Identifying Site Specific Methylation in tRNAs and Target Substrates of RNA Methyltransferase NSun2

Currently, DNA methylation is one of the most broadly studied and well-characterized epigenetic modifications associated with gene silencing. The biological importance of 5-mC as a major epigenetic modification in phenotype and gene expression has been widely recognized. DNA hypomethylation is likely caused by methyl-deficiency due to a variety of environmental influences and has been proposed as a molecular marker in multiple biological processes such as cancer. The quantification of 5-mC content or global methylation in diseased or environmentally impacted cells could provide useful information for detection and analysis of disease. A less widely studied but potentially equally important modification is that of methylated RNA. Cytosine methylation (5-mC) of RNA is not new to the field of epigenetics however the functional relevance of this modification remains unknown. The known RNA methyltransferases are DNMT2 and NSun2; whose target substrate is tRNA. The researchers at Welcome Trust – Medical Research Council Cambridge Stem Cell Institute in the UK, have used an innovative technique called miCLIP (individual-nucleotide-resolution crosslinking and immunoprecipitation method) to identify site specific methylation in tRNAs and other target substrates of NSun2 – namely messenger and noncoding RNAs (ncRNAs).

Their findings are summarized below:

  • Approximately 90% of the 312 miCLIP-identified mRNAs remained unchanged in the absence of NSun2, indicating that expression of the NSUN2 gene is unnecessary for mRNA stability.
  • In addition substrate tRNA, miCLIP along with bisulfite sequencing, identified several non-coding RNA NSun2 targets in both human fibroblasts and HEK293 cells. Several targets were confirmed from previous findings along with two newly identified targets of vault ncRNA (vtRNA) in HEK293 cells, vtRNA1.2 and vtRNA1.3.
  • Human vtRNAs can be processed into small regulatory RNAs (svRNA) differently than microRNAs. The authors demonstrated that in the absence of NSun2-mediated methylation, vtRNA processing into svRNA is altered which affects the levels of svRNA-regulated mRNAs. The authors conclude that alternate processing of this pathway may contribute to symptoms found in humans with NSun2 deficiency such as disorders associated with intellectual disabilities.

You can read more about this interesting work here: Shobbir Hussain, et al. NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs. (Cell Reports 4, 255–261, 2013)

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