Genetics biweekly vol.59, 27th June —11th July
TL;DR
- The function of non-coding RNA in the cell has long been a mystery to researchers. Unlike coding RNA, non-coding RNA does not produce proteins — yet it exists in large quantities. A research team has now discovered an important function of antisense RNA (asRNA): the researchers found that asRNA acts as a ‘superhighway’ in cell transport and thus accelerates gene expression.
- A decade-long study has discovered huge genetic potential that is untapped in modern wheat varieties.
- The ketogenic diet has its fanatics and detractors among dieters, but either way, the diet has a scientifically documented impact on memory in mice. While uncovering how the high fat, low carbohydrate diet boosts memory in older mice, scientists identified a new molecular signaling pathway that improves synapse function and helps explain the diet’s benefit on brain health and aging.
- In mammals, only 3% of the genome consists of coding genes which, when transcribed into proteins, ensure the biological functions of the organism and the in-utero development of future individuals. But genes do not function alone. They are controlled by other sequences in the genome, called enhancers, which, like switches, activate or deactivate them as required. A team has now identified and located 2700 enhancers — among millions of non-coding genetic sequences — that precisely regulate the genes responsible for bone growth. This discovery sheds light on one of the major factors influencing the size of individuals in adulthood, and explains why their failure could be the cause of certain bone malformations.
- Some species of tardigrades are highly and unusually resilient to various extreme conditions fatal to most other forms of life. The genetic basis for these exceptional abilities remains elusive. Researchers have now successfully edited genes using the CRISPR technique in a highly resilient tardigrade species previously impossible to study with genome-editing tools. The successful delivery of CRISPR to an asexual tardigrade species directly produces gene-edited offspring. The design and editing of specific tardigrade genes allow researchers to investigate which are responsible for tardigrade resilience and how such resilience can work.
- And more!
Overview
Genetic technology is defined as the term that includes a range of activities concerned with the understanding of gene expression, advantages of natural genetic variation, modifying genes and transferring genes to new hosts. Genes are found in all living organisms and are transferred from one generation to the next. Gene technology encompasses several techniques including marker-assisted breeding, RNAi, and genetic modification. Only some gene technologies produce genetically modified organisms.
Modern genetic technologies like genome editing would not be possible without all the previous generations of genetic technologies that have enabled scientists to discover what genes are, what they do, and how DNA can be modified to add, remove, or replace genes. You can find major genetic technologies development milestones via the link.
Gene Technology Market
According to Global Genetic Engineering Market Research Report: The genetic engineering market is projected to grow from USD 1.36 Billion in 2023 to USD 7.73 Billion by 2032, exhibiting a compound annual growth rate (CAGR) of 24.20% during the forecast period (2023–2032).
Growing demand for synthetic genes and increased use of CRISPR genome editing technology across various biotechnology industries are the key market drivers enhancing the market growth. In addition, it’s projected that increased government financing, a rise in the output of genetically modified crops, and an increase in genomics studies will all contribute to the expansion.
Latest Research
dsRNA formation leads to preferential nuclear export and gene expression
by Ivo Coban, Jan-Philipp Lamping, Anna Greta Hirsch, Sarah Wasilewski, Orr Shomroni, Oliver Giesbrecht, Gabriela Salinas, Heike Krebber in Nature
The function of non-coding RNA in the cell has long been a mystery to researchers. Unlike coding RNA, non-coding RNA does not produce proteins — yet it exists in large quantities. A research team from the University of Göttingen has now discovered an important function of antisense RNA (asRNA): the researchers found that asRNA acts as a “superhighway” in cell transport and thus accelerates gene expression.
RNA (ribonucleic acid) plays a central role in the translation of DNA information into proteins. There are different types of RNA, one of which is known as messenger RNA (mRNA). Messenger RNA is a type of coding RNA and its job is to transmit the building instructions for proteins from the DNA in the cell nucleus out into the cytoplasm, where other cell components translate them into proteins. In addition to coding RNA, there are large quantities of non-coding RNA. Much of the non-coding RNA is produced as the complementary strand to mRNA and is therefore referred to as antisense RNA (asRNA). Their function has been unclear for a long time.
“It seemed unbelievable to me that a cell would produce RNAs without a purpose,” says Professor Heike Krebber from Göttingen University’s Institute of Microbiology and Genetics. “This is contrary to nature.”
