Articles tagged with Genomic Dna
The study observed changes in A/B compartments of mouse embryonic stem cells, correlating with gene expression and replication timing changes. Chromosome conformation changes preceded gene expression changes, suggesting a physical mechanism for transcriptional regulation.
Yale scientists identify two proteins P300 and Brd4 as essential for activating the zebrafish genome after fertilization, allowing embryonic development to proceed. The discovery provides new insights into how life begins at a molecular level.
Researchers have discovered that DNA base editors can induce tens of thousands of off-target RNA single nucleotide variants (SNVs). To address this issue, they engineered deaminases to eliminate the off-target effects, providing a solution for the clinical application of these methods.
Researchers have characterized extensive structural variants in three family trios, uncovering 818,054 small insertions and deletions and 27,622 SVs per genome. Many of these variations are missed by routine sequencing technologies, revealing a vast genetic repertoire that can inform new disease associations and diagnostic methods.
Biologists have discovered 'doppelganger' lake frogs with distinct mitochondrial DNA, allowing them to better adapt to their environment. The study, conducted in collaboration with Japanese colleagues, aims to understand how the genome protects itself from foreign DNA.
Researchers identified 1,148 hot spots with unusually high numbers of structural variants in the genome, including sections near genes linked to sense of smell, blood function, and immunity. The study suggests balancing selection drives adaptation and malleability of human DNA.
Researchers have established a novel method to study DNA replication in individual cells, allowing them to gain insights into the mechanisms that maintain genomic DNA stability. The 'scRepli-seq' method revealed that genome replication profiles were highly conserved among cells and reflected the organization of chromatin compartments.
Researchers at the Wellcome Sanger Institute and Pacific Biosciences successfully assembled the genetic code of a single Anopheles coluzzii mosquito, opening doors to understanding genetic diversity in insects. The breakthrough reduces DNA needed for genome sequencing by an order of magnitude, enabling studies on previously inaccessibl...
A team of Johns Hopkins scientists analyzed DNA sequences from 910 individuals of African descent and found 300 million base pairs of genetic material missing from the current human genome reference. This discovery highlights the need for more diverse reference genomes to better understand genetic variations across populations.
Researchers at University of Pennsylvania have developed a new method to sequence epigenetic marks on DNA, allowing for more precise detection of disease earlier and with increased precision. The method uses APOBEC DNA deaminases to differentiate between two common epigenetic marks, methylation and hydroxmethylation.
Researchers used a twin study to identify factors influencing chemical modifications to DNA across the genome, finding epigenetic marks are more similar between identical twins due to genetic variation. Environmental exposures like smoking and obesity also show partly genetic control.
A CNIC-coordinated project will investigate the oxidative phosphorylation system (OXPHOS) and its structural heterogeneity, with potential implications for metabolic plasticity. Researchers from various countries and specialties will collaborate to develop new methods and gain a deeper understanding of this fundamental biological process.
Researchers found that satellite DNA, once thought to be 'junk,' is essential for holding the genome together and ensuring cell survival. This conserved function is critical for chromosomes to bundle correctly inside the nucleus.
Salk scientists discover that maternal behavior changes brain cells in mice by altering L1 gene copy number and methylation. This correlation suggests a unique role for the jumping gene L1 in shaping brain development.
Researchers from the University of Seville have discovered that genes located near nuclear pores contribute to maintaining genome stability. The study found that anchoring DNA to the pore during transcription prevents DNA-RNA hybrids, a natural source of genome instability.
Scientists have identified a novel mechanism safeguarding mitochondrial DNA, which encodes for essential parts of cellular respiration machinery. The study reveals that an unusual enzyme called PrimPol can re-initiate replication after damage, helping to prevent double-strand breaks and mitochondrial dysfunction.
A study has characterized all of the circular DNA in the worm <em>C. elegans</em> and three human cell types, revealing different sets of circles in different cell varieties. The researchers used a 50-year-old lab technique called density gradient centrifugation to separate and purify the circular DNA.
Researchers developed a new imaging approach called ChromEMT to visualize the three-dimensional structure of chromatin, resolving long-standing debates about its organization. The study reveals that local nucleosome structure combined with global 3D organization determines gene expression and cell fate.
The study found that the red vizcacha rat's genome grew quickly due to the expansion of highly repetitive elements, rather than whole genome duplication. This mechanism is also thought to contribute to 'genomic baggage' in humans, influencing disease susceptibility.
Researchers have identified the KMT2A gene translocations as a common underlying cause of infant and treatment-related leukemias. The Penn/CHOP team has also found that topoisomerase II cleavage clusters in specific regions of the genome, which may play a role in DNA damage repair and cancer development.
