Transposase-Accessible Chromatin Assay for Fast and Sensitive Epigenomic Profiling

November 18, 2013 WhatIsEpigenetics

Scientists at Stanford University School of Medicine have developed a rapid and sensitive method for integrative epigenomic analysis called assay for transposase-accessible chromatin using sequencing (ATAC-seq).This assay is based on direct in vitro transposition of sequencing adaptors into native chromatin, which captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. By using ATAC-seq, the scientists discovered classes of DNA-binding [more…]

RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

November 18, 2013 Milka Rodriguez

Circadian rhythms are the physiological changes that follow a roughly 24-hour cycle, such as the sleep-wake cycle. They are found in most living things including animals, plants and fungi. The mammalian circadian biological clock regulates metabolism via a negative transcription-translation feedback loop of clock genes. Histone protein methylation is an epigenetic modification which has been suggested to be involved in circadian clock regulation; however, the role of RNA methylation in this process is still unknown. The most common and abundant [more…]

Accurately Telling the Age of Human Tissues and Cells by DNA Methylation Clock

November 11, 2013 WhatIsEpigenetics

External signs of the human body’s age can be given by wrinkles and graying hair. However, these signs may not be accurate to tell the age of human tissues and cells that construct your body. Geneticist and biomathematician Steve Horvath at the University of California Los Angeles has developed a multi-tissue predictor of age that enables one to estimate the age of most tissues and cell types based on DNA methylation that can selectively switch off genes. This age predictor was [more…]

Vitamin C Modulates TET1 Function During Somatic Cell Reprogramming

November 1, 2013 Milka Rodriguez

Cellular reprogramming of somatic cells to a pluripotent state (an undetermined state in which a cell is capable of differentiating to all of the various cell types of the body) is accompanied by several epigenetic changes including genome-wide resetting of DNA methylation status. Vitamin C, an essential nutrient for humans, is involved in several metabolic pathways and in the prevention of conditions such as scurvy. Vitamin C was recently found to promote the generation of induced pluripotent stem cells (iPSCs) [more…]

Simple Blood Test of DNA Methylation Markers Promises Early Diagnosis of Pancreatic Cancer

November 1, 2013 WhatIsEpigenetics

The scientists at Johns Hopkins University used a genome-wide pharmacologic transcriptome approach to identify two novel cancer-specific DNA methylation markers in cultured pancreatic cancer cells: BNC1 and ADAMTS1. Using a nanoparticle-enabled MOB (Methylation On Beads) technology, they found that these two markers are also frequently detected in serum samples of pancreatic cancer patients (N = 42) with a sensitivity for BNC1 of 79% and for ADAMTS1 of 48%, while the specificity was 89% for BNC1 and 92% for ADAMTS1. Overall [more…]