Krebber’s team discovered that asRNA combines with mRNA, which is then preferentially transported from the cell nucleus into the cytoplasm. This means that the cell translates the information from the mRNA into proteins faster than would be the case without asRNA. Therefore, asRNA serves as a “booster” for gene expression. This is necessary for the cell in many situations, for example when confronted with harmful environmental conditions or stress. This work is the next step from the team’s earlier basic research, also published in Nature, which showed that mRNAs activated under stress are no longer subject to quality control.
The new research findings about asRNAs solve the long-standing question of why the cell sometimes produces large quantities of asRNA. “In biology, this is particularly striking because the cell expends a lot of energy on asRNA production,” explains Krebber. The mechanism that has now been discovered explains how cells can react abruptly to external influences to produce the necessary proteins immediately and in large quantities in order to adapt to environmental conditions or, for example, to enter a certain stage of development. “This new understanding brings asRNAs into the focus of the question of how diseases develop and how they can be combated,” says Krebber.
Harnessing landrace diversity empowers wheat breeding
by Shifeng Cheng, Cong Feng, Luzie U. Wingen, Hong Cheng, et al in Nature
A decade-long collaborative study has discovered huge genetic potential that is untapped in modern wheat varieties.
The international study reveals that at least 60% of the genetic diversity found in a historic collection of wheat is unused providing an unprecedented opportunity to improve modern wheat and sustainably feed a growing global population.
To make this discovery, a cross-institutional collaboration led by Dr Simon Griffiths, at the John Innes Centre and Professor Shifeng Cheng at the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), studied the A.E. Watkins Landrace Collection, a historic collection of local varieties of wheat which are no longer grown anywhere in the world and compared this with modern wheats.
The achievement is the result of a consortium joint effort, Professor Cheng says, “We built a collaborative and complementary consortium with full openness, making resources in germplasm, genomic and phenotypic datasets, publicly available through the Watkins Worldwide Wheat Genomics to Breeding Portal. Our effort has facilitated and accelerated many existing projects both in fundamental research and in breeding practices.”
One of the key factors that contributes to the success is the in-depth phenotyping, covering experimental stations from the UK (three locations) and field evaluation (five locations) from northern to southern China. In total, 137 traits were surveyed in this study. This work was particularly underpinned by Rothamsted Research, who worked as a phenotyping hub to add understanding of the qualities and characteristics of the wheat, to connect the crop to the genetic sequence.
The team built a wheat genomic variation map, a haplotype-phenotype association map. The landrace-cultivar comparison revealed that modern wheat varieties only make use of 40% of the genetic diversity found in the Watkins Collection.
The remaining diversity represents a goldmine of potential to improve modern wheat, says Dr Griffiths, group leader at the John Innes Centre, and an author of the paper, “This missing 60% discovered in this study is full of beneficial genes that we need to feed people sustainably. Over the last ten thousand years we’ve tended to select for traits which increase yield and improve disease resistance.”
“We’ve found that the Watkins landraces are packed full of useful variation which is simply absent in modern wheat, and it is imperative to deploy this into modern breeding. What’s exciting is that genes and traits are already being discovered using the data and tools developed over the past decade.”
The A.E. Watkins landrace collection of bread wheat (Watkins collection) assembled in the 1920s and 1930s from 32 countries, represents the most comprehensive collection of historic wheat anywhere in the world.
The collection provides a snapshot of the diversity of cultivated wheat before the advent of modern, systematic plant breeding and shows how the genetic variation is dispersed in clusters, or ancestral groups, around the world. “We can retrace the novel, functional and beneficial diversity that were lost in modern wheats after the ‘Green Revolution’ in the 20th century, and have the opportunity to add them back into elites in the breeding programmes,” says Professor Cheng.
Genomics and bioinformatics analysis completed by researchers at the Agricultural Genomics Institute at Shenzhen, allowed the consortium to see where modern wheat came from. They discovered that globally, wheat varieties originate from central and western Europe, with just two of the seven ancestral groups in the Watkins collection being used in modern plant breeding.
Using three complementary association genetics approaches (QTL mapping, GWAS and NAM GWAS), the team discovered hundreds of Watkins-unique haplotypes that can confer superior traits in modern wheats, informing breeders to know what accessions carry what useful genetic loci or alleles in their breeding programmes.
Key traits already found in this untapped diversity include nitrogen use efficiency, slug resistance and resilience to pests and diseases.
Dr Griffiths adds, “There are genes which will enable plant breeders to increase the efficiency of nitrogen use in wheat, if we can get these into modern varieties that farmers can grow, they will need to apply less fertilizer, saving money and reducing emissions.”
