Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5′ termini

Toczydłowska-Socha, Diana; Zielinska, Magdalena M.; Kurkowska, Małgorzata; Astha,; Almeida, Catarina; Stefaniak, Filip; Purta, Elżbieta; Bujnicki, Janusz

doi:10.1098/rstb.2018.0161

Cited by 20 publications

(21 citation statements)

References 48 publications

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“…Indeed, CMTR1 has reduced activity on mRNAs with highly structured 5= UTRs and, as such, these structured 5= UTRs may require unwinding by the helicase DHX15 for methylation by CMTR1. Interestingly, DHX15 activity is increased by CMTR1 binding (41,48). Therefore, CMTR1 likely acts in concert with DHX15 to regulate the expression of certain ISGs.…”

Section: Discussionmentioning

confidence: 99%

The mRNA Cap 2′- O -Methyltransferase CMTR1 Regulates the Expression of Certain Interferon-Stimulated Genes

Williams

Gokhale

Snider

et al. 2020

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Type I interferons (IFN) initiate an antiviral state through a signal transduction cascade that leads to the induction of hundreds of IFN-stimulated genes (ISGs) to restrict viral infection. Recently, RNA modifications on both host and viral RNAs have been described as regulators of infection. However, the impact of host mRNA cap modifications on the IFN response and how this regulates viral infection are unknown. Here, we reveal that CMTR1, an ISG that catalyzes 2′-O-methylation of the first transcribed nucleotide in cellular mRNA (Cap 1), promotes the protein expression of specific ISGs that contribute to the antiviral response. Depletion of CMTR1 reduces the IFN-induced protein levels of ISG15, MX1, and IFITM1, without affecting their transcript abundance. However, CMTR1 depletion does not significantly affect the IFN-induced protein or transcript abundance of IFIT1 and IFIT3. Importantly, knockdown of IFIT1, which acts with IFIT3 to inhibit the translation of RNAs lacking Cap 1 2′-O-methylation, restores protein expression of ISG15, MX1, and IFITM1 in cells depleted of CMTR1. Finally, we found that CMTR1 plays a role in restricting RNA virus replication, likely by ensuring the expression of specific antiviral ISGs. Taken together, these data reveal that CMTR1 is required to establish an antiviral state by ensuring the protein expression of a subset of ISGs during the type I IFN response. IMPORTANCE Induction of an efficient type I IFN response is important to control viral infection. We show that the host 2′-O-methyltransferase CMTR1 facilitates the protein expression of ISGs in human cells by preventing IFIT1 from inhibiting the translation of those mRNAs lacking cap 2′-O-methylation. Thus, CMTR1 promotes the IFN-mediated antiviral response.

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Section: Discussionmentioning

confidence: 99%

The mRNA Cap 2′- O -Methyltransferase CMTR1 Regulates the Expression of Certain Interferon-Stimulated Genes

Williams

Gokhale

Snider

et al. 2020

mSphere

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“…Alternatively, the non-CMTR1 regulated ISG IFIT3 may only have low levels of Cap 1, and so it may not be as sensitive to changes in CMTR1 and resulting decrease in Cap 1 levels that would enable IFIT1 sensing and translational inhibition. Indeed, CMTR1 has reduced activity on mRNAs with highly structured 5’ UTRs and as such these structured 5’ UTRs require unwinding by the helicase DHX15 helicase for efficient Cap 1 formation (41, 48). Finally, it is possible that CMTR1 depletion preferentially affects the levels of Cap 1 in ISGs with highly structured 5’ UTRs which are not efficiently 2’O methylated, thereby specifically resulting in reduced translation of these transcripts following CMTR1 depletion.…”

Section: Discussionmentioning

confidence: 99%

The mRNA cap 2’O methyltransferase CMTR1 regulates the expression of certain interferon-stimulated genes

Williams

Gokhale

Snider

et al. 2020

Preprint

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AbstractType I interferons (IFN) initiate an antiviral state through a signal transduction cascade that leads to the induction of hundreds of IFN-stimulated genes (ISGs) to restrict viral infection. Recently, RNA modifications on both host and viral RNAs have been described as regulators of infection. However, the impact of host mRNA cap modifications on the IFN response and how this regulates viral infection is unknown. Here, we reveal that CMTR1, an ISG that catalyzes 2’O methylation of the first transcribed nucleotide in cellular mRNA (Cap 1), promotes the protein expression of specific ISGs that contribute to the antiviral response. Depletion of CMTR1 reduces the IFN-induced protein levels of ISG15, MX1, and IFITM1, without affecting their transcript abundance. However, CMTR1 depletion does not significantly affect the IFN-induced protein or transcript abundance of IFIT1 and IFIT3. Importantly, knockdown of IFIT1, which acts with IFIT3 to inhibit the translation of RNAs lacking Cap 1 2’O methylation, restores protein expression of ISG15, MX1, and IFITM1 in cells depleted of CMTR1. Finally, we found that CMTR1 plays a role in restricting RNA virus replication, likely by ensuring the expression of specific antiviral ISGs. Taken together, these data reveal that CMTR1 is required to establish an antiviral state by ensuring the protein expression of a subset of ISGs during the type I IFN response.ImportanceInduction of an efficient type I IFN response is important to control viral infection. We show that the host 2’O methyltransferase CMTR1 facilitates the protein expression of ISGs in human cells by preventing IFIT1 from inhibiting the translation of these mRNAs lacking cap 2’O methylation. Thus, CMTR1 promotes the IFN-mediated antiviral response.

