Back to Shapiro: organisms remove DNA in fetuses (Evolution)

by David Turell , Tuesday, December 05, 2023, 19:29 (352 days ago) @ David Turell

A common event:

https://www.the-scientist.com/features/downsizing-dna-71512?utm_campaign=TS_eTOC_2023&a...

"Marie Delattre, a biologist...has studied the nematode Mesorhabditis belari for nearly a decade now. The microscopic worm first caught her attention for its unconventional approach to reproduction, where only a small fraction of offspring keep their male parent’s DNA.

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"During this brief point in the worms’ development, part of their genomes appeared to vanish.

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"Even after more than a century of research, there are still many unanswered questions about programmed DNA elimination.

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"Recent technologies such as DNA sequencing have bolstered researchers’ efforts to probe this process. By comparing sequences of the genomes of germ cells and somatic cells from the same organism, researchers can look for long stretches in the germline genome that are absent from the somatic genome. These studies have shown that species can eliminate anywhere between 0.5 percent and 90 percent of their genomes.

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"...regardless of species, the eliminated regions include large stretches of repeated DNA sequences, which typically do not encode the instructions for proteins.

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"Programmed DNA elimination pops up on almost every branch of the tree of life, but the processes are as diverse as the flora and fauna that use them. The nematodes and unicellular ciliates seem to slice their genomes into small pieces and remove a subset. Vertebrates seem to be more likely to remove full chromosomes.

"These different approaches involve the same set of core steps: part of the genome is marked for elimination, and as the cell divides, this DNA is shunted out of the nucleus and ultimately removed from the cell. In ciliates and worms, the cell also needs to slice up the DNA into fragments. How this happens in cells is still largely unknown. But studies from Wang, Delattre, and others are starting to piece together the process.

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"Researchers still don’t know how the lagging chromosomes or discarded DNA fragments are chosen. In worms, Delattre uses detailed maps of the genome and RNA measurements to figure out how the cell knows where to fragment the DNA and what proteins make the cuts.

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"Another explanation is that eliminated genes might play a role in germ cells during reproduction, where they may need to make an arsenal of proteins that are unnecessary in other cells of the body. Studies in Ascaris and in zebra finches revealed that their eliminated genes have functions in sex organs like the testes, where germ cells originate.

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"It’s also possible that programmed DNA elimination could play diverse r oles in different species. “I would say, at this point, that they’re different processes,” Suh said. Smith agreed and noted that the evolutionary history of DNA elimination is still hazy. He speculated that each major branch of life may have independently developed the ability to eliminate DNA. “They’re doing similar things, but they got there through very different evolutionary trajectories,” he said.

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"For now, many scientists agree that the next step is to study programmed DNA elimination in more species. “We probably don’t know the majority of species that actually do this,” Smith said.

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"Every songbird eliminates at least one chromosome, but in some cases it’s the biggest chromosome; in other species it’s the smallest one. The genes on the eliminated chromosomes can be completely different between species but they have one thing in common: Some of the gene sequences are very similar to those found on retained chromosomes, a trend that hasn’t yet been observed in other types of animals.9

“'It gets more and more confusing with every species,” Suh said."

Comment: yes, the whole of all genomes is a mystery, yet to unravel. Here we see purposeful editing for elimination, while in bacteria we see editing only for improvement, an opposite event.