Fertilizer use in agriculture is expensive and contributes to emissions of greenhouse gases, reducing its use could help agriculture to move towards net zero. Enhancing nitrogen use efficiency in crops and reducing agriculture’s nitrogen footprint is currently a big challenge globally, especially for countries like China.
To achieve this unprecedented research feat, the team developed a core set of 119 landraces which represented the breadth of the genetic variation within the Watkins collection. This diversity set was then crossed and back crossed them into modern wheat to make a collection of 12,000 lines of wheat that are now stored in the Germplasm Resource Unit at the John Innes Centre. This means that for the first time in 100 years these lost traits have been incorporated into modern wheat, and the data and tools are already being used to improve crops.
This research establishes a framework for wheat whole-genome design pre-breeding by connecting genomics to phenomics and to breeding practice. “We implemented a pre-breeding strategy to decode, discover, design and deliver progress in breeding,” says Dr Griffiths. “Indeed, the genomics revolution is leading to the genetic revolution and a breeding revolution,” says Shifeng Cheng. This study was truly a collaborative, long-term, endeavour and couldn’t have been completed without international cooperation and long-term funding.
In collaboration with UK commercial plant breeders the team have created the freely available breeder’s toolkit, a set of online resources which are open source and accessible globally for anyone to use. The toolkit provides an integrated set of tools for the research and breeding communities allows others to access and use new, beneficial diversity to deliver sustainable, resilient wheat now and into the future. These germplasms, the resources and toolkits developed in this study, are still under further investigation in various experimental stations in China. We can expect that these efforts will significantly contribute to wheat genetic improvement and breeding in China.
Ketogenic diet administration later in life improves memory by modifying the synaptic cortical proteome via the PKA signaling pathway in aging mice
by Diego Acuña-Catalán, Samah Shah, Cameron Wehrfritz, et al in Cell Reports Medicine
The ketogenic diet has its fanatics and detractors among dieters, but either way, the diet has a scientifically documented impact on memory in mice. Whlie uncovering how the high fat, low carbohydrate diet boosts memory in older mice, Buck scientists and a team from the University of Chile identified a new molecular signaling pathway that improves synapse function and helps explain the diet’s benefit on brain health and aging. The findings provide new directions for targeting the memory effects on a molecular level, without requiring a ketogenic diet or even the byproducts of it.
“Our work indicates that the effects of the ketogenic diet benefit brain function broadly, and we provide a mechanism of action that offers a strategy for the maintenance and improvement of this function during aging,” said the study’s senior author, Christian González-Billault, PhD, who is a professor at the Universidad de Chile and director of their Geroscience Center for Brain Health and Metabolism, and adjunct professor at the Buck Institute.
“Building off our previous work showing that a ketogenic diet improves healthspan and memory in aging mice, this new work indicates that we can start with older animals and still improve the health of the aging brain, and that the changes begin to happen relatively quickly,” said John Newman, MD, PhD, whose laboratory at Buck collaborated with Dr. González-Billault on the study. Newman is both an assistant professor at the Buck Institute, and a geriatrician at University of California, San Francisco. “It is the most detailed study to date of the ketogenic diet and aging brain in mice.”
More than a century ago, researchers observed that rats that consumed less food lived longer. “We now know that being able to manipulate lifespan is not about specifically eating less,” said Newman, but actually is related to signals inside cells that turn on and off specific pathways in response to available nutrients. Many of those pathways are related to aging, such as controlling protein turnover and metabolism.
Some of those signals are the ketone bodies, which consist of acetoacetate (AcAc), β-hydroxybutyrate (BHB) and to a much lesser extent, acetone. These molecules are routinely produced in the liver. They ramp up when glucose is in short supply, whether due to caloric restriction, intense exercise or low carbohydrate intake, such as with a ketogenic diet.
Seven years ago, Newman led a team that published the first proof of the concept that if a ketogenic diet exposes mice to increased levels of ketone bodies over much of their adult life, it helps them to live longer and age in a more healthy way. “The most striking effect on their health as they aged was that their memory was preserved; it was possibly even better than when they were younger,” he said.
The current study, designed to answer what part of the ketogenic diet was having the effect and how it was affecting the brain on a molecular level to improve memory, was led by González-Billault in a collaboration with scientists at the Buck. Mice on a ketogenic diet are fed a ratio of 90 percent calories from fat and 10 percent from protein, while mice on a control diet received the same amount of protein but only 13 percent fat. The test mice, of “advanced age” of more than two years old, received one week of the ketogenic diet, cycled with one week of the control diet, to keep the mice from overeating and becoming obese.