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“…We observed no statistically significant difference between any two of these three samples in the relative expression of any enzyme examined ( Supplementary Figure S12 ), suggesting that the differences in the level of m 7 Gpppm 6 A cap are likely due to other factors. We speculate that two such factors are secondary structure of 5’ ends of mRNAs (69) and helicase activity that is critical for CMTR1-mediated 2’- O -methylation of cap 1 in mRNAs harboring highly structured 5’ ends (70). Further studies are needed to fully address this question.…”

Section: Discussionmentioning

confidence: 99%

Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA

Wang

Chew

Lai

et al. 2019

Preprint

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6 7 Chemical modification of transcripts with 5' caps occurs in all organisms. Here we report a 8 systems-level mass spectrometry-based technique, CapQuant, for quantitative analysis of the 9 cap epitranscriptome in any organism. The method was piloted with 21 canonical caps -10 m 7 GpppN, m 7 GpppNm, GpppN, GpppNm, and m 2,2,7 GpppG -and 5 "metabolite" caps -NAD, 11 FAD, UDP-Glc, UDP-GlcNAc, and dpCoA. Applying CapQuant to RNA from purified dengue 12 virus, Escherichia coli, yeast, mice, and humans, we discovered four new cap structures in 13 humans and mice (FAD, UDP-Glc, UDP-GlcNAc, and m 7 Gpppm 6 A), cell-and tissue-specific 14 variations in cap methylation, and surprisingly high proportions of caps lacking 2'-O-methylation, 15 such as m 7 Gpppm 6 A in mammals and m 7 GpppA in dengue virus, and we did not detect cap 16 m 1 A/m 1 Am in humans. CapQuant accurately captured the preference for purine nucleotides at 17 eukaryotic transcription start sites and the correlation between metabolite levels and metabolite 18 caps. The mystery around cap m 1 A/m 1 Am analysis remains unresolved. 19 20 21 cap structure involves -phosphate methylation of unprocessed 5'-triphosphate (mPPPN) on 1 small RNAs such as mammalian U6 and 7SK, mouse B2, and plant U3 RNAs (7). 2 A variety of non-canonical caps involving nucleotide metabolites (Figure 1A) have also recently 3 been described (8,9). For example, nicotinamide adenine dinucleotide (NAD) and coenzyme A 4 (CoA) were found as cap-like structures in bacterial small RNAs (10) and the NAD cap was also 5 found in yeast and human mRNA and non-coding RNAs (11). Julius and Yuzenkova expanded 6 the potential repertoire of caps by demonstrating that a variety of nucleotide metabolites could 7 initiate transcription by bacterial RNA polymerase (RNA Pol) in vitro, including flavin adenine 8 dinucleotide (FAD), uridine diphosphate glucose (UDP-Glc), and uridine diphosphate N-9 acetylglucosamine (UDP-GlcNAc) (9). They also showed that capping with NAD and UDP 10 analogs by bacterial RNA Pol is promoter-specific and stimulates promoter escape (9), 11 suggesting a role for metabolite caps in regulating gene expression. For example, the NAD cap 12 has been shown to influence RNA stability and turnover, and is a substrate for decapping 13 enzymes (11). However, the lack of sensitive and specific analytical methods has hindered the 14 systematic study of the cap landscape dynamics in cells. 15Analysis of RNA cap structures has traditionally relied on radioisotope labeling and enzymatic 16 hydrolysis, followed by thin-layer and other types of chromatography to resolve cap structures 17 (12)(13)(14). While sensitive, the radiolabeling approach lacks specificity (12) and has the potential 18 to create cellular toxicity artifacts (15,16). While two-dimensional electrophoresis (14) allows 19 multiple caps analysis, it (i) lacks specificity for identifying intact cap structures, (ii) is limited to 20 NpppN caps, (iii) does not provide absolute quantification, and (iv) is semi-quantitative at b...

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Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5′ termini

Cited by 20 publications

References 48 publications

The mRNA Cap 2′- O -Methyltransferase CMTR1 Regulates the Expression of Certain Interferon-Stimulated Genes

The mRNA Cap 2′- O -Methyltransferase CMTR1 Regulates the Expression of Certain Interferon-Stimulated Genes

The mRNA cap 2’O methyltransferase CMTR1 regulates the expression of certain interferon-stimulated genes

Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA

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