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Yi C and Pan T  (2011) Cellular dynamics of RNA modification. Acc Chem Res 44(12):1380-8

Abstract: Five decades of research have identified more than 100 ribonucleosides that are post-transcriptionally modified. Many modified nucleosides are conserved throughout bacteria, archaea, and eukaryotes, while some are unique to each branch of life. However, the cellular and functional dynamics of RNA modification remain largely unexplored, mostly because of the lack of functional hypotheses and experimental methods for quantification and large-scale analysis. Many RNA modifications are not essential for life, which parallels the observation that many well-characterized protein and DNA modifications are not essential for life. Instead, increasing evidence indicates that RNA modifications can play regulatory roles in cells, especially in response to stress conditions. In this Account, we review some examples of RNA modification that are dynamically controlled in cells. We also discuss some recently developed methods that have enhanced the ability to study the cellular dynamics of RNA modification. We discuss four specific examples of RNA modification in detail here. We begin with 4-thio uridine (s(4)U), which can act as a cellular sensor of near-UV light. Then we consider queuosine (Q), which is a potential biomarker for malignancy. Next we examine N(6)-methyl adenine (m(6)A), which is the prevalent modification in eukaryotic messenger RNAs (mRNAs). Finally, we discuss pseudouridine (?), which is inducible by nutrient deprivation. We then consider two recent technical advances that have stimulated the study of the cellular dynamics in modified ribonucleosides. The first is a genome-wide method that combines primer extension with a microarray. It was used to study the N(1)-methyl adenine (m(1)A) hypomodification in human transfer RNA (tRNA). The second is a quantitative mass spectrometric method used to investigate dynamic changes in a wide range of tRNA modifications under stress conditions in yeast. In addition, we discuss potential mechanisms that control dynamic regulation of RNA modifications as well as hypotheses for discovering potential RNA demodification enzymes. We conclude by highlighting the need to develop new tools and to generate additional hypotheses for how these modifications function in cells. The study of the cellular dynamics of modified RNA remains a largely open area for new development, which underscores the rich potential for important advances as researchers drive this emerging field to the next level.

Status: Published Type: Journal Article PubMed ID: 21615108

Topics addressed in this paper

Number of different genes curated to this paper: 48

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Topics Genes linked to topics (#1 - 10 )
GCD1 GCD11 GCD2 GCD6 GCD7 GCN3 IME1 IME2 IME4 PUS1
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Topics Genes linked to topics (#11 - 20 )
PUS7 SNR81 SOE1 SUI2 SUI3 SUP11 SUP2 SUP3 SUP4 SUP5
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Topics Genes linked to topics (#21 - 30 )
SUP6 SUP7 SUP8 tE(UUC)B tE(UUC)C tE(UUC)E1 tE(UUC)E2 tE(UUC)E3 tE(UUC)G2 tE(UUC)G3
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Jump to Summary Chart for:
  • To find other papers on a gene and topic, click on the colored ball in the appropriate box.
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  • To go to the Locus page for a gene, click on the gene name.

Topics Genes linked to topics (#31 - 40 )
tE(UUC)I tE(UUC)J tE(UUC)K tE(UUC)L tE(UUC)M tE(UUC)P tR(UCU)B tR(UCU)D tR(UCU)E tR(UCU)G1
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Topics Genes linked to topics (#41 - 48 )
tR(UCU)G2 tR(UCU)G3 tR(UCU)J1 tR(UCU)J2 tR(UCU)K tR(UCU)M1 tR(UCU)M2 TRM9
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