A study by the University of Edinburgh reveals that dynamic DNA properties can ward off gene damage and promote genome organization. The research highlights the importance of scaffold attachment factor A in forming a protective chromatin mesh that allows for flexible and responsive cell signals.
A team of researchers used computational modeling to understand DNA knotting in nanochannels, a challenge in genome mapping. They found that experimental results are not consistent with simulations, but the data may come from other sources.
Scientists have determined the first 3D structures of intact mammalian genomes from individual cells, showing how chromosomes fold together inside cell nuclei. This knowledge can help study gene interactions, regulation, and development, with potential applications in understanding diseases.
Researchers have developed a new method of genetic engineering that creates artificial restriction enzymes with enhanced sequence specificity and defined sticky ends. This technology has the potential to revolutionize genomic research and gene editing by improving precision and reducing obstacles posed by existing restriction enzymes.
Researchers from the University of Granada have discovered 62 satellite DNA families in the migratory locust, a species with no previously known satellite DNA. This discovery expands the genetic information available to date about the species, revealing new insights into its genome and potential applications for chromosome identification.
A team of researchers has successfully developed a genome editing technique that induces target point mutation without cutting the DNA. This technique offers high-level editing operations with reduced cytotoxicity, making it suitable for gene therapy, disease research, and organism breeding.
A new type of transposable element was discovered in certain bird genomes, which also occurred in nematode worms that are human parasites. The finding reveals that these modern human parasite species were birds from 25-17 million years ago.
A team co-led by Penn Medicine researcher discovers that a mysterious lncRNA has no obvious function in regulating its neighbor's gene expression, but the DNA from which it originates does. The study reveals a new mechanism for enhancer functions in the genome, pointing to a broader role of non-coding DNA and RNA.
Researchers at CNIO have discovered a code of signals that regulates the concentration of proteins involved in genome duplication. The USP7 protein acts as a traffic officer, eliminating ubiquitin marks to favor protein accumulation and DNA copying. This balance is essential for accurate genome replication.
New study confirms Neanderthal DNA has a subtle but significant impact on modern human biology, including associations with skin lesions, nicotine addiction, depression, and blood coagulation. The research uses anonymized electronic health records and genomes to test the effects of archaic genetic variants on clinical traits.
Researchers at IBS created multiplex Digenome-seq to detect errors in CRISPR-Cas9 processes. The tool uses cell-free genomic DNA and sgRNA to identify on- and off-target sites, providing precise analysis results.
Two studies on yeast reveal that gene expression among tandem DNA repeats varies substantially depending on position within the array. These findings provide key information about DNA architecture in cells, highlighting the central role of chromosome architecture in regulating these sequences.
Scientists at the University of Minnesota and BioNano Genomics have developed a new method to analyze DNA sequences in nanochannels, enabling more accurate genome mapping. By analyzing the probability distributions of DNA barcode label separations, researchers can identify structural oddities and improve the accuracy of genome maps.
A streamlined PITCh system enables efficient genome editing for inserting foreign DNA into targeted genomic loci. This method can aid rapid research progress in fields like drug screening and human disease modeling.
Researchers have developed a new technique that maps genomic contact points to shed light on the parts of the genome involved in autoimmune diseases. This approach identified novel candidate genes relating to the risk of developing conditions like rheumatoid arthritis and type 1 diabetes.
Researchers found that tardigrades have a massive amount of foreign DNA, with around 17.5% coming from non-tardigrade sources, primarily bacteria. This challenges conventional views on how DNA is inherited and raises new questions about the connection between foreign DNA and extreme environment survival.
Scientists classify all gene promoters into two distinct types differing in nucleosome stability, with one type found at highly expressed growth-related genes and the other at less frequently expressed genes. The study reveals the role of dynamic nucleosomes in increasing access to promoter DNA for transcription initiation.
The sequenced ancient human genome from Africa reveals a significant wave of migration back into the continent around 3,000 years ago, affecting all populations across the African continent. This migration predates the 'Eurasian backflow' event and shares genetic similarities with Early Neolithic farmers who brought agriculture to Europe.
Researchers analyzed copy number variation across 236 genomes from 125 populations to identify patterns of ancestry and genetic subpopulations. DNA deletions are more reflective of selection, while duplications highlight these variations.
A team of researchers from the University of Cambridge and the Babraham Institute has discovered that a naturally occurring modified DNA base, 5-formylcytosine (5fC), is stably incorporated in the DNA of many mammalian tissues. This rare 'extra' base may play a key role in regulating gene activity.
