Bailey et al. 2021 (PRJNA774874)
General Details
| Title | Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling |
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| Organism | |
| Number of Samples | 33 |
| Release Date | 2021/10/26 00:00 |
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| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP343289 |
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| ENA | SRP343289 |
| GEO | |
| BioProject | PRJNA774874 |
Publication
| Title | |
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| Authors | Bailey AD,Talkish J,Ding H,Igel H,Duran A,Mantripragada S,Paten B,Ares M |
| Journal | eLife |
| Publication Date | 2022 Apr 6 |
| Abstract | Nucleotides in RNA and DNA are chemically modified by numerous enzymes that alter their function. Eukaryotic ribosomal RNA (rRNA) is modified at more than 100 locations, particularly at highly conserved and functionally important nucleotides. During ribosome biogenesis, modifications are added at various stages of assembly. The existence of differently modified classes of ribosomes in normal cells is unknown because no method exists to simultaneously evaluate the modification status at all sites within a single rRNA molecule. Using a combination of yeast genetics and nanopore direct RNA sequencing, we developed a reliable method to track the modification status of single rRNA molecules at 37 sites in 18 S rRNA and 73 sites in 25 S rRNA. We use our method to characterize patterns of modification heterogeneity and identify concerted modification of nucleotides found near functional centers of the ribosome. Distinct, undermodified subpopulations of rRNAs accumulate upon loss of Dbp3 or Prp43 RNA helicases, suggesting overlapping roles in ribosome biogenesis. Modification profiles are surprisingly resistant to change in response to many genetic and acute environmental conditions that affect translation, ribosome biogenesis, and pre-mRNA splicing. The ability to capture single-molecule RNA modification profiles provides new insights into the roles of nucleotide modifications in RNA function. © 2022, Bailey et al. |
| PMC | PMC9045821 |
| PMID | 35384842 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR16584057 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA |  |
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| SRR16584066 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | Cycloheximide | |
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| SRR16584067 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584068 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584069 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584070 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584071 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584072 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584073 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584074 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584075 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584076 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584077 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584078 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584079 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584080 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584081 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584082 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584083 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584084 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584085 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584086 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584087 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584088 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584089 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584058 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584059 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584060 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584061 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584062 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584063 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584064 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| SRR16584065 | PRJNA774874 | Saccharomyces cerevisiae | ribosomal RNA | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
ⓘ For more Information on the columns shown here see: About