Tag Archives: genome

Worms Share Memories With Others by Swapping RNA, Wild Study Reveals

A ghastly bout of food poisoning isn’t an experience to forget. The commonly studied microscopic nematode Caenorhabditis elegans not only ensures it remembers, it genetically embeds the threat of skanky meals into its kids to force them to stay clear as well.

 

And if by some misfortune one of those worms goes belly-up anyway? The warning encoded in RNA can leak out of their disintegrating body, potentially to be picked up by any passing member of the species.

This remarkable means of memory transfer was spotted by researchers from Princeton University’s Murphy Lab in the US as a part of a series of studies on inherited behaviors in the nematode.

Due to the existence of a fairly strict barrier between the germ cells that give rise to a new generation and the parent’s own body cells, it was once believed events affecting a parent’s physiology couldn’t be imprinted on their offspring.

That view has gone out the window with discoveries of environmental stresses in animals like C. elegans changing the way genes are switched on not only in their offspring, but in their offspring’s own children… and so on, for generations down the line.

It’s not just a worm thing, either. Genes in the offspring of fruit flies and even mice can be tweaked by cues in their parent’s environment, effectively changing the biological functions of future generations.

 

Last year, researchers at molecular biologist Coleen Murphy’s lab published their findings on C. elegans reactions to consuming the bacterium Pseudomonas aeruginosa – an appealing food source that quickly turns nasty in their digestive system.

The team discovered that worms absorbed strands of RNA from their toxic meal through their intestines, among which was a stretch of non-coding RNA called P11.

This slither of nucleic acid was found to bind to a corresponding code in the worm’s genome – a gene called maco-1 – which was already known to play a role in sensory perception. As a result, the worm ‘learns’ to steer clear of P. aeruginosa in the future.

Amazingly, this behavioral shift also affects a mother worm’s descendants, teaching at least the next four generations to avoid this particular microbial meal as well.

This latest experiment demonstrates that genetic memory isn’t strictly a family affair, with evidence that it can be transmitted laterally from worm to worm.

Tragically, the teacher has to be pulped first.

“We found that one worm can learn to avoid this pathogenic bacterium and if we grind up that worm, or even just use the media the worms are swimming in, and give that media or the crushed-worm lysate to naïve worms, those worms now ‘learn’ to avoid the pathogen as well,” says Murphy.

 

Investigations of nematodes incapable of learning this avoidance trick suggested that in spite of maco-1’s established role in avoiding P. aeruginosa, the gene’s presence alone couldn’t explain why the behavior was inherited. Something else was happening.

So the team went on the hunt for other factors behind the quirky neurological adaptation.

(Murphy Lab)

Chief suspect was an itinerant ‘jumping’ gene called Cer1, already known to have the right characteristics to move from one part of a genome to another like a virus.

“What we discovered is that a retrotransposon called Cer1 that forms viral-like particles seems to carry a memory not only between tissues (from the worm’s germline to its neurons) but also between individuals,” says Murphy. Worms that naturally lacked Cer1, or had it edited out, simply couldn’t resist taking a nibble of P. aeruginosa.

This whole learning experience isn’t without its risks. The retrotransposon’s jumping behavior can also cause harm as it inserts itself into parts of the animal’s genome, suggesting there has to be a benefit to its costs.

Fascinating as they are now, hints that behavior-altering experiences can be inherited would have been surprisingly controversial half a century ago, when American animal psychologist James V. McConnell shot to fame – and infamy – over suggestions that flatworms could inherit memories by consuming other, more educated flatworms.

McConnell’s chapter in the history of biology has since influenced debate over the permeability of that barrier between parent and child, and whether one generation’s experiences of the world can directly affect the way the next approaches it.

The extent to which this might happen in humans is still being explored, yet there are tantalizing signs we’re not exempt, either.

This research was published in Cell.

 

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Researchers develop an engineered ‘mini’ CRISPR genome editing system

CRISPR-associated protein Cas9 (white) from Staphylococcus aureus based on Protein Database ID 5AXW. Credit: Thomas Splettstoesser (Wikipedia, CC BY-SA 4.0)

The common analogy for CRISPR gene editing is that it works like molecular scissors, cutting out select sections of DNA. Stanley Qi, assistant professor of bioengineering at Stanford University, likes that analogy, but he thinks it’s time to reimagine CRISPR as a Swiss Army knife.

