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Category: genetics – Page 15

Scientists chart over 140,000 DNA loops to map human chromosomes in the nucleus

One of the most detailed 3D maps of how the human chromosomes are organized and folded within a cell’s nucleus is published in Nature.

Chromosomes are thread-like structures that carry a cell’s genetic information inside the nucleus. Rather than existing as loose strands or only as the familiar X-shapes seen in textbooks, chromosomes fold into specific three-dimensional forms. How they fold, the structures they form, and their placement play crucial roles in maintaining proper cellular functions, gene expression, and DNA replication.

The team involved in the 4D Nucleome Project, whose goal was to understand the 3D organization of human chromosomes in the nucleus and how it changes over time, identified over 140,000 DNA looping interactions in human embryonic stem cells and fibroblasts. They also presented computational methods that can predict genome folding solely from its DNA sequence, making it easier to determine how genetic variations—including those linked to disease—affect genome structure and function.

Cardiovascular Disease Biomarker Deep Dive (Test #7 In 2025)

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Chromosome shattering in cancer

Cancer cells often contain an abnormal number of chromosomes as a result of incorrect chromosome segregation during cell division.

These fragments of genetic material can be encapsulated by a membrane, forming small nucleus-like structures called micronuclei. These structures often rupture, exposing chromatin (DNA and associated proteins) to the harsh environment of the cytoplasm, which can lead to large-scale DNA damage in a process called chromothripsis, or chromosome shattering and scrambling.

In a new Science study, researchers report that the cytoplasmic protein NEDD4-binding protein 2 may be responsible for chromothripsis.

Learn more in a new.

A protein that cuts double-stranded DNA contributes to chromosome scrambling in human cancer cells.

Stanley Clarke and Marcin Imieliński Authors Info & Affiliations

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Pressing pause: A small genetic stop may have helped complex life evolve

Humans have it. So does Drosophila. But not yeast. That “it” is a small pause at the start of gene activity—a brief molecular halt that may have helped life evolve from simple cells to complex animals.

A new study by Charles Danko, associate professor in life science and technology at Cornell’s Baker Institute for Animal Health and in the Department of Biomedical Sciences in the College of Veterinary Medicine, and colleagues explores how this key step in gene regulation—promoter-proximal pausing—evolved across species.

Promoter-proximal pausing occurs just after a cell’s molecular “copy machine”– RNA polymerase II—is activated. The polymerase temporarily stops, usually after about 20 to 60 nucleotides or “letters” of the gene, waiting for further signals.

How ancient viral DNA shapes early embryonic development

A new study from the MRC Laboratory of Medical Sciences (LMS) in London, UK reveals how ancient viral DNA once written off as “junk” plays a crucial role in the earliest moments of life. The research, published in Science Advances, begins to untangle the role of an ancient viral DNA element called MERVL in mouse embryonic development and provides new insights into a human muscle wasting disease.

Transposable elements are stretches of DNA that can move around the genome. Many of these DNA sequences originate from long ago, when viruses inserted their genetic material into our ancestors’ genomes during infection. Today, these viral transposable elements make up around 8–10% of the mammalian genome.

Once disregarded as “junk” DNA, we now know that many transposable elements play an important role in influencing how genes are turned on and off, especially during early development. They have a variety of beneficial and harmful roles in the body, for example, some help regulate normal immune responses, while others can disrupt genes and contribute to diseases like cancer.

Epigenetic Age Prediction Remains Stable Across Common Variants and Diverse Ancestries

Epigenetic clocks, based on DNA methylation profiles at CpG sites, are widely recognized as reliable biomarkers of biological aging. However, common single-nucleotide polymorphisms (cSNPs), genomic variants that can overlap CpG sites, may affect DNA methylation profiles in ways that potentially interfere with the accuracy of epigenetic clocks. Moreover, because the prevalence of cSNPs varies across populations, such cSNP-CpG overlaps may differentially affect the age predictions of epigenetic clocks in diverse cohorts. Here, we present the first systematic cross-ancestry evaluation of cSNP robustness in the epigenetic clock, examining how cSNP-CpG overlaps affect the performance of epigenetic clocks across nine major genomic ancestry groups. We employed three complementary strategies: (a) testing whether cSNP-CpG overlaps are overrepresented in established epigenetic clocks or particular populations, (b) evaluating whether overlapping CpG sites correspond to the most influential aging predictors within clock models, and © simulating the effects of cSNP-associated methylation changes on predicted biological age. Our findings indicate that cSNP-CpG overlaps are not enriched among the CpG sites used in current epigenetic clocks, nor do they tend to involve the most influential sites. Furthermore, our simulation analysis revealed that current epigenetic clocks appear robust to cSNP-related methylation variations. Our findings underscore the overall stability of current epigenetic clocks, even in the presence of population-specific cSNP-CpG overlaps that are known to affect DNA methylation levels.

The authors have declared no competing interest.

Study examines oligodendrocyte dynamics throughout the progression of multiple sclerosis

Multiple sclerosis (MS) is a chronic autoimmune disease characterized by the disruption of nerve signals and various associated neurological symptoms, ranging from vision problems to numbness, weakness, fatigue and cognitive impairments. These symptoms emerge when the immune system starts to attack mature oligodendrocytes (MOLs), specialized cells that produce the protective sheath surrounding nerve fibers (i.e., myelin).

There are several subtypes of MOLs, which might exhibit different immune cell-like genetic responses in patients diagnosed with MS. While various studies have investigated the neural and molecular underpinnings of MS, how these different cell subtypes respond as the disease progresses has not yet been elucidated.

Researchers at Karolinska Institute in Sweden recently carried out a mouse study aimed at mapping how different MOL subtypes might differ in their sensitivity to neuroinflammation across different stages of MS.

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