Rich diet marks messenger RNA molecules for degradation in old, conserved mechanism
The scheme determines the placement of methylation signatures like post-it notes at specific sites on a messenger RNA (mRNA) marking molecules for degradation, a new study on the microscopic model worm, Caenorhabditis elegans, reveals.
The results of this study carried out in collaboration by scientists from the University of Geneva (UNIGE), Switzerland and the Norwegian University of Science and Technology (NTNU) are published in an article entitled “Splice site m6Methylation prevents binding of U2AF35 to inhibit RNA splicing, ”in the journal Cell.
Methylation of RNA is essential. Previous studies show that mice without RNA methylation die at an early embryonic stage.
In this study, the laboratories of Ramesh Pillai, PhD, and Florian Steiner, PhD, professors in the molecular biology department of the Faculty of Sciences of UNIGE, showed for the first time that methylation at the end of the intron of a particular gene (S-adenosylmethionine synthetase or SAM synthetase), blocks the splicing machinery – the process that removes unnecessary non-coding sequences (introns) from the gene, leaving only the protein-coding sequences (exons) in a mature messenger RNA.
The intron of the SAM synthetase gene, whose immature mRNA is specifically methylated at the tail of the intron, cannot be removed and the functional protein cannot be produced.
“It is therefore a self-regulatory mechanism since the gene involved in the production of a key factor necessary for methylation is itself regulated by methylation!” explained Mateusz Mendel, researcher in the molecular biology department of the Faculty of Sciences of UNIGE and first author of this study.
This methylation of the methyl donor gene depends on the amount of nutrients in the diet of the worms.
“When nutrients are plentiful, mRNA is methylated, gene splicing is blocked and the level of methyl donors decreases, which limits the number of possible methylation reactions. On the other hand, when there are few nutrients, there is no methylation of the particular RNA of this gene, so the splicing is not blocked and the synthesis of the methyl donors increases, ”said Kamila Delaney, PhD, researcher in the department of molecule biology at the Faculty of Sciences of UNIGE.
SAM levels are highly regulated in living organisms. This is accomplished by regulating the RNA splicing of SAM synthetase. Under conditions of high SAM, the SAM synthetase pre-mRNA is methylated to directly inhibit splicing, intron retention, and mRNA decay. On the other hand, low levels of SAM stimulate splicing.
The authors showed that although mammalian pre-mRNA SAM synthetase is not regulated by this mechanism, inhibition of intron tail methylation splicing is retained in mammals. The researchers also showed that the modification works by physically preventing an essential component of the splicing machinery (U2AF35) from recognizing the back end of the intron splice site.
This study highlights the crucial role of methylation in the regulation of splicing, in particular in the response to changes in the environment, such as the availability of nutrients.