We gather the best tips, advice and wisdom from you guys at the bench and publish them to help each other improve in the lab.
What could you add to this collection? Click here to explore how you could contribute to Bitesize Bio.
Epigenetics is the study of heritable changes in the phenotype of a cell or an organism that are not encoded by the genome (hence epi which means ‘above’ in Greek, and genetikos which means ‘origin’).
In this article, we’ll discuss DNA methylation, a common epigenetic modification: both what it is, and how it can be detected and quantified.
Our genome stores information in the form of DNA molecules. Most of us are familiar with the genomic architecture, which consists of DNA wrapped around histone proteins to form nucleosomes, which are then packaged into highly condensed chromatin. Our genome sequence remains generally constant, with the exception of genetic mutations that can lead to deleterious results such as cancer. Epigenetic changes, however, which are not encoded in the DNA sequence, are reversible and dynamic, and are also heritable. These epigenetic modifications reflect adaptations to our environment, life-style, diet, and other external factors. Thus, the mammalian genome can be modified at either the chromatin or the DNA level.
DNA consists of four nucleotide building blocks: cytosine, guanine, adenine, and thymine. Cytosine residues can undergo an epigenetic modification called methylation, catalyzed by the enzyme DNA methyltransferase, that results in the addition of a methyl group to the carbon-5 position, yielding 5-methylcytosine (5-mC). Additionally, 5-mC can be enzymatically oxidized to 5-hydroxymethylcytosine (5-hmC) by the TET1/2/3 enzymes. These DNA methylation events are thought to regulate gene expression, and there is increasing evidence that these modifications are linked to embryonic stem cell function, development, normal tissue function, and disease progression. However, 5-hmC and 5-mC are believed to have different functional roles in the mammalian genome, and it is possible that these changes may represent early epigenetic biomarkers for different pathogeneses.
In our recent webinar on Bitesize Bio, Dr. Sriharsa Pradham of New England Biolabs discussed various techniques for detecting 5-hmC and 5-mC modifications, both globally and within specific sequences. Dr. Pradham presented a very robust and easy-to-use protocol that employs the EpiMark 5-hmC and 5-mC analysis kit.
The power of this approach is that it can determine enrichment for specific methylation modifications locally and on a genome-wide level. For instance, you could determine global 5-hmC levels in normal vs. cancer samples, possibly identifying epigenetic biomarkers for a particular cancer.
How could you use this technology in your reseaarch?
ps: Don’t forget to check out our webinar on detecting 5-hmC and 5-mC modifications!Photo Credits