Eukaryotic 5-methylcytosine (m5C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease

Bohnsack, Katherine E.; Höbartner, Claudia; Bohnsack, Markus T.

doi:10.3390/genes10020102

Cited by 329 publications

(335 citation statements)

References 88 publications

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“…They have mostly been characterised as either targeting tRNA (NSUN2, 3 and 6; TRDMT1) or rRNA (NSUN1, 4 and 5) (Sibbritt et al 2013;Bohnsack et al 2019). Despite their seemingly 'housekeeping' functions, these MTases display complex expression patterns during development and disease, especially in cancer, and mutations in several of them cause human genetic disease (Chi and Delgado-Olguin 2013;Blanco and Frye 2014;Begik et al 2019;Bohnsack et al 2019). One explanation for their complex biology might be that these MTases modify additional substrates outside of the tRNA and rRNA realm.…”

Section: Introductionmentioning

confidence: 99%

Multiple links between 5-methylcytosine content of mRNA and translation

Schümann

Zhang²,

Sibbritt

et al. 2020

Preprint

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Abstract5-methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. We obtained ∼1,000 candidate m5C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m5C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m5C sites in mRNAs are enriched in 5’UTRs and near start codons, and are commonly embedded in a local context reminiscent of the NSUN2-dependent m5C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association. Altogether, these findings emphasise the major role of NSUN2 in making this mark transcriptome-wide and further substantiate a functional interdependence of cytosine methylation level with mRNA translation.

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Section: Introductionmentioning

confidence: 99%

Multiple links between 5-methylcytosine content of mRNA and translation

Schümann

Zhang²,

Sibbritt

et al. 2020

Preprint

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“…Surprisingly, we detected that the amount of 5‐methylcytosine (5mC) signal increased by 20% in KD morulae (Figure A,B). The increase in 5mC may be attributed by the aberrant conversion to 5‐hydroxymethylcytosine (5hmC) by Tet (ten‐eleven translocation methyl‐cytosine dioxygenase) family enzymes . However, we found there is no significant change in 5hmC signal intensity (Figure A,B).…”

Section: Resultsmentioning

confidence: 65%

“…The increase in 5mC may be attributed by the aberrant conversion to 5-hydroxymethylcytosine (5hmC) by Tet (ten-eleven translocation methyl-cytosine dioxygenase) family enzymes. 11 However, we found there is no significant change in 5hmC signal intensity ( Figure 6A,B). Chromatin architecture undergoes extensive reprogramming after fertilization.…”

Section: Dna Methylation In Morulaementioning

confidence: 64%

“…1 Nucleolar protein 2 belongs to the NOL1/NOP2/SUN domain (NSUN) family of proteins, which all have enzymatic activity in catalyzing C5 methylation of RNA cytosine (m 5 C), an abundant RNA modification. 11 In yeast, NOP2 has been identified as a 25S rRNA methyltransferase at C2870 position, 12 and is required for the synthesis of the large subunit of the ribosome. 13 Interestingly, the presence of NOP2 rather than its m 5 C modification activity is required for rRNA processing.…”

Section: Introductionmentioning

confidence: 99%

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The nucleolar protein NOP2 is required for nucleolar maturation and ribosome biogenesis during preimplantation development in mammals

Wang

et al. 2019

FASEB j.

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The maternal nucleolus plays an indispensable role in zygotic genome activation (ZGA) and early embryonic development in mice. During oocyte-to-embryo transition, the nucleolus is subject to substantial transformation. Despite the primary role of the nucleolus is ribosome biogenesis, accumulating evidence has uncovered its functions in various other cell processes. However, the regulation of nucleolar maturation and ribosome biogenesis and the molecules involved remain unclear during early embryonic development. In this study, we observed that nucleolar protein 2 (NOP2) is restrictedly localized within the nucleolus, first detected in the late two-cell embryos, and increases to a peak level at the eight-cell stage in mice. RNAi-mediated NOP2 depletion leads to a developmental arrest during the morula-to-blastocyst transition. RNA-seq analyses reveal that 208 genes are differentially expressed, including multiple lineage-specific genes and several genes encoding ribosome proteins.Indeed, we observe a failure of the first lineage specification with reduced TEA domain transcription factor 4(TEAD4) (trophectoderm-specific), tir na nog (NANOG), and kruppel-like factor 4 (KLF4) (inner cell mass-specific). Importantly, by Transm ission Electron Microscopy (TEM), we noted a decrease in the ratio of the nucleolus size and an increase in the ratio of the size of the nucleolus precursor body, suggesting the nucleolar maturation is disrupted. Moreover, both qPCR and Fluorescence I n Situ Hybridization (FISH) data showcase a significant decrease in the abundance of ribosome RNAs. Similarly, NOP2 depletion causes reduced developmental potential and decreased rRNA level in bovine early embryos, suggesting a functional 2716 |

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“…In eukaryotes, m 5 C is present in a wide variety of RNA species, including tRNA, rRNA, mRNA, and viral RNA (17-20) ( Figure 1A). m 5 C is introduced by the NOL1/NOP2/SUN domain (NSUN) family of enzymes, as well as by DNMT2 (21).…”

Section: Introductionmentioning

confidence: 99%

Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs

Shinoda

Kitagawa

Nakagawa

et al. 2019

Preprint

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Post-transcriptional modifications in mitochondrial tRNAs (mt-tRNAs) play critical roles in mitochondrial protein synthesis, which produces respiratory chain complexes. In this study, we used mass spectrometric analysis to map 5-methylcytidine (m 5 C) at positions 48-50 in eight mouse and six human mt-tRNAs. We also confirmed the absence of m 5 C in mt-tRNAs isolated from Nsun2 knockout (KO) mice, as well as from NSUN2 KO human culture cells. In addition, we successfully reconstituted m 5 C at positions 48-50 of mt-tRNA in vitro with NSUN2 protein in the presence of S-adenosylmethionine (SAM).Although NSUN2 is predominantly localized to the nucleus and introduces m 5 C into cytoplasmic tRNAs and mRNAs, structured illumination microscopy (SIM) clearly revealed NSUN2 foci inside mitochondria. These observations provide novel insights into the role of NSUN2 in the physiology and pathology of mitochondrial functions.

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Eukaryotic 5-methylcytosine (m5C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease

Cited by 329 publications

References 88 publications

Multiple links between 5-methylcytosine content of mRNA and translation

Multiple links between 5-methylcytosine content of mRNA and translation

The nucleolar protein NOP2 is required for nucleolar maturation and ribosome biogenesis during preimplantation development in mammals

Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs

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