Human evolution; new genes from non-coding DNA (Introduction)

by David Turell , Friday, January 13, 2023, 17:53 (680 days ago) @ David Turell

New research in Rhesus monkeys:

https://www.sciencemagazinedigital.org/sciencemagazine/library/item/13_january_2023/407...

"Biologists have shone a light on an evolutionary mystery: how stretches of seemingly useless DNA can become meaningful, protein-coding genes. New genes are known to arise when existing ones are accidentally duplicated, freeing one copy to evolve novel or additional functions. But some genes seem to evolve from stretches of DNA once disparaged as “junk.”

"Now, a study has identified mutations that play a key part in this process: They enable RNA encoded by this DNA to slip out of the cell nucleus into the cell cytoplasm, where it can be translated into a protein. The study highlights 74 human protein genes that appear to have evolved this way, including some that may have helped drive the evolution of our large and complex brains.

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"A decade ago, Chuan-Yun Li, an evolutionary biologist at Peking University, and colleagues discovered that some human protein genes bear a striking resemblance to DNA sequences in rhesus monkeys that get transcribed into long noncoding RNAs (lncRNAs), which don’t make proteins or usually have any other purpose. How those stretches of monkey DNA could have become true protein-coding genes was a mystery, but Li’s postdoc, Ni A. An, discovered a clue.

"Many lncRNAs, An found, have a hard time exiting the nucleus and traveling to ribosomes, the organelles that translate messenger RNA (mRNA) into proteins. The researchers then searched for differences between protein-coding genes whose mRNA got out of the nucleus and DNA sequences whose RNAs did not. Stretches of DNA known as U1 elements seemed to be the key: When transcribed into RNA they make the strand too sticky to escape. In protein-coding genes, mutations have altered or eliminated the U1 elements to make the RNA less sticky.

“'This makes perfect sense because for an RNA to be translated, it needs to go the cytoplasm [where ribosomes are found] first,” says Maria Del Mar Albà, an evolutionary biologist at Hospital del Mar Medical Research Institute in Barcelona.

"In search of genes that originated this way, Li’s team scoured the human and chimpanzee genomes for protein-coding genes that had lncRNA counterparts in rhesus monkeys, as well as the crucial U1 element mutations. Dozens fit the bill, including nine that are active in the human brain. To learn what they do, Li’s collaborator Baoyang Hu, a neuroscientist from the Chinese Academy of Sciences Institute of Zoology, grew clumps of human brain tissue called cortical organoids with and without each of these genes. Two of them made the organoids grow slightly bigger than normal.

"When Hu introduced the genes into mice, their brains also grew larger and developed a bigger cortex, the wrinkly outer layer of the mammalian brain that in humans is responsible for high-level functions such as reasoning and language. One of the genes also caused the animals’ brains to develop more humanlike ridges and grooves, and mice that carried it performed better on tests of cognitive function and memory than mice lacking this gene. Li and Hu’s team says it will soon report these findings in Advanced Science.

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"Long adds other reasons to be cautious about concluding the genes had a role in human brain expansion: Organoids are far simpler tissues than the brain itself, he notes, and human and mouse brains have evolved along very different paths.

"But Long doesn’t doubt that many key genes do emerge from noncoding sequences. His own group has found that most of the recognizable de novo genes in rice were once lncRNAs, and that lncRNAs also helped form new genes in bamboo."

Comment: Long non-coding RNA was a black-box area until this work showed how they contribute to new gene formation. This looks like dhw's wish for cells innate ability to do their own designing. which then brings up the issue of purpose in biology. To design requires first developing a theoretical purposeful goal, which can only come from mental activity. The only other way is to be given exquisitely detailed instructions to follow. So, we come back to my usual point: it is easier for God to do it Himself, than get involved with the rigmarole of providing a huge set of detailed instructions.