CpGT and MethylGPT – Large AI Models Lay the Foundation for Advanced DNA Methylation AnalysisNovember 27, 2024Vast amounts of DNA methylation data have paved the way for epigenetic clocks to significantly advance aging research; however, generative artificial intelligence (AI) may have now laid the foundation for more transformative insights into DNA methylation. Two preprints report the application of transformer architecture to develop “foundation” or large AI models trained on vast DNA […]
“Epi-bit” Encoded Images of Tigers and Pandas Reveal the Epigenetic Future of DNA-based Memory StorageNovember 10, 2024A memorable musical number from Cats muses on the loss of “Memory;” however, an unforgettable new feline-related study now describes the encoding of images of tigers (and pandas!) using printed epigenetic bits (“epi-bits”) on DNA as a novel storage approach for our data and dearest recollections. Can epi-bits make any memory loss a thing of […]
scEpiAge Brings Single-cell Resolution to Epigenetic Clock HeterogeneitySeptember 23, 2024DNA methylation-based epigenetic clock construction has generally relied on bulk datasets representing findings from thousands or millions of cells, and now, a new single-cell epigenetic clock age predictor known as scEpiAge may help to resolve the impact of heterogeneity. Can improved resolution offer more profound insight into the aging process? A team led by Marc […]
Chrom-seq Uses ‘Readers’ to See Which RNAs Put Epigenetic Marks on ChromatinAugust 20, 2024Reading glasses, or “readers,” help you see text and other fine details up close. Inspired by our desire for increased resolution, a talented team is using histone readers to more clearly see which long noncoding RNAs (lncRNAs) interact with particular histone modifications. Their method, called Chrom-seq, doesn’t require highly pure antibodies or crosslinking, making it […]
PaleoHi-C Makes a “Mammoth” Genome Architecture DiscoveryJuly 22, 2024Certain scientific findings may be considered colossal or even epic in scale; however, few compare to a “mammoth” new study describing the three-dimensional genome architecture of preserved cells from a 52,000-year-old animal skin sample thanks to a primeval-sounding yet cutting-edge technique known as PaleoHi-C! Epigenetics research goes pre-historic! A veritable “stampede” of researchers led by […]
cfDNA Methylation Analysis Captures the Double Trouble of Inflammaging!July 1, 2024Analyzing cell-free (cf)DNA methylation from liquid biopsies represents a non-invasive approach to profile various diseases, but what if it could help us understand the devious duo of inflammaging – aging and inflammation? A talented team has dealt with this “double trouble” by applying enzymatic methyl-seq (EM-seq) to evaluate cfDNA methylation patterns. Researchers headed by Jian-Ping […]
No Epigenetic Modification is an Island: How Reader Proteins Functionally Interpret Complex Chromatin StatesMarch 25, 2024Like no man is an island and instead relies on those surrounding them, single epigenetic modifications generally do not function in solitary. Now, an absorbing new study from a synergistic epigenomics squad reports how epigenetic reader proteins functionally interpret chromatin states made up of complex combinations of disparate epigenetic modifications. A highly collaborative team guided […]
reChIP Doubles Down on Low-input Profiling of Bivalent ChromatinMarch 5, 2024Sometimes, when you’re dealt the right hand, doubling down is a sound strategy. Although it can be a risky move in blackjack, a new ChIP-seq method makes it a sure thing when you’re dealing with bivalent chromatin. The strategy, which includes important preparation steps and two rounds of chromatin immunoprecipitation (ChIP), provides sensitive genome-wide profiles […]
FORGEdb Deciphers Genetic Variants and Disease Mechanisms to Tell Whether Your Gene Regulation Mechanism is a Touchdown or a Field Goal!February 26, 2024Performing experiments to understand gene regulation and do not want to miss any extra points? Well, FORGEdb may be the method for you! Building on previous research, this new method can help scientists unravel the mysteries behind complex diseases by identifying candidate functional variants and uncovering target genes and mechanisms. Developed by a team led […]
SIMPLE-seq Collaborates Chemistries to Report Single-Cell 5mC and 5hmCFebruary 20, 2024Collaborations work best when team members’ abilities complement each other. That’s what makes SIMPLE-seq work so well—it’s a simple, easy combination of two methods that complement each other to provide both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) datasets in one experiment in single cells and molecules. Continuing on the recent theme of methods that report both 5mC […]