The benefits of the ketogenic diet, said, González-Billault, were demonstrated through neurophysiological and behavioral experiments with the mice that test how well the mechanisms involved in memory generation, storage, and retrieval function in aged animals. When these showed that the ketogenic diet appeared to benefit how well the synapses responsible for memory worked, they took a deep dive into the protein composition at these synapses in the hippocampus, in a collaboration with Buck professor Birgit Schilling, PhD, who directs the Proteomics and Mass Spectrometry Center.
“Surprisingly, we saw that the ketogenic diet caused dramatic changes in the proteins of the synapse,” said Schilling. Even more surprising, she said, was that the changes started after a relatively brief exposure to the diet (tested after only one week on the diet) and only became more pronounced over time (tested again after six weeks and a year).
Further testing indicated that in synapses, a particular signaling pathway (protein kinase A, which is critical to synapse activity) was activated by the ketogenic diet. In isolated cells, the team then showed that it appears that BHB, the main ketone body produced in a ketogenic diet, is activating this pathway. This leads to the idea, said González-Billault, that ketone bodies (specifically BHB) play a crucial role not only as an energy source, but also as a signaling molecule.
“BHB is almost certainly not the only molecule in play, but we think this is an important part of understanding how the ketogenic diet and ketone bodies work,” said Newman “This is the first study to really connect deep molecular mechanisms of ketone bodies all the way through to improving the aging brain.”
Looking forward, he said, the next step would be to see if the same memory protection could be achieved by using BHB alone, or possibly going even more targeted than that by manipulating the protein kinase A signaling pathway directly. “If we could recreate some of the big-picture effects on synapse function and memory just by manipulating that signaling pathway in the right cells,” he said, “we wouldn’t even need to eat a ketogenic diet in the end.”
Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development
by Fabrice Darbellay, Anna Ramisch, Lucille Lopez-Delisle, Michael Kosicki, Antonella Rauseo, Zahra Jouini, Axel Visel, Guillaume Andrey in Nature Communications
In mammals, only 3% of the genome consists of coding genes which, when transcribed into proteins, ensure the biological functions of the organism and the in-utero development of future individuals. But genes do not function alone. They are controlled by other sequences in the genome, called enhancers, which, like switches, activate or deactivate them as required. A team from the University of Geneva (UNIGE) has identified and located 2700 enhancers — among millions of non-coding genetic sequences — that precisely regulate the genes responsible for bone growth. This discovery sheds light on one of the major factors influencing the size of individuals in adulthood, and explains why their failure could be the cause of certain bone malformations.
Tall or short, our height is largely inherited from our parents. Furthermore, many genetic diseases affect bone growth, the exact cause of which often remains unknown. What if an explanation could be found not in the genes themselves, but in other parts of the genome responsible for activating them? Guillaume Andrey, assistant professor in the Department of Genetic Medicine and Development at the UNIGE Faculty of Medicine and at the Geneva Institute of Genetics and Genomics (IGE3), who led this research, explains: ‘’Short DNA sequences — known as enhancers — give the signal for transcription of DNA into RNA, which is then translated into proteins. While the genes that regulate bone formation and their location in the genome are already well known, it is not the case for the switches that control them.”
Guillaume Andrey and his team have developed an innovative experimental technique, rewarded in 2023 with the Swiss 3R Competence Centre Prize, which makes it possible to obtain mouse embryos carrying a precise genetic configuration from murine stem cells. ‘’In this case, our mouse embryos have fluorescent bones that are visible by imaging, enabling us to isolate the cells of interest to us and analyse how the enhancers work during bone development,’’ explains Fabrice Darbellay, a post-doctoral researcher in Professor Andrey’s laboratory and first author of this work.
The team monitored the activity of chromatin, the structure in which DNA is packaged, specifically in fluorescent bone cells. Using markers of gene activation, the scientists were able to identify precisely which regulatory sequences came into action to control the genes responsible for building bone. They then confirmed their discovery by selectively deactivating the enhancers without affecting the coding gene. ‘’We then observed a loss of activation of the genes in question, which indicates both that we had identified the right switches and that their role is indeed crucial to the proper functioning of the gene,’’ explains Fabrice Darbellay.
