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 […]
Engineering (Epi)Genomes with CRISPR-CasMarch 14, 2013To really figure out what genes really do, you gotta get in there and get your hands dirty. That usually means deleting or modifying genes, or other regulatory regions. In a recent “Research Highlight” article, researchers at Johns Hopkins reviewed the three main ways to do this, including the increasingly popular CRISPR/Cas system. To engineer […]
DNA Methylation in Cancer Goes the Distance via EnhancersMarch 14, 2013We like having all the important things close by—a stash of chocolate, a latte, and the remote control. But sometimes important things are far away. Take enhancers, for example. Enhancers are often pretty far from the genes whose transcription they are “enhancing.” And now, it turns out that DNA methylation at these enhancers can affect […]