METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation

Abstract

Summary 7-methylguanosine (m7G) is present at mRNA caps and at defined internal positions within tRNAs and rRNAs. However, its detection within low-abundance mRNAs and microRNAs (miRNAs) has been hampered by a lack of sensitive detection strategies. Here, we adapt a chemical reactivity assay to detect internal m7G in miRNAs. Using this technique (Borohydride Reduction sequencing [BoRed-seq]) alongside RNA immunoprecipitation, we identify m7G within a subset of miRNAs that inhibit cell migration. We show that the METTL1 methyltransferase mediates m7G methylation within miRNAs and that this enzyme regulates cell migration via its catalytic activity. Using refined mass spectrometry methods, we map m7G to a single guanosine within the let-7e-5p miRNA. We show that METTL1-mediated methylation augments let-7 miRNA processing by disrupting an inhibitory secondary structure within the primary miRNA transcript (pri-miRNA). These results identify METTL1-dependent N7-methylation of guanosine as a new RNA modification pathway that regulates miRNA structure, biogenesis, and cell migration.

Visualizing a protonated RNA state that modulates microRNA-21 maturation

“…Here, by integrating structural, dynamic, and functional analyses on miR-21 precursor, we showed that the intrinsic conformational plasticity of miRNA processing intermediates can serve as a new layer of regulation for miRNA biogenesis. Often, structural changes in pri-/pre-miRNAs can be induced upon binding to protein regulators 23 , nucleotide modifications such as ADAR1-mediated adenine-to-inosine editing 24 and METTL1-mediated methylation 25 , and disease-linked mutations 26 . RNA structural motifs are also important factors in recognition by processing machineries for miRNA biogenesis, where altering primary and/or precursor structures of a target miRNA can further lead to altered biogenesis, inducing a change in physiological outcomes 3 .…”

“…that possess a UGU motif in the apical loops are preferentially processed by the Microprocessor 19,20 , pre-miRNAs encoding a two-nucleotide distance between the cleavage sites and the apical bulge/loop structures are more accurately processed by Dicer 21 , and miRNAs that feature stable basal stems in pri-miRNAs and flexible apical loops in pri-/pre-miRNAs are more efficiently processed by biogenesis machineries 22 . In addition, altering secondary structures and even primary sequences of pri-/pre-miRNAs via protein binding 23 , enzymatic-driven nucleotide modification 24,25 and disease-linked mutation 26 can further influence the outcome of miRNA biogenesis 3 . During these regulatory processes, it is often perceived that protein factors act on the largely passive primary and precursor miRNAs to direct their maturation outcome.…”

“…Even those clustered on the same primary transcript can be differentially processed in a tissue-specific manner 3-5 . Over the past decade, it has been shown that specific sequences and structures of primary and precursor miRNAs can be recognized by processing machineries and protein factors for regulation [16][17][18][19][20][21][22][23][24][25][26] . For example, pri-miRNAs…”

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

“…Here we identify two RMPs (TRDMT1 and METTL1) whose expression is significantly enriched in epididymis (Figure S3), one of which (TRDMT1) was recently shown to be involvedin the transmission of diet-induced paternal phenotypes across generations [53]. Whether METTL1 plays a role in intergenerational inheritance is yet to be deciphered; however, recent insights showing its role in miRNA maturation [58] suggest that this enzyme might be playing a role in miRNA-acquired inheritance of information.…”

“…We then investigated whether specific RMPs also showed increased expression patterns in epididymis, relative to other tissues ( Figure S3D). Our analysis identified two RMPs as epididymisenriched: (i) TRDMT1 -also known as DNMT2-, a N5-methyladenosine (m 5 C) methyltransferase modifying position 38 in specific tRNAs [57], and (ii) METTL1, a N7-methylguanosine (m 7 G) tRNA methyltransferase, which has been recently shown to act not only on tRNAs, but also on miRNAs, promoting their maturation [58]. Interestingly, TRDMT1 has been shown to play a major role in the transmission of paternal epigenetic information across generations [53]; however, whether METTL1 is involved in the transmission of such information is yet to be determined.…”