Identification and Quantification of Modified Nucleosides in <i>Saccharomyces cerevisiae</i> mRNAs

Tardu, Mehmet; Jones, Joshua D.; Kennedy, Robert T.; Lin, Qishan; Koutmou, Kristin S.

doi:10.1021/acschembio.9b00369

Cited by 79 publications

(123 citation statements)

References 37 publications

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“…A volume of 4 ll (96 to 487 ng/ll) total RNA was used to evaluate levels of cm 5 U, mcm 5 U, and mcm 5 s 2 U, by LC-MS/MS using a similar method as described (Basanta-Sanchez et al, 2016;Tardu et al, 2019). Briefly, prior to UHPLC-MS analysis, each sample was mixed with 0.4 pg/ll of internal standard (IS), isotopically labeled guanosine, [ 13 C][ 15 N]-G. The enzymatic digestion was carried out using Nucleoside Digestion Mix (New England BioLabs) according to the manufacturer's instructions.…”

Section: Quantification and Analysis Of Trna Levelsmentioning

confidence: 99%

Translational offsetting as a mode of estrogen receptor α‐dependent regulation of gene expression

et al. 2019

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Estrogen receptor alpha (ERα) activity is associated with increased cancer cell proliferation. Studies aiming to understand the impact of ERα on cancer‐associated phenotypes have largely been limited to its transcriptional activity. Herein, we demonstrate that ERα coordinates its transcriptional output with selective modulation of mRNA translation. Importantly, translational perturbations caused by depletion of ERα largely manifest as “translational offsetting” of the transcriptome, whereby amounts of translated mRNAs and corresponding protein levels are maintained constant despite changes in mRNA abundance. Transcripts whose levels, but not polysome association, are reduced following ERα depletion lack features which limit translation efficiency including structured 5′UTRs and miRNA target sites. In contrast, mRNAs induced upon ERα depletion whose polysome association remains unaltered are enriched in codons requiring U34‐modified tRNAs for efficient decoding. Consistently, ERα regulates levels of U34‐modifying enzymes and thereby controls levels of U34‐modified tRNAs. These findings unravel a hitherto unprecedented mechanism of ERα‐dependent orchestration of transcriptional and translational programs that may be a pervasive mechanism of proteome maintenance in hormone‐dependent cancers.

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Section: Quantification and Analysis Of Trna Levelsmentioning

confidence: 99%

Translational offsetting as a mode of estrogen receptor α‐dependent regulation of gene expression

et al. 2019

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“…Analysis of mRNA modification abundances under different conditions may provide insight into modification‐mediated mechanisms activated by environmental stress or disease. Consistent with this possibility, both the abundances and distributions of mRNAs modifications are dependent on environmental conditions, cell‐type, disease, and organism (Table ; Carlile et al, ; Chu et al, ; X. Cui, Liang, et al, ; Duan et al, ; X. Li et al, ; Ma et al, ; S. Schwartz et al, ; Tardu et al, ; Zhou et al, ). Nucleoside methylations and acetylations exhibit the largest changes in mRNA modification abundance as a result of shifting cellular environments (Tardu et al, ).…”

Section: Current Quantitative Perspective On Mrna Modificationsmentioning

confidence: 86%

“…Consistent with this possibility, both the abundances and distributions of mRNAs modifications are dependent on environmental conditions, cell‐type, disease, and organism (Table ; Carlile et al, ; Chu et al, ; X. Cui, Liang, et al, ; Duan et al, ; X. Li et al, ; Ma et al, ; S. Schwartz et al, ; Tardu et al, ; Zhou et al, ). Nucleoside methylations and acetylations exhibit the largest changes in mRNA modification abundance as a result of shifting cellular environments (Tardu et al, ). In line with this observation, the metabolites used by enzymes to catalyze methyl‐ and acetyl‐ modifications (S‐adenosylmethionine and acetyl‐CoA) also fluctuate significantly in response to cellular conditions (Anstee & Day, ; Pietrocola, Galluzzi, Bravo‐San Pedro, Madeo, & Kroemer, ; L. Shi & Tu, ).…”

