A Chemical Signature for Cytidine Acetylation in RNA

Thomas, Justin M.; Briney, Chloe A.; Nance, Kellie D.; Lopez, Jeffrey E.; Thorpe, Abigail L.; Fox, Stephen D.; Bortolin-Cavaillé, Marie-Line; Sas‐Chen, Aldema; Arango, Daniel; Oberdoerffer, Shalini; Cavaillé, Jérôme; Andrésson, Þorkell; Meier, Jordan L.

doi:10.1021/jacs.8b06636

Cited by 75 publications

(91 citation statements)

References 29 publications

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“…modifications and the presence of N 4 -actetylcytidines observed here is reminiscent of previous studies concerning two hyperthermophilic crenarchaea (Sulfolobus solfataricus and Pyrodictium occultum) 30,31 . In order to confirm the positions of ac 4 C in the 16S rRNA sequence, we performed reverse transcription mapping on borohydride-reduced 16S rRNA as described 32 ( Fig. 2b and Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

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Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

et al. 2020

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Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA i Met. Here, we determine the cryo-EM structure of a 30S: mRNA:aIF1A:aIF2:GTP:Met-tRNA i Met complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N 4-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.

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Section: Resultsmentioning

confidence: 99%

“…16S rRNA was prepared from purified P. abyssi 30S subunits 12 using a standard phenol-ether extraction protocol. 16S rRNA reduction was performed as described 32 . Totally, 3 µg of rRNA was incubated with either sodium borohydride (100 mM in H 2 O) or water (control sample) in a final reaction volume of 50 µL.…”

Section: Methodsmentioning

confidence: 99%

Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

et al. 2020

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“…The region surrounding the translation start site seems to be especially enriched with ac 4 C peaks. The study could have benefited from quantitative and single-nucleotide resolution mapping using a chemical approach that was recently described by some of the authors (Thomas et al, 2018).…”

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confidence: 99%

N4-acetylation of Cytidine in mRNA by NAT10 Regulates Stability and Translation

Dominissini

Rechavi

2018

Cell

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“…The discovery of ac 4 C and f 5 C in yeast mRNAs provides a rational motivation for the development of mapping methods (e.g. based on tools such as those developed in the Meier lab (Sinclair et al 2017;Thomas et al 2018)) and transcriptome-wide localization studies of these modifications. More broadly, our findings demonstrate the power of quantitative UHPLC-MS/MS as a tool for mRNA modification discovery.…”

Section: Resultsmentioning

confidence: 99%

Identification and quantification of modified nucleosides inSaccharomyces cerevisiaemRNAs

Tardu

Lin

Koutmou

2018

Preprint

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Shortened title: mRNA modification quantification and discovery by UHPLC-MS/MSABSTRACT Post-transcriptional nucleoside modifications have long been recognized as key modulators of non-coding RNA structure and function. There is an emerging appreciation that the chemical modification of protein-coding messenger RNAs (mRNAs) also plays critical roles in the cell. Although there are over 100 known RNA modifications found in biology only a handful have been identified in mRNAs. We sought to identify and quantify modifications present in the mRNAs of yeast cells using a high throughput ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method that measures the levels of 36 types of RNA nucleosides in parallel. We detected the presence of six modified nucleosides in mRNAs at relatively high abundances: N7methylguanosine, N6-methyladenosine, 2'-O-methylguanosine, 2'-O-methylcytosine, N4acetylcytidine and 5-formylcytidine. Additionally, we investigated how the levels of mRNA modifications vary in response to cellular stress. We find that the concentrations of mRNA modifications including N6-methyladenosine and N4-acetylcytidine change in response to heat stress, glucose starvation and/or oxidative stress. This work expands the repertoire of potential chemical modifications in mRNAs, and utilizes a high-throughput approach to search for modifications that highlights the value of integrating massspectrometry tools in the mRNA modification discovery and characterization pipeline.

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A Chemical Signature for Cytidine Acetylation in RNA

Cited by 75 publications

References 29 publications

Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

N4-acetylation of Cytidine in mRNA by NAT10 Regulates Stability and Translation

Identification and quantification of modified nucleosides inSaccharomyces cerevisiaemRNAs

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