing seeing such an important role the heterochromatin plays in gene evolution.”

***

"About a decade ago, researchers discovered that new genes don’t just confer new functions; some may actually be necessary for survival. In the fruit fly Drosophila melanogaster, as many as 30 percent of essential genes are “new,” with some arising as recently as 3 million years ago — a flash in evolutionary timescales. The discovery overturned a long-held belief that important genes don’t really change much over the course of evolution.

***

"The team found that one of the new essential genes, dubbed Nicknack, issues instructions for a protein that binds to heterochromatin, although the details remain unknown.

***

"They tested this theory by swapping the gene from D. simulans into the D. melanogaster fly, expecting that if the genes were the same, the trade would have no effect. But instead, the female files survived the swap just fine, but all the males died. Malik thinks the difference between the sexes has to do with heterochromatin: The Y chromosome contains a lot of it.

“'It’s as if [D.] simulans’ [Nicknack gene] comes in with its hand tied behind its back,” Malik says. “It’s good enough to do its function in female flies, but in male flies, where there is a huge block of heterochromatin, it can’t.” In other words, the gene from one species is no match for its counterpart in the other.

"The result suggests that in the 2.5 million years since the two species split, D. melanogaster evolved its own version of Nicknack. And because the swap adversely affected the males, with their abundance of heterochromatin in the Y chromosome, the researchers concluded that Nicknack must play some crucial role in regulating heterochromatin. And since heterochromatin evolves so rapidly, the Nicknack gene has to evolve rapidly too, so it doesn’t become obsolete."

Comment: This study suggests much support for my theory that God dabbles as evolution proceeds. And. of course, more 'junk DNA' disappears.

Another report also covers this study:

https://www.quantamagazine.org/scientists-find-vital-genes-evolving-in-genomes-junkyard...

To dig deeper into this puzzling result, Kasinathan looked for clues to the functions of Nicknack and Oddjob, two essential ZAD-ZNF genes that evolved quickly.

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According to Malik, this explains why Oddjob and Nicknack evolve so rapidly: They have to adjust to the changing DNA environment of the heterochromatin to remain functional. In some ways, they are like the genes of the immune system, which change quickly to keep up with rapidly evolving pathogens in a kind of arms race. But in this case, Malik said, “It’s almost like an arms race happening in the genome, just to preserve an essential function.”

***

Species today face problems that their ancestors didn’t, and those new problems require new solutions. But “what if it’s actually the evolution of these heterochromatin sequences that created the need for this essential function first?” Malik asked.

“The essential function itself may not be conserved, and that’s a heretical concept,” he continued. “We’re not just saying that the essential genes are not conserved. We are actually saying that it’s possible that the essential functions are not conserved, because it’s all context-specific.” (My bold)

Kasinathan and Malik are now turning their attention to the other ZAD-ZNF transcription factors, many of which also localize to the heterochromatin. “This compartment of the genome that we basically ignored because it’s so gene-poor … is actually, at least for the ZAD-ZNFs, the answer to this paradox of young genes becoming essential,” Malik said.

“If you’re interested in centromere function, if you only look at the genes that are totally conserved across humans, yeast and flies, you could be missing really important genes that are potential therapeutic targets,” Malik said. “We’ve let our intuition and dogma kind of bias us to the point where we might be missing a lot of important biology.”

Comment: The bold suggest s God edits as necessary