Section: Current Quantitative Perspective On Mrna Modificationsmentioning

confidence: 86%

“…Therefore, the heterogeneity of modification occupancy introduces challenges for interpreting data collected by these methods. The analysis of such data is further complicated by the fact that most enzymes that catalyze mRNA modification also catalyze the incorporation of the same functional groups into ncRNA species essential to protein translation (e.g., tRNAs, ribosomal RNA [rRNA]; Arango et al, ; X. Li et al, ; S. Schwartz et al, ; Tardu et al, ; Xu et al, ). Since translation and decay rates are coupled, these potential perturbations to the translation machinery can make complicate efforts to deconvolute the impacts of modifications on ncRNAs from those on mRNAs by these methods (Figure ; Presnyak et al, ; Radhakrishnan et al, ).…”

Section: Quantitative Approaches For Studying Mrna Modification Levelmentioning

confidence: 99%

“…Several modifications, Ψ, ac 4 C, Cm, and Gm, have abundances approaching those of m 6 A (Arango et al, ; X. Li et al, ; Tardu et al, ; You et al, ). These modifications have been less well studied than m 6 A, but their prevalence and localization in mRNA coding regions suggests that they might also play roles in regulating mRNA function (Arango et al, ; Carlile et al, ; X. Li et al, ; Lovejoy et al, ; Nakamoto, Lovejoy, Cygan, & Boothroyd, ; S. Schwartz et al, ; L. Sun et al, ; You et al, ).…”

Section: Current Quantitative Perspective On Mrna Modificationsmentioning

confidence: 99%

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A molecular‐level perspective on the frequency, distribution, and consequences of messenger RNA modifications

2020

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Cells use chemical modifications to alter the sterics, charge, and conformations of large biomolecules, modulating their biogenesis, function, and stability. Until recently post‐transcriptional RNA modifications were thought to be largely limited to nonprotein coding RNA species. However, this dogma has rapidly transformed with the discovery of a host of modifications in protein coding messenger RNAs (mRNAs). Recent advancements in genome‐wide sequencing technologies have enabled the identification of mRNA modifications as a potential new frontier in gene regulation—leading to the development of the epitranscriptome field. As a result, there has been a flurry of multiple groundbreaking discoveries, including new modifications, nucleoside modifying enzymes (“writers” and “erasers”), and RNA binding proteins that recognize chemical modifications (“readers”). These discoveries opened the door to understanding how post‐transcriptional mRNA modifications can modulate the mRNA lifecycle, and established a link between the epitranscriptome and human health and disease. Despite a rapidly growing recognition of their importance, fundamental questions regarding the identity, prevalence, and functional consequences of mRNA modifications remain to be answered. Here, we highlight quantitative studies that characterize mRNA modification abundance, frequency, and interactions with cellular machinery. As the field progresses, we see a need for the further integration of quantitative and reductionist approaches to complement transcriptome wide studies in order to establish a molecular‐level framework for understanding the consequences of mRNA chemical modifications on biological processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Processing > RNA Editing and Modification

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NAT10 Promotes Prostate Cancer Growth and Metastasis by Acetylating mRNAs of HMGA1 and KRT8

Li,

Hong,

et al. 2024

Advanced Science

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N4‐acetylcytidine (ac4C) is essential for the development and migration of tumor cells. According to earlier research, N‐acetyltransferase 10 (NAT10) can increase messenger RNAs (mRNAs) stability by catalyzing the synthesis of ac4C. However, little is known about NAT10 expression and its role in the acetylation modifications in prostate cancer (PCa). Thus, the biological function of NAT10 in PCa is investigated in this study. Compared to paraneoplastic tissues, the expression of NAT10 is significantly higher in PCa. The NAT10 expression is strongly correlated with the pathological grade, clinical stage, Gleason score, T‐stage, and N‐stage of PCa. NAT10 has the ability to advance the cell cycle and the epithelial‐mesenchymal transition (EMT), both of which raise the malignancy of tumor cells. Mechanistically, NAT10 enhance the stability of high mobility group AT‐hook 1 (HMGA1) by acetylating its mRNA, thereby promoting cell cycle progression to improve cell proliferation. In addition, NAT10 improve the stability of Keratin 8 (KRT8) by acetylating its mRNA, which promotes the progression of EMT to improve cell migration. This findings provide a potential prognostic or therapeutic target for PCa.

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Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs

Cited by 79 publications

References 37 publications

Translational offsetting as a mode of estrogen receptor α‐dependent regulation of gene expression

Translational offsetting as a mode of estrogen receptor α‐dependent regulation of gene expression

A molecular‐level perspective on the frequency, distribution, and consequences of messenger RNA modifications

NAT10 Promotes Prostate Cancer Growth and Metastasis by Acetylating mRNAs of HMGA1 and KRT8

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