Dynamic RNA Methylation Emerges as New Player in the Epigenetic LandscapeApril 29, 2013Methylation is a hot topic in the field of epigenetics whether it’s occurring on the cytosines of DNA or its histone protein friends. With a relatively well-known set of enzymes, methylation marks are dynamically modified in order to regulate gene expression. However, the revisiting of a RNA modification discovered in the 70’s has come to […]
SCANning Single Molecules to Pinpoint Co-Occurrence of Epigenetic MarksApril 24, 2013Just because two people live on the same street doesn’t necessarily mean they live that close to each other or in the same house, yet that’s what you often have to assume when using ChIP to detect epigenetic modifications. Either that, or you have to use tons of sample and/or a labor-intensive method to figure […]
RNA Methylation in lncRNAs Does XISTApril 24, 2013Building on work from the 1970s, the era of orange shag carpet and bell bottoms, researchers report that poly(A) RNA gets methylated on cytosines, just like other RNAs and DNA. These methylated cytosines—in the long non-coding RNAs (lncRNAs) HOTAIR and XIST—could also be important for their functions. Methylated cytosines in DNA are old news, and […]
5-hmC as a Cancer DiagnosticApril 24, 2013We’ve heard that DNA methylation can get messed up in cancer, but what about 5-hydroxymethylation (5-hmC)? In a recent report, researchers say that 5-hmC profiles could serve as epigenetic signatures of cancer. The U.K. and Swiss team wanted to know if they could zero in on a signature or biomarker for liver cancer—specifically for liver […]
Guide: Getting Started with Genome-Wide 5-mC and 5-hmC SequencingApril 10, 2013With recent advances in sample preparation, highthroughput sequencing, and bioinformatics, researchers looking to study DNA methylation and hydroxymethylation now have several options for investigating these epigenetic modifications on a genome-wide scale. The following technologies offer varying levels of resolving power, with some offering regional estimates of DNA methylation status, while others provide quantitative values at […]
Vitamin C Helps Cells Get their 5hmC OnApril 9, 2013Pass the SunnyD. According to a paper just out in the Journal of Biological Chemistry, vitamin C, also known as ascorbic acid, may have a role in epigenetic regulation, specifically 5-hmC regulation. Gaofeng Wang at the University of Miami Miller School of Medicine and colleagues demonstrated that this critical dietary nutrient is involved in hydroxylation […]
Global Chromatin Dynamics Key in Stem Cell DifferentiationApril 5, 2013Human embryonic stem cells (hESCs) are experts are keeping their options open, and now a scientist reports how—it turns out that Oct-4 keeps chromatin in the right state to maintain pluripotency. In a single-author paper, Xuejun Parsons, who is at the San Diego Regenerative Medicine Institute and Xcelthera, lays it all out. She’d developed a […]
DNA Methylation Covers Up Potential Polycomb Binding SitesApril 3, 2013Just like a bossy older sister, DNA methylation tells the Polycomb complex where it can and cannot bind. That’s the gist of a recent paper showing that removing DNA methylation actually frees up the Polycomb machinery to bind to new places, changing gene expression. DNA methylation is linked to Polycomb repression, but the question of […]
HpaII and MspI Strike Again in 5hmC Sequencing with HMST-SeqMarch 24, 2013It’s hard to tell some things apart—for instance, with her new haircut, Miley Cyrus could almost be mistaken for Pink. Well, almost. Anyhow, if you’re trying to tell 5-methylcytosines (5-mCs) from 5-hydroxymethylcytosines (5-hmCs) from each other, you’re in luck because there’s a new method for that—one that’s inexpensive and selective. Sure, some methods for doing […]
DNA Methylation Tells Splicing Machinery Where to CutMarch 21, 2013In a recent paper, researchers say that DNA methylation, nucleosomes, and the “GC architecture” of an exon and its flanking introns may actually act as a big “cut here” sign stuck to the DNA or RNA to show where splicing is supposed to happen. Evidence that DNA methylation and nucleosomes are linked to splicing has […]