“CRISPR can be as simple as a cutter, or more advanced as a regulator, an editor, a labeler or imager. Many applications are emerging from this exciting field,” said Qi, who is also an assistant professor of chemical and systems biology in the Stanford School of Medicine and a Stanford ChEM-H institute scholar.

The many different CRISPR systems in use or being clinically tested for gene therapy of diseases in the eye, liver and brain, however, remain limited in their scope because they all suffer from the same flaw: they’re too large and, therefore, too hard to deliver into cells, tissues or living organisms.

In a paper published Sept. 3 in Molecular Cell, Qi and his collaborators announce what they believe is a major step forward for CRISPR: An efficient, multi-purpose, mini CRISPR system. Whereas the commonly used CRISPR systems—with names like Cas9 and Cas12a denoting various versions of CRISPR-associated (Cas) proteins—are made of about 1000 to 1500 amino acids, their “CasMINI” has 529.

The researchers confirmed in experiments that CasMINI could delete, activate and edit genetic code just like its beefier counterparts. Its smaller size means it should be easier to deliver into human cells and the human body, making it a potential tool for treating diverse ailments, including eye disease, organ degeneration and genetic diseases generally.

Persistent effort

To make the system as small as possible, the researchers decided to start with the CRISPR protein Cas12f (also known as Cas14), because it contains only about 400 to 700 amino acids. However, like other CRISPR proteins, Cas12f naturally originates from Archaea—single-celled organisms—which means it is not well-suited to mammalian cells, let alone human cells or bodies. Only a few CRISPR proteins are known to work in mammalian cells without modification. Unfortunately, CAS12f is not one of them. This makes it an enticing challenge for bioengineers like Qi.

“We thought, ‘Okay, millions of years of evolution have not been able to turn this CRISPR system into something that functions in the human body. Can we change that in just one or two years?'” said Qi. “To my knowledge, we have, for the first time, turned a nonworking CRISPR into a working one.”

Indeed, Xiaoshu Xu, a postdoctoral scholar in the Qi lab and lead author of the paper, saw no activity of the natural Cas12f in human cells. Xu and Qi hypothesized that the issue was that human genome DNA is more complicated and less accessible than microbial DNA, making it hard for Cas12f to find its target in cells. By looking at the computationally predicted structure of the Cas12f system, she carefully chose about 40 mutations in the protein that could potentially bypass this limitation and established a pipeline for testing many protein variants at a time. A working variant would, in theory, turn a human cell green by activating green fluorescent protein (GFP) in its genome.

“At first, this system did not work at all for a year,” Xu said. “But after iterations of bioengineering, we saw some engineered proteins start to turn on, like magic. It made us really appreciate the power of synthetic biology and bioengineering.”

The first successful results were modest, but they excited Xu and encouraged her to push forward because it meant the system worked. Over many additional iterations, she was able to further improve the protein’s performance. “We started with seeing only two cells showing a green signal, and now after engineering, almost every cell is green under the microscope,” Xu said.

“At some moment, I had to stop her,” recalled Qi. “I said ‘That’s good for now. You’ve made a pretty good system. We should think about how this molecule can be used for applications.'”

In addition to protein engineering, the researchers also engineered the RNA that guides the Cas protein to its target DNA. Modifications to both components were crucial to making the CasMINI system work in human cells. They tested CasMINI’s ability to delete and edit genes in lab-based human cells, including genes related to HIV infection, anti-tumor immune response and anemia. It worked on almost every gene they tested, with robust responses in several.

Opening the door

The researchers have already begun assembling collaborations with other scientists to pursue gene therapies. They are also interested in how they could contribute to advances in RNA technologies—like what has been used to develop the mRNA COVID-19 vaccines—where size can also be a limiting factor.

“This ability to engineer these systems has been desired in the field since the early days of CRISPR, and I feel like we did our part to move toward that reality,” said Qi. “And this engineering approach can be so broadly helpful. That’s what excites me—opening the door on new possibilities.”