Of the 2700 switches identified in mice, 2400 are found in humans. ‘’Each chromosome is a long strand of DNA. Like pearls on a necklace, the enhancers and the genes they control form little balls of DNA on the same chromosomal thread. It is this physical proximity that enables them to interact in such a controlled way,’’ explains Guillaume Andrey. Variations in the activity of these regions could also explain the differences in size between human beings: the activity of bone cells is indeed linked to the size of bones and therefore of individuals.
Moreover, many bone diseases cannot be explained by a mutation affecting the sequence of a known gene. The answer could be found elsewhere, and more precisely in the non-coding but regulatory regions of the genome. ‘’There are already a few documented cases where a mutation in the switches rather than in the genes themselves is the cause of bone disease. It is therefore very likely that the number of cases is underestimated, especially when the patients’ genes appear normal,’’ the authors explain. And beyond bone disease, failures of these various, as yet little-understood genetic switches could be the cause of many other developmental pathologies.
Single-step generation of homozygous knockout/knock-in individuals in an extremotolerant parthenogenetic tardigrade using DIPA-CRISPR
by Koyuki Kondo, Akihiro Tanaka, Takekazu Kunieda in PLOS Genetics
Some species of tardigrades are highly and unusually resilient to various extreme conditions fatal to most other forms of life. The genetic basis for these exceptional abilities remains elusive. For the first time, researchers from the University of Tokyo successfully edited genes using the CRISPR technique in a highly resilient tardigrade species previously impossible to study with genome-editing tools. The successful delivery of CRISPR to an asexual tardigrade species directly produces gene-edited offspring. The design and editing of specific tardigrade genes allow researchers to investigate which are responsible for tardigrade resilience and how such resilience can work.
If you’ve heard about tardigrades, then you’ve no doubt heard about their uncommon abilities to survive things like extreme heat, cold, drought, and even the vacuum of space, which different members of the species possess. So naturally, they attract researchers keen to explore these novelties, not just out of curiosity, but also to look at what applications might one day be possible if we learn their secrets.
“To understand tardigrades’ superpowers, we first need to understand the way their genes function,” said Associate Professor Takekazu Kunieda from the Department of Biological Sciences. “My team and I have developed a method to edit genes — adding, removing or overwriting them — like you would do on computer data, in a very tolerant species of tardigrade, Ramazzottius varieornatus. This can now allow researchers to study tardigrade genetic traits as they might more established lab-based animals, such as fruit flies or nematodes.”
The team used a recently developed technique called direct parental CRISPR (DIPA-CRISPR), based on the now-famous CRISPR gene-editing technique, which can serve as a genetic scalpel to cut and modify specific genes more efficiently than ever before. DIPA-CRISPR has the advantage of being able to affect the genome of a target organism’s offspring and had previously been shown to work on insects, but this is the first time it’s been used on the noninsect organisms that include tardigrades. Ramazzottius varieornatus is an all-female species that reproduces asexually, and almost all offspring turned out to have two identical copies of the same edited code, unlike other animals, making it an ideal candidate for DIPA-CRISPR.
“We simply needed to inject CRISPR tools programmed to target specific genes for removal into the body of a parent to obtain modified offspring, known as ‘knock-out’ editing,” said Koyuki Kondo, project researcher at the time of the study (currently assistant professor at the Department of Life Science at Chiba Institute of Technology). “We could also obtain gene-modified offspring by injection of extra DNA fragments we want to include; this is called ‘knock-in’ editing. The availability of knock-in editing allows researchers to precisely edit tardigrade genomes, allowing them to, for example, control the way individual genes are expressed, or exhibit the genes’ functions.”
The main resilience trait this species demonstrates is their ability to survive extreme dehydration for long periods. This was previously shown to be partially due to a special kind of gel protein in their cells. And this trait is interesting as it has also been applied to human cells. Kunieda and other tardigrade researchers think it’s worth exploring whether something like an entire human organ could one day be successfully dehydrated and rehydrated without degradation. If that is possible, it could revolutionize the way organs are donated, transported and used in surgery to save lives.
“I understand some people feel anxious about gene editing, but we performed the gene-editing experiments under well-controlled conditions and secured the edited organisms in a closed compartment,” said Kunieda. “CRISPR can be an incredible tool for understanding life and aiding in useful applications that can positively impact the world. Tardigrades not only offer us a glimpse at what medical advances might be possible, but their range of remarkable traits means they had an incredible evolutionary story, one we hope to tell as we compare their genomes to closely related creatures using our new DIPA-CRIPSR-based technique.”
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