Beyond the epigenome and into the epitranscriptome

Transcriptome-wide mapping of the modified base N6-methyladenosine in RNA joins discoveries of methyl-binding proteins and demethylating enzymes to herald the field of ‘epitranscriptomics’ – dynamic post-transcriptional regulation of mRNA analogous to the better known reversible epigenetic modifications of DNA and histone proteins.

HFSP Long-Term Fellow Dan Dominissini and colleagues
authored on Tue, 10 February 2015

HFSP Long-Term Fellow Dan Dominissini was awarded the 2014 Science & SciLifeLab prize in the genomics and proteomics category for his work on RNA methylation. The prize, a joint enterprise of Science magazine and SciLifeLab, the Swedish national center for molecular biosciences, is awarded annually to four young scientists for their outstanding contribution to the life sciences.

This year’s award recognized the emerging field of epitranscriptomics. Namely, that an extensive and dynamic repertoire of chemical groups decorates RNA to expand its 4-letter vocabulary, thereby helping it fulfill its many roles in a variety of biological processes. To date, well over a hundred nucleotide modifications have been identified in diverse types of RNA molecules; every position of pyrimidine and purine rings can be post-transcriptionally modified, with methylation predominating. RNA thus joins both DNA and proteins in being subject to dynamic and reversible chemical modifications. But unlike the latter two, the functions of RNA modifications and their molecular underpinnings are far from understood.  

Figure: Post-transcriptional regulation of RNA by reversible adenosine methylation. Human and mouse mRNA transcripts are punctuated by m6A at specific, highly conserved, discrete locations: around stop codons, within long internal exons, and at transcription start sites (A). Methylation, a dynamic modification, is installed by a nuclear methyltransferase complex (writers)—composed of METTL3, METTL14, and WTAP—and removed by at least 2 demethylases (erasers), ALKBH5 and FTO. Methyl-specific binding proteins (readers), primarily of the YTH-domain family, bind to modified transcripts and mediate the effect (B).

One such prevalent and essential modification is methylation of the N6 position of adenosine to create N6-methyladenosine (m6A). A newly developed approach for detection of m6A positions, called m6A-seq, enabled the first transcriptome-wide glimpse of the human and mouse methylomes. It revealed that methylation non-randomly punctuates thousands of positions along most expressed transcripts to form a unique pattern that is also remarkably conserved along evolution:  m6A is strongly enriched around stop codons, within unusually long internal exons and at transcription start sites.

Analysis of this pattern in relation to other transcript processing levels exposed its control over transcript stability and splicing patterns, and the dynamic nature of its deposition under changing physiological conditions. The parallel discoveries of two specific m6A demethylases, FTO and ALKBH5, underscored the dynamic nature of this modification. The work further illuminated a mechanism through which methyl groups exert their influence over RNA metabolism. Much like the seminal discovery of proteins that bind 5-methylcytosine in DNA - a family of proteins found in all eukaryotes (the YTH-domain family of RNA binding proteins), but of hitherto unknown function, was shown to specifically bind m6A in RNA.

The distinct topology and conservation of m6A sites, in conjunction with its dynamic deposition, control over transcript stability and splicing patterns, and existence of specific binding proteins – all point to a novel and fundamental role in regulation of gene expression. Uncovering the m6A methylome opens new avenues for correlating methylation with other transcript processing levels. This approach is a forerunner that has since spawned many studies by a growing number of groups around the world. It provides reference and paves the way for uncovering of other RNA modifications, together constituting a new realm of regulation, recently coined epitranscriptomics.

Reference

Genomics and Proteomics. Roadmap to the epitranscriptome. D. Dominissini, Science 346, 1192 (2014).

Pubmed link