Australian researchers discovered that a single genetic change in Smchd1 affects its function in the cell, leading to debilitating muscle wasting in FSHD. This fundamental understanding could help develop future treatments for the currently untreatable disease.
Researchers developed coupled microcantilevers that can measure mass on the order of nanograms in a liquid environment with only a 1 percent margin of error. This enables weighing individual molecules, ideal for biological processes such as DNA hybridization and protein characterization.
A genome-wide study found that malnutrition in the first 10 weeks of pregnancy is associated with changes in DNA methylation, which can suppress genes involved in growth, development, and metabolism. These findings have significant implications for understanding the long-term effects of prenatal nutrition on health outcomes.
A new study reveals that carnivorous bladderwort Utricularia gibba packs an impressive number of genes into its tiny genome, outperforming well-known plant species. The plant's unique genetic architecture allows it to thrive in aquatic environments, boasting floating branches and miniature traps that capture prey using vacuum pressure.
Researchers found that C2H2-ZF transcription factors evolved to defend the genome from self-replicating parasitic DNA, known as selfish DNA. These proteins eventually took control of genes, including those involved in brain and heart development.
A genomic test helped doctors solve a medical mystery for a boy with painful spasms. Whole exome sequencing identified the rare condition Episodic ataxia type 1, allowing for targeted treatment and symptom relief. The patient's motor and cognitive functioning have improved since medication was started.
Researchers have identified widespread incorporation of ribonucleotides in genomic DNA, with hotspots found in nuclear and mitochondrial DNA. The Ribose-seq technique allows for the precise location of ribonucleotides, which can affect genome stability and function.
A new computational method can identify positions in the human genome that play a role in cell function, revealing insights into genetic regulation and potential applications in personalized medicine. The study found that 4.2 to 7.5 percent of nucleotides in the human genome have influenced fitness since humans diverged from chimpanzees.
A new study using DNA barcoding confirms that most Ginkgo biloba supplements contain the expected species, while others may be adulterated or contain incorrect materials. The research provides a validated method for supplement manufacturers to ensure quality control and may help consumers avoid toxic or ineffective products.
Researchers at Harvard University have developed a method to efficiently deliver genome-editing proteins into cells, bypassing the need for DNA delivery. The new system uses commercially-available cationic lipids to introduce proteins into cells, offering hope for treating genetic diseases, including deafness.
Scientists have developed a new method to isolate plant nuclear DNA from organellar DNA using the human methyl-binding domain. This approach enables rapid and simple separation of genome sequences, reducing wasted data and increasing efficiency in genomic studies.
Researchers found that only 8.2% of human DNA has a clear function, with most being 'junk' DNA. This figure challenges the previous claim of 80% functional DNA, highlighting the need for a more precise definition of 'function'.
Researchers at Duke University mapped fragile sites across the entire yeast genome, finding they occur in areas where DNA replication slows or stalls. These sites are linked to genetic abnormalities seen in solid tumors and can lead to chromosome instability.
Researchers have unveiled a biological process that explains how DNA can be damaged during genome replication, which relies on protein RPA. Cells use this protein as 'band aids' to protect DNA temporarily during replication, but if they run out, DNA breaks severely and cells cannot divide.
Researchers at Salk Institute discovered a patchwork of genetic variation in individual brain neurons, contrary to the long-held belief that each cell possesses identical DNA code. The study found that up to 41% of neurons have unique, massive copy number variations (CNVs) that arose spontaneously.
Scientists at Ludwig-Maximilians-Universität München discovered a mechanism that allows chromosomal DNA to be locally displaced from nucleosomes for transcription. The FACT complex interacts with histone subunits and detaches stretches of packaged DNA from the nucleosome core, releasing it from its tight wrapping.
Researchers have developed a new method for precisely altering the genomes of living cells, enabling targeted gene insertion and deletion with increased accuracy. This breakthrough technology has far-reaching potential applications in biofuel production, disease research, and therapy development.
A new study by Ohio State University researchers found that mobile DNA elements, called transposons, can significantly disrupt gene expression and cause biological variation in mice. The study discovered that these elements can influence gene expression even when located far away from the affected gene.
A new study reveals two mechanisms by which cells remove embedded ribonucleotides from DNA: the mismatch repair system and RNase H. This research provides insights into how cells maintain genomic integrity and potentially opens up new avenues for understanding RNA-driven DNA evolution.
Researchers at RIKEN have uncovered a key epigenetic mechanism by which Arabidopsis protects cells from harmful DNA elements. The discovery sheds light on the complex interplay between DNA methylation and histone modification, revealing how plants silence transposons and prevent gene disruption.