Most biologists are aware of chemical modification of DNA in the form of 5-methylcytosine (mC), the eponymous ‘5th base’.
Moving to the 6th base
The fields of epigenetics and epigenomics are increasingly having an impact on our understanding of biology and a subsequent impact on medicine. Some biologists are aware of the wider range of DNA modifications that are found in biology, the most notable new example is 5-hydroxy-methylcytosine (now referred to as the ‘6th base’). To date there are well over 100 other nucleotide analogues.
These modifications, and those of histones, have been shown to have important roles in the regulation of gene expression and function, and analyzing these using Bisulfite-sequencing, ChIP-seq and/or other methods has become almost routine.
Rising to the challenge
Recently a broader awareness of the ‘epitranscriptome’, the modification of RNA, has become much wider. The NGS community has risen to the challenge of analyzing these and modified the MeDIP-seq methods to allow MeRIP analysis, (Methylated-RNAImmunopreciPitation).
Now the first commercial product is available to allow reliable bisulfite treatment of RNA to convert methylated Cytosines to Uracil. The EZ RNA Methylation from Zymo Research (http://www.zymoresearch.com) uses their spin-column format to create an easy workflow for RNA conversion and desulphonation that delivers high C<U conversion rates.
The kit was recently used in a paper which shows that regulatory long non-coding RNAs are methylated at specific cytosines, and that this methylation affects binding to chromatin-associated protein complexes (1).
Analysis of poly-adenylated RNA methylation is just getting started.