Tianhe-1A at the National Supercomputer center in Tianjin, China, is currently the world’s fastest supercomputer. Tianhe means “Milky Way” in English…or the river in the sky. It strikes me as a lovely, but ironic name. Although, I suppose this “river of stars” is moving fast, in the context of the universe.
That Milky Way idea coincidentally reminded me of how Epigenetics is being aided by rapid technique developments. Epigeneticists are calling for cheaper sequencing methods, paired with standardised data analysis methods. At the bench, you must carefully plan for the optimal utility of your currently available methods. However, it’s also important to your lab practice, to keep updated in this fast paced field. A major goal of the Epiexperts networking site, is for users to be able to efficiently communicate about the latest research trends and techniques. We all want to promote progress in the field.
Since defining the functional roles of 5-hmC is such a hot topic, today I’m noting a couple techniques which demonstrate progress that has been made towards experimentally differentiating 5-hydroxymehtylated cytosine from 5-methylated cytosine.
Some clever β-glucosyltransferase (β-GT) based methods to do 5-hmC genome wide profiling, were developed and published by a couple groups. Szwagierczak et al. Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res. (2010) takes a look at the relationship of the Tet family of enzymes and 5-hmC in mouse ESCs, embryoid body, and adult tissues. The work done by Chun-Xiao Song et al. 12 December, 2010. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine Nature Biotechnology, produced some interesting results looking at the aging brains of mice. (Great, a new way to tell when we are getting old. Just kidding!) Similar commercially available PCR based kits from Zymo and New England Biolabs can also fit into these types of high throughput workflows.
Another method we are hearing about is the 3rd generation fluorophore sequencing technology, called SMRT (single molecule real time) from Pacific Biosciences. This real time sequencing platform detects epigenetic modifications (including hydroxymethatylated cytosine) based on polymerase kinetic signatures. The authors state that the method will “likely enable mapping of methylation patterns within even highly repetitive genomic regions”. Since these SMRT platforms have now made their way into some research institutions, hopefully we’ll be hearing more details about how that works out soon.
Often times when when we look back, it appears that time was moving much faster than we experienced while we were in that time. (I’ve heard people say a watched gel never runs!) With these types of 5-hmC profiling techniques as toeholds, I’m eagerly awaiting future research news. If anyone wants to note a new 5-hmC profiling paper or recent talk, please do so. I am continually inspired by scientists’ creativity and invention.