Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation

Abstract

Over 150 types of RNA modifications are identified in RNA molecules. Transcriptome profiling is one of the key steps in decoding the epitranscriptomic panorama of these chemical modifications and their potential functions. N 7-methylguanosine (m 7 G) is one of the most abundant modifications present in tRNA, rRNA and mRNA 5′cap, and has critical roles in regulating RNA processing, metabolism and function. Besides its presence at the cap position in mRNAs, m 7 G is also identified in internal mRNA regions. However, its transcriptome-wide distribution and dynamic regulation within internal mRNA regions remain unknown. Here, we have established m 7 G individual-nucleotide-resolution cross-linking and immunoprecipitation with sequencing (m 7 G miCLIP-seq) to specifically detect internal mRNA m 7 G modification. Using this approach, we revealed that m 7 G is enriched at the 5′UTR region and AG-rich contexts, a feature that is well-conserved across different human/mouse cell lines and mouse tissues. Strikingly, the internal m 7 G modification is dynamically regulated under both H 2 O 2 and heat shock treatments, with remarkable accumulations in the CDS and 3′UTR regions, and functions in promoting mRNA translation efficiency. Consistently, a PCNA 3′UTR minigene reporter harboring the native m 7 G modification site displays both enriched m 7 G modification and increased mRNA translation upon H 2 O 2 treatment compared to the m 7 G site-mutated minigene reporter (G to A). Taken together, our findings unravel the dynamic profiles of internal mRNA m 7 G methylome and highlight m 7 G as a novel epitranscriptomic marker with regulatory roles in translation.

The emerging role of RNA modifications in the regulation of mRNA stability

“…Finally, the presence of internal N 7methylguanosine (m 7 G) in mRNA is known to promote translation. The positive charge of internal m 7 G may affect the RNA secondary structure and thereby affect the mRNA stability 105,106 .…”

Mapping the epigenetic modifications of DNA and RNA

“…m 7 G is a well-known mRNA cap modification. It is also prevalent in tRNA and recently has been identified in mRNA as well (Chu et al, 2018 ; Malbec et al, 2019 ; Zhang et al, 2019a ). METTL1-WDR4, known as a tRNA m 7 G methyltransferase complex, installs a subset of internal m 7 G in mRNA (Fig.…”

“…m 7 G-MeRIP-Seq used m 7 G-specific antibody to identified over 2,000 internal m 7 G peaks in the mammalian transcriptome (Zhang et al, 2019a ). m 7 G miCLIP-Seq utilized cross-linking-induced truncation and mutation to detect m 7 G (Malbec et al, 2019 ). m 7 G-Seq adopted a reduction-induced depurination reaction to generate a basic site at m 7 G positions, which can be further labeled with biotin and subsequently pulled down.…”

“…The labeled m 7 G sites in RNA can cause misincorporation during RT, thus achieving the base-resolution map of m 7 G methylome (Zhang et al, 2019a ). Benefiting from high-throughput detection strategies, two groups independently found that internal m 7 G in mRNA plays regulatory roles in translation (Malbec et al, 2019 ; Zhang et al, 2019a ). Considering that METTL1-modified m 7 G in tRNA is also required for translation and modification enzymes are shared between mRNA and tRNA (Lin et al, 2018 ), it would be interesting to separately probe its function in mRNA.…”

N6-methyladenosine (m6A) methylation in ischemia–reperfusion injury

“…RNA methylation accounts for over 60% of all RNA modifications 12,13 . Methylation modifications have been identified on all four ribonucleotides (A, U, C, and G) including N6-methyladenosine (m 6 A), 5methylcytosine (m 5 C) 14 , 3-methyluracil (m 3 U) 15 , N7methylguanosine (m 7 G) 16 , and so on. Among them, m 6 A methylation is the most common type of RNA methylation in mRNA 17 .…”