Epitranscriptomics: Epigenetic landscaping’s new level

Mike Yee

Epigenetics involves regulation or changes to gene expression that occur on the level other than the sequence of the DNA, and that have wide-ranging effects on protein production and cell functions. Epigenetic marks include DNA methylation such as those found on CpG sites, histone post-translational modifications, and RNA-associated silencing that can affect the output. However, what we know about epigenetics—classically described by Conrad Washington as a rolling landscape—is ever expanding, and is an area of study recently hailed as a gold rush.

Recent studies led by Dr. Chuan He on what is now called epitranscriptomics have brought the role of RNA methylation as yet another layer of epigenetic regulation into the limelight. Dr. He and his lab focused on understanding the specific role—substrate and function—of FTO (fat mass and obesity-associated protein), previously known to demethylate ssDNA and ssRNA. Briefly, to analyze FTO’s abilities, they performed a comparison of HPLC profiles of ssRNA, ssDNA, and RNA stem-loop in the presence or absence of FTO, and found that FTO removed the methyl mark on N6-methyladenosine (m6A) on ssRNA—a mark previously discovered decades ago, in 1974. They also performed mass spectrometric analysis of m6A in the presence or absence of siRNA against FTO in HeLa and 293FT cells, and found that m6A levels increased with SIRNA against FTO. In another experiment using immunofluorescent imaging, they showed that FTO was colocalized with nuclear transcriptional machinery, but the addition of a transcriptional inhibitor reduced the number of foci for FTO along with an associated reduction in phosphorylated RNA Polymerase II. Altogether, what they showed for the first time was that a specific mark of RNA methylation, m6A, could be reversed, pointing to a previously unknown mechanism for epigenetic regulation on the level of RNA.

As of 2012, 12,000 methylation sites were revealed on mRNA. The m6A mark has been found in the nematode Caenorhabditis elegans, the algae Chlamydomonas, and the fruit fly Drosophila, with papers published on these works in 2015 by Dr. He and his associates. Also published in 2015, m6A has been found to be regulated by miRNAs, and this regulates cell pluripotency. Dr. He and colleagues also published a 2016 article in which they reported on a new RNA modification site: N1-methyladenosine (m¹A).

What are the cellular functions and roles for a mark such as m6A and the epigenetic mechanism of RNA methylation. That is the subject discussed in these reviews. Multiple studies have analyzed the molecular roles of RNA methylation and RNA methyltransferases, but one study has analyzed the role of an RNA methyltransferase in regulating microRNA processing that then affects the invasiveness of MDA-MB-231 triple-negative breast cancer cells. Another review gives an overview of the diverse roles of RNA methyltransferases specifically involving m6A and 5-methylcytidine (m5C) in development and pathology.

When Dr. He and his group began working on this, more than 100 marks were known to exist on RNA, and the list keeps growing. There is a very handy resource called MODOMICS that is a database with a wide berth of information on RNA modifications, including sequences, pathways involved, and protein interactions. With such an abundance of RNA modifications to analyze and so many functions to explore from the molecular level through to the cellular and disease models, it’s no wonder that scientists are digging into this awakening field—or proverbial golden mountain.

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Mike has a Ph.D. in Biomedical Sciences from the University of California, Riverside, a M.S. in Cell and Molecular Biology from San Francisco State University, and a B.A. in English from the University of California, Berkeley.

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