Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA774874 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: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 18S rRNA and 73 sites in 25S 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 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.
2021-12-03 | GSE186634 | GEO
Project description: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.
| S-EPMC9045821 | biostudies-literature
Project description:Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling
| PRJEB48183 | ENA
Project description:Synthesized DNA with unnatural nucleotides Synthetic Genomics
| PRJNA89669 | ENA
Project description:Transcriptome-wide methodology is developed to capture and sequence decay intermediates deriving from direct NMD targets. Results demonstrate that mammalian-cell NMD generates decay intermediates in a process that involves the covalent addition of nontemplated U, C, G and A nucleotides to 3'-ends. Variations of this methodology demonstrate that these decay intermediates arise co-translationally.
2018-07-05 | GSE111818 | GEO
Project description:The effect of nucleotides on the intestinal microbiota of zebrafish
| PRJEB19156 | ENA
Project description:Complex multicellular organisms have evolved numerous cell types with many different functions. Comparative transcriptomic data yields valuable insights into cell type, tissue, and organ evolution. However, interpreting this data requires understanding how transcriptomes evolve. A particularly difficult problem is that cell type transcriptomes may not evolve independently, a key assumption of most evolutionary analyses. Non-independence of cell types can occur when cell types share regulatory mechanisms. This leads to concerted evolution in gene expression across different cell types, confounding efforts to unravel the history of cell type evolution, and identify cell type-specific patterns of expression. Here we present a statistical model to estimate the level of concerted transcriptome evolution and apply it to published and new data. The results indicate that tissues undergo pervasive concerted evolution in gene expression. Tissues related by morphology or developmental lineage exhibit higher levels of concerted evolution. Concerted evolution also causes tissues from the same species to be more similar in gene expression to each other than to homologous tissues in another species. This result may explain why some tissue transcriptomes cluster by species rather than homology. Our analysis of bird skin appendages data suggests levels of concerted evolution also varies with phylogenetic age of the tissue. Our study illustrates the importance of accounting for concerted evolution when interpreting comparative transcriptome data, and should serve as a foundation for future investigations of cell type evolution.
2017-10-13 | GSE89040 | GEO
Project description:Novel approaches were used to generate the DNA sequence information for the rhesus GeneChip (2005). The purpose of this experiment was to test its reliability and validity of the rhesus macaque GeneChip across different tissues and centers. Keywords: reliability To test the reliability of the rhesus GeneChip across different centers, RNA was isolated from five sources: cerebral cortex, pancreas, thymus, testis, and an immortalized fibroblast cell line. Aliquots of this RNA were sent to each of three centers: Yerkes National Primate Research Center, Oregon National Primate Research Center and the University of Nebraska Medical Center. Each center labeled the samples and hybridized them to two rhesus macaque GeneChips.
2010-06-11 | E-GEOD-7094 | biostudies-arrayexpress
Project description:NMD-degradome sequencing reveals ribosome-bound intermediates with 3'-end nontemplated nucleotides
| PRJNA438276 | ENA
Project description:Normal kidney, liver, spleen, and Universal RNA from Stratagene were expression profiled across five centers (UCLA, Duke, TGen, Children's National Medical Center in Washington, DC, and University of Pennsylvania) using the Affymetrix, spotted Operon, Agilent, and Amersham arrays to identify differences in expression between microarray platforms as well as centers. To compare the four microarray platforms as well as the reproducibility across the centers. There will be expression differences between the five centers. The following array types were profiled at the centers: UCLA: Affymetrix, Amersham, Agilent TGen: Affymetrix (3000 scanner) Children's: Affymetrix (2500 scanner) Duke: Operon Oligo University of Penn.: Affymetrix Series_author: Consortium,,Cross Platform Keywords: other. This dataset is part of the TransQST collection.
2004-11-24 | E-GEOD-2004 | biostudies-arrayexpress