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Epigenetics

Unlocking the Secrets of Your DNA: How Ancient Viral Sequences Regulate Gene Expression

What scientists once dismissed as junk DNA may actually be some of the most powerful code in our genome. A new international study reveals that ancient viral DNA buried in our genes plays an active role in controlling how other genes are turned on or off, especially during early human development. These sequences, originally from long-extinct viruses, have evolved to act like tiny genetic switches. Using new analysis tools and large-scale experiments, researchers discovered that certain viral DNA fragments are especially strong at activating genes and may even have helped shape what makes humans different from other primates.

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Unlocking the Secrets of Your DNA: How Ancient Viral Sequences Regulate Gene Expression

For years, scientists have been fascinated by the vast expanse of “junk” DNA embedded in our genome. Long dismissed as genetic leftovers with no useful function, these sequences have now been found to play powerful roles in regulating gene expression. A recent international study has shed light on a family of sequences called MER11, revealing their importance in early human development and providing a model for understanding how “junk” DNA can evolve into regulatory elements.

Transposable elements (TEs) are repetitive DNA sequences that originated from ancient viruses. They make up nearly half of the human genome, and while they were once thought to serve no useful function, recent research has found that some of them act like “genetic switches,” controlling the activity of nearby genes in specific cell types.

However, because TEs are highly repetitive and often nearly identical in sequence, they can be difficult to study. The researchers developed a new method for classifying TEs, grouping MER11 sequences based on their evolutionary relationships and how well they were conserved in primate genomes. This approach allowed them to divide MER11A/B/C into four distinct subfamilies, namely, MER11_G1 through G4, ranging from oldest to youngest.

The new classification revealed previously hidden patterns of gene regulatory potential. By comparing the MER11 subfamilies to various epigenetic markers, which are chemical tags on DNA and associated proteins that influence gene activity, researchers found that this new classification aligned more closely with actual regulatory function compared with previous methods.

To directly test whether MER11 sequences can control gene expression, the team used a technique called lentiMPRA (lentiviral massively parallel reporter assay). This method allows thousands of DNA sequences to be tested at once by inserting them into cells and measuring how much each one boosts gene activity. The researchers applied this method to nearly 7000 MER11 sequences from humans and other primates, and measured their effects in human stem cells and early-stage neural cells.

The results showed that the youngest subfamily, MER11_G4, exhibited a strong ability to activate gene expression. It also had a distinct set of regulatory “motifs,” which are short stretches of DNA that serve as docking sites for transcription factors, the proteins that control when genes are turned on. These motifs can dramatically influence how genes respond to developmental signals or environmental cues.

Further analysis revealed that the MER11_G4 sequences in humans, chimpanzees, and macaques had each accumulated slightly different changes over time. In humans and chimpanzees, some sequences gained mutations that could increase their regulatory potential during early development.

This study offers a model for understanding how “junk” DNA can evolve into regulatory elements with important biological roles. By tracing the evolution of these sequences and directly testing their function, researchers have demonstrated how ancient viral DNA has been co-opted into shaping gene activity in primates.

“Our genome was sequenced long ago, but the function of many of its parts remain unknown,” said Dr. Inoue, a corresponding author on the study. Transposable elements are thought to play important roles in genome evolution, and their significance is expected to become clearer as research continues to advance.

Disability

Unlocking Skin Renewal: Vitamin C Activates “Youth Genes” to Reverse Age-Related Thinning

Japanese researchers have found that vitamin C can thicken skin by switching on genes that boost skin cell growth, helping reverse age-related thinning. It works by reactivating DNA through a process that lets cells regenerate more effectively—potentially a game-changer for aging skin.

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The skin serves as our body’s first line of defense against external threats. As we age, however, the epidermis – the outermost layer of skin – gradually becomes thinner and loses its protective strength. Research has long emphasized the benefits of vitamin C (VC) in maintaining skin health and promoting antioxidant properties.

Recently, a team of researchers in Japan made an exciting discovery: VC helps thicken the skin by directly activating genes that control skin cell growth and development. Their findings, published online in the Journal of Investigative Dermatology, suggest that VC may restore skin function by reactivating genes essential for epidermal renewal.

Led by Dr. Akihito Ishigami, Vice President of the Division of Biology and Medical Sciences at Tokyo Metropolitan Institute for Geriatrics and Gerontology, the study used human epidermal equivalents – laboratory-grown models that closely mimic real human skin. In this model, skin cells are exposed to air on the surface while being nourished from underneath by a liquid nutrient medium.

The researchers applied VC at concentrations comparable to those typically transported from the bloodstream into the epidermis and found that VC-treated skin showed a thicker epidermal cell layer without significantly affecting the stratum corneum (the outer layer composed of dead cells) on day seven. By day 14, the inner layer was even thicker, and the outer layer was found to be thinner, suggesting that VC promotes the formation and division of keratinocytes.