New CRISPR-Cas system cuts virus RNA


More information:
Engineered Miniature CRISPR-Cas System for Mammalian Genome Regulation and Editing, Molecular Cell (2021). DOI: 10.1016/j.molcel.2021.08.008, https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00648-1

Citation:
Researchers develop an engineered ‘mini’ CRISPR genome editing system (2021, September 3)
retrieved 3 September 2021
from https://phys.org/news/2021-09-mini-crispr-genome.html

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Scientists Shorten Daddy Long-Legs’ Iconic Limbs to Figure Out How They Got So Gangly

Through a process known as RNA interference (RNAi), scientists have been able to modify the genetic make-up of the daddy long-legs arachnid so that its distinctive spindly limbs become twice as short.

 

This process – which uses a gene’s own DNA sequence and small fragments of RNA to turn the gene off – was applied to the Phalangium opilio species, one of the most common species of daddy long-legs in the world.

The result is effectively a daddy short-legs instead of a daddy long-legs. The team behind the work is hoping that the experiments can teach us more about how these elongated limbs evolved in the first place.

“We anticipate that the genome of P. opilio will facilitate the development of more sophisticated tools for functional genetics, toward refining the understanding of how daddy long-legs make their long legs,” write the researchers in their published paper.

After sequencing the genome of P. opilio, researchers identified three genes that act as a map for various body parts. Two of those genes were then found to be turned on in the legs of the arachnid embryos.

Turning off or silencing the genes in other embryos produced daddy long-legs that were different: two or more of their legs were shorter than normal and had transformed into pedipalps, which are limbs used specifically for handling food.

 

The team then turned off the third gene thought to be linked to building legs in embryos. The legs didn’t turn into pedipalps, but they did get shorter and lose their tarsomeres, the knuckle-like joints used for grip. Similar experiments have been run on fruit flies.

“Looking forward, we are interested in understanding how genes give rise to novel features of arachnids, such as spider fangs and scorpion pinchers, and also leveraging the genome to develop the first transgenic harvestmen,” geneticist Guilherme Gainett, from the University of Wisconsin-Madison, told CNET.

Technically, the P. opilio species isn’t a spider but rather a close relative, which makes these creatures useful for figuring out how the multitude of different arachnids on our planet evolved. Not all daddy long-legs have legs that can wrap around twigs and other objects like these bugs can, for example.

The thinking is that the spider genome duplicated in the distant past, giving these creatures a wide choice of genes to use for their own unique evolutionary journeys – there could be a link between more complex genomes and greater organism variation.

This latest research should prove useful in future work to trace back the development of P. opilio and other arachnids, to establish if long and spindly legs were indeed something that evolved separately in each group of arthropods.

“The effectiveness of single and double RNAi in this system makes P. opilio an opportune point of comparison for future investigations of arachnid body plan evolution,” write the researchers in their published paper.

The research is published in Proceedings of the Royal Society B: Biological Sciences.

 

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A Shockingly Small Percentage of Our DNA Is Uniquely ‘Human’, Study Finds

By now you might have heard the factoid that modern humans share a pretty large chunk of our genomes with bananas. But delving down much deeper, how much of our genome is uniquely Homo sapiens.

 

A new study has suggested that number could be as small as 1.5 percent, with the rest being shared with our ancient relatives such as Neanderthals and Denisovans.

“We generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins,” the team wrote in their new paper.

“We find that only 1.5 to 7 percent of the modern human genome is uniquely human.”

Untangling what is ours and what came from our ancient kin is a difficult task. How do you tell which genetic variants are due to interbreeding (also called admixing) of Neanderthals and Homo sapiens for example, rather than variants that were passed onto both species from a common ancestor?

The team wanted to create a system that could identify both admixture events as well as this shared inheritance – called incomplete lineage sorting – that would help tell us which regions of our genome are unique to us.

They created an algorithm called SARGE – Speedy Ancestral Recombination Graph Estimator – so they could map how our genes have weaved through time and species, separating and joining back together at different points using something called ancestral recombination graphs.

 

They ran SARGE on 279 modern human genomes from Africa and elsewhere, two high-quality Neanderthal genomes, and one high-quality Denisovan genome.

“Using the resulting ancestral recombination graph, we map Neanderthal and Denisovan ancestry, incomplete lineage sorting, and the absence of both across modern human genomes,” the team wrote.

“We find evidence of at least one wave of Neanderthal admixture into the ancestors of all non-Africans.”

Along with the 1.5 to 7 percent of the genome that’s unique to modern humans, they also found “evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function”.

