Old Dog, New Tricks? Cytosine Methylation in Long Non-Coding RNAs
Cytosine methylation (5-mC) in DNA is very common, and is generally associated with repression of gene expression. DNA methylation was the first discovered type of epigenetic modification and remains one of the most actively investigated epigenetic processes, especially with respect to its use as a valuable biomarker for cancer and other human diseases. The presence of RNA methylation has been known for years, however, the functional relevance and importance of this modification remains largely unknown. According to Dr. Alexandra Lusser, an internationally recognized expert in epigenetics research, “Internal RNA modifications in poly(A)-RNAs may play diverse roles, including [regulation of] splicing, RNA stability, transport or interaction with protein binding partners.” A recent paper by Dr. Lusser’s group in Austria describes the identification of specific sites of RNA methylation in XIST and HOTAIR, which are two of the best-characterized long non-coding RNA molecules, and they discuss potential roles for 5-mC in RNA.
HOTAIR is a long non-coding RNA associated with promoting metastasis in lung cancer and is known to interact with several chromatin-modifying enzymes, such as the polycomb-repressive complex 2 (PRC2) and the histone lysine demethylase complex consisting of LSD1, REST, and CoREST. The authors identified one particular site, cystosine 1683, which appeared to be invariably methylated in HOTAIR transcripts, in both normal and cancer cells, suggesting that it might play an important role in the activity of this RNA molecule.
XIST is arguably the most studied long non-coding RNA, and is critical for the inactivation of one of the X chromosomes in all female cells. XIST is known to bind directly to PRC2, and this interaction is important for X chromosome inactivation. In contrast to HOTAIR, there were no cytosine residues in XIST that were always methylated. However, several cytosines did show a methylation frequency of ~20%, suggesting that methylation might play an important role in modulating the function of XIST. The authors next chemically synthesized a fragment of the XIST RNA that was methylated at the five cytosines that they discovered to have the highest levels of methylation. They then demonstrated that methylation of this RNA molecule interfered with PRC2 binding, relative to the unmethylated XIST RNA fragment, providing a possible molecular role for RNA modification. Dr. Lusser states that “Our data so far favor the idea that methylation directly interferes with the binding of PRC2. Since C5 methylation in cytosine should not affect base pairing, it is less likely that it will lead to major structural changes.”
While investigation of the importance and role of RNA methylation in biology is still an emerging research area, RNA is clearly extensively modified. In fact, over 100 different RNA modifications have already been reported (http://mods.rna.albany.edu/mods/). The existence of these modifications suggests that epigenetic mechanisms play critical roles in the regulation of many RNA-mediated activities. The study of RNA modification is a rapidly expanding field and much remains to be learned about the function and applications of RNA methylation. For example, Dr. Lusser points out that “There is definitely potential for this mechanism to be used as a biomarker… in different types of cancer.” What are your thoughts? Do you think RNA methylation is important to cellular biology, and if so, what are its roles?
Amort T, Soulière MF, Wille A, Jia XY, Fiegl H, Wörle H, Micura R, & Lusser A (2013). Long non-coding RNAs as targets for cytosine methylation. RNA biology, 10 (6) PMID: 23595112