Importantly, the study revealed that VC helps skin cells grow by reactivating genes associated with cell proliferation. This process occurs through DNA demethylation – a process in which methyl groups are removed from DNA, allowing for gene expression and promoting cell growth.

The researchers further identified over 10,138 hypomethylated differentially methylated regions in VC-treated skin and observed a 1.6- to 75.2-fold increase in the expression of 12 key proliferation-related genes. When a TET enzyme inhibitor was applied, these effects were reversed, confirming that VC functions through TET-mediated DNA demethylation.

These findings reveal how VC promotes skin renewal by triggering genetic pathways involved in growth and repair. This suggests that VC may be particularly helpful for older adults or those with damaged or thinning skin, boosting the skin’s natural capacity to regenerate and strengthen itself.

“We found that VC helps thicken the skin by encouraging keratinocyte proliferation through DNA demethylation, making it a promising treatment for thinning skin, especially in older adults,” concludes Dr. Ishigami.

This study was supported by grants from the Japan Society for the Promotion of Science (JSPS) KAKENHI: grant number 19K05902.

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Diseases and Conditions

Unraveling the Mysteries of Cohesin: A Protein That Forms Loops in the Human Genome

Cohesin is a protein that forms a ring-shaped complex which wraps and alters the DNA molecule shape. It moves through the DNA and creates specific loops in the genetic material which determine the architecture of the genome and gene expression. Some mutations in the genes of the cohesion complex are responsible for rare diseases (cohesinopathies), such as the Cornelia de Lange syndrome (SCdL) or Roberts syndrome, which affect several organs and cause malformations during development.

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Cohesin, a protein complex that forms loops in the human genome, plays a crucial role in determining the architecture of our genetic material and regulating gene expression. However, its function and behavior have remained somewhat mysterious until now.

Researcher Professor Eva Estébanez-Perpiñá from the University of Barcelona, along with her team and international collaborators, has made significant strides in understanding how cohesin works. Their study, published in Nucleic Acids Research, sheds light on the protein’s interaction with chromatin structure and its role in altering gene expression.

Cohesin consists of four subunits: SMC1, SMC3, SCC1/RAD21, and STAG (also known as SA or SCC2). Previous studies had identified 25 proteins that regulate these subunits and their biological function. Estébanez-Perpiñá’s team has now discovered how the NIPBL protein interacts with both MAU2 and the glucocorticoid receptor (GR), a transcription factor essential for cellular functions.

This ternary complex, comprising NIPBL, MAU2, and GR, modulates transcription by facilitating the interaction of GR with these two proteins. When GR interacts with NIPBL and MAU2, it alters chromatin structure and affects gene expression. This discovery has significant implications for understanding Cornelia de Lange syndrome, a rare disease caused by mutations in genes involved in cohesin formation.

The researchers used advanced microscopic techniques to visualize real-time molecular complexes binding to chromatin, as well as biochemical and biophysical methods to analyze the complex from different structural and cellular perspectives.

Their findings not only improve our comprehension of cohesin’s role but also highlight its potential involvement in other diseases, such as asthma and autoimmune pathologies. As research continues, scientists will likely uncover more about this enigmatic protein and its intricate relationships with chromatin structure and gene expression.

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Children's Health

The Lasting Impact of Early Teenage Obesity on Future Generations

A new study suggests that boys who become overweight in their early teens risk damaging the genes of their future children, increasing their chances of developing asthma, obesity and low lung function.

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The article you provided raises critical concerns about the potential consequences of early teenage obesity on future generations. A recent study published in Communications Biology has shed light on the biological mechanism behind this issue, revealing that boys who become overweight in their early teens may pass on harmful epigenetic traits to their children.

Researchers from the University of Southampton and the University of Bergen in Norway investigated the epigenetic profiles of 339 people, aged 7 to 51. They found that fathers who gained weight during adolescence were more likely to have epigenetic changes in over 2,000 sites in 1,962 genes linked with adipogenesis (formation of fat cells) and lipid metabolism in their children.

These epigenetic changes can regulate gene expression and are associated with asthma, obesity, and low lung function. The study found that the effect was more pronounced in female children than male children, with different genes involved.

The findings have significant implications for public health and may be a game-changer in public health intervention strategies. As Professor Cecilie Svanes from the University of Bergen noted, “A failure to address obesity in young teenagers today could damage the health of future generations, further entrenching health inequalities for decades to come.”

The research was funded by the Norwegian Research Council and highlights the importance of addressing childhood obesity globally. As Prof John Holloway from the University of Southampton and the National Institute for Health and Care Research (NIHR) Southampton Biomedical Research Centre added, “Childhood obesity is increasing globally, and the results of this study demonstrate that this is a concern not only for the health of the population now but also for generations to come.”

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