The researchers explain that most of those genes that were uniquely ours were not genes with unknown functions, instead they were well known genes which coded for proteins used in the brain.

Obviously, this is not even close to the end of the story. For starters, between 1.5 and 7 percent is a pretty large range and the team think they can make it more specific with more genomes and more research.

There have also been plenty of other analyses looking at the percentage of DNA we take from our ancient cousins, so it’s unlikely this will be the last word on the matter.

 

Plus, SARGE isn’t able to tell the researchers why those bursts of adaptive changes happened when they did.

However, the team already has some ideas.

“It’s extremely tempting to speculate that one or more of these bursts had something to do the incredibly social behavior humans have – mediated in large part by our expert control of speech and language,” University of California, Santa Cruz paleogeneticist and one of the researchers, Richard Green, told Business Insider.

The research has been published in Science Advances.

 

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Human Genome Mostly Overlaps With Neanderthals, Other Human Ancestors

  • Just 1.5% to 7% of the human genome is unique to our species, a new study suggests.
  • Neanderthals, Denisovans, and other ancestors share most of the same genes found in modern humans. 
  • Genes unique to humans are involved in brain development, which may be what sets our species apart. 

Humans like to think they’re special, but our genes suggest that’s far from the case.

No more than 7% of the human genome is unique to Homo sapiens, according to a study published Friday in the journal Science Advances. 

We share the remaining chunks of our genetic material with other human ancestors, or hominins, including our Neanderthal cousins and the Denisovans first discovered in east Asia.

“The evolutionary family tree shows there are regions of our genome that make us uniquely human,” Richard Green, director of the paleogenomics lab at the University of California, Santa Cruz and co-author of the new study, told Insider. “Now we have a catalog of those, and it’s a surprisingly small fraction of the genome.”

Anthropologists already knew that our hominin ancestors all interacted and interbred — exchanging genes and stone technologies that altered the course of our species’ evolution. But these new findings further underscore just how frequently that intermingling happened in the last 300,000 years or so, since the first known population of modern humans emerged. 

“More or less everywhere we look, admixture is not the exception at all, but rather the rule,” Green said.

Genetic evidence suggests our ancestors interbred with mysterious hominins 



An exhibit shows the life of a neanderthal family in a cave in the new Neanderthal Museum in the northern town of Krapina, Croatia, February 25, 2010.

Reuters/Nikola Solic


To construct a hominin family tree, Green’s team sequenced and compared genomes from 279 modern humans — sampled from people all over the world — to ancient genomes from one Denisovan and two Neanderthals. Then, the researchers used a computer algorithm to determine out how each of those individuals are related to each other.

The analysis tool, which Green said took years to develop, helped them distinguish what parts of the human genome are devoid of admixture — meaning these sets of genes aren’t seen in Neanderthals or Denisovans. 

The algorithm also highlighted what genes humans inherited from an even older ancestor, one that lived 500,000 years ago or so, that eventually gave rise to our species as well as Neanderthals and other hominins.

The study results suggest mysterious populations of human ancestors that scientists haven’t even discovered yet may have interbred with Neanderthals and Denisovans before these species mixed with modern humans, Green added.

Genes unique to humans are related to our brain development



A scientist at work in a laboratory at the Max Planck Institute for Evolutionary Anthropology analyzing ancient DNA.

Max Planck Institute for Evolutionary Anthropology


Researchers have already identified many of the human genes that resulted from cross-species trysts, but this is the first study to pinpoint what regions of genes were completely devoid of admixture, according to Green.

His group found these uniquely human regions of our genome were “incredibly enriched for genes that have to do with neural development,” Green said.

While Neanderthals have similarly large, if not larger, heads than humans do, that cranium size tells us little about how well their brains work compared to ours.

“Now we know human-specific stuff has to do with brain function,” Green said.

And most of these uniquely human genes came out during two distinct bursts of evolution — one that happened 600,000 years ago and another 200,000 years ago — the study found.

One of those evolutionary waves could’ve laid the genetic groundwork for human communication, Green said.

“It’s extremely tempting to speculate that one or more of these bursts had something to do the incredibly social behavior humans have — mediated in large part by our expert control of speech and language,” he said.

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Coronavirus Texas: New York, California and Brazil COVID-19 variants detected in Houston Methodist genome study

HOUSTON, Texas (KTRK) — The Houston area is now facing at least five different variants of COVID-19 with the addition of three from New York, Brazil and California.

Study findings released Thursday by the infectious diseases team at Houston Methodist showed the additional three variants have been detected among the 20,453 coronavirus genomes in the area examined since the start of the pandemic.

SEE ALSO: Researchers find worrying new coronavirus variant in New York City

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Two separate teams of researchers said this week they have found a worrying new coronavirus variant in New York City. Meanwhile, hope is on the horizon for a third U.S. COVID vaccine.

The Houston Methodist study is the first to identify the three new variants in the greater Houston area.

Breaking down all the COVID-19 variants identified in the U.S. right now

Variants from the United Kingdom and South Africa have already been confirmed by city and county-level health officials, who have described them as being more contagious.

SEE MORE: Everything you need to know about South African COVID-19 variant

The findings come from the hospital system’s nation-leading genome sequencing study. Methodist’s team processes as many as 1,700 samples a week. All four variants were detected in the most recent batches of genomes, the hospital told ABC13.

How wastewater is helping officials detect COVID-19 variants

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ABC13 sat down with the city of Houston’s health authority to see how the variant can impact COVID-19 testing and the vaccine.

Follow Marla Carter on Facebook, Twitter and Instagram.

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Bizarre Coelacanth Hasn’t Spent 65 Million Years Unchanged After All, Its Genome Reveals

In 1938, a living relic, thought 65 million years long extinct, was accidentally captured in a trawl net off the coast of South Africa.

The 2-metre (6.5-foot) long coelacanth (Latimeria chalumnae) turned out to be one of our closest fish relatives – looking largely unchanged since its most recent appearance in the fossil record back from the time of non-avian dinosaurs.

 

Now new genetic evidence shows this deep-sea predator has undergone hidden, but widespread evolution at a genetic level – by hijacking genes from other species.

While searching genetic databases for the ancestral version of a human gene involved in gene regulation, CGGBP1, University of Toronto molecular geneticist Isaac Yellan unexpectedly found coelacanth strangely has many variations of this gene.

Even more unusually, these different variations of the CGGBP genes didn’t all share a common ancestor with each other. This suggests that at some points around 10 million years ago, 62 of these genes were swiped by the coelacanth from other, unrelated species – through horizontal gene transfer.

These genes, with their ability to ‘jump’ around and even between genomes a bit like viruses, are known as transposons.

If they happen to jump into the right place in the genome, cellular machinery will copy them just like any other gene. But they can also jump into the wrong place, where they can be harmful and so are thought of as parasitic.

Occasionally though, they can end up in a position that’s useful to their host species and end up losing their ability to jump around but are conserved within their new place in the genome, which is what seems to have happened in the coelacanth, several times over.

 

“Horizontal gene transfer fuzzies up the picture of where the transposons came from but we know from other species that it can occur via parasitism,” said Yellan. “The most likely explanation is that they were introduced multiple times throughout evolutionary history.”

While it’s common to find transposons like these in many species, it’s unusual to find so many.

Test tube experiments and computer modelling demonstrated at least eight of the proteins that these genes code for bind to distinct repeated sequences of DNA, suggesting that – like the human version – they are involved in gene regulation. Some of them are only expressed in specific tissues.

“We don’t know what these 62 genes are doing, but many of them encode DNA binding proteins and probably have a role in gene regulation, where even subtle changes are important in evolution,” explained University of Toronto molecular geneticist Tim Hughes.

Coelacanth have leg-like lobed fins and are more closely related to us and our closest fishy relatives, the lungfish, than other types of fish. Our very distant shared ancestor means the coelacanth’s genome has the potential to help us unravel many mysteries about our own evolution.

 

Unfortunately, these fish are rarely seen and endangered, so opportunities to study them are limited. But the information we have from them is already proving fruitful.

A recent study on their genes suggests our bitter receptors may have roles beyond protecting us from toxic substances, like metabolic regulation and hormone sensing. Now coelacanth genes have demonstrated transposons potentially play a larger role than we realise in tetrapod evolution.

“Our findings provide a rather striking example of this phenomenon of transposons contributing to the host genome,” said Hughe.

This research was published in Molecular Biology and Evolution.

 

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