ArticleGenome biology2015
Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
46 citing papers in PubMed, 90 citations in OpenAlex.
- TRiC/CCT chaperonin governs RNA polymerase II activity in the nucleus to support RNA homeostasis.Molecular cell · 2026Article
- Transcriptional activity during seed imbibition is conserved, robust and required for germination.Nature communications · 2026Article
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
- StaggR: an interactive R/Shiny application for planning and visualizing staggered experimental protocols.F1000Research · 2025Article
- Multiple direct and indirect roles of the Paf1 complex in transcription elongation, splicing, and histone modifications.Cell reports · 2024Article
- Multiple direct and indirect roles of Paf1C in elongation, splicing, and histone post-translational modifications.bioRxiv : the preprint server for biology · 2024Article
- Post-transcriptional regulation shapes the transcriptome of quiescent budding yeast.Nucleic acids research · 2024Article
- Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain.RNA (New York, N.Y.) · 2024Article
- Transcriptome-Wide Analysis of mRNA Adenylation Status in Yeast Using Nanopore Sequencing.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Impact on splicing inRNA (New York, N.Y.) · 2023Article
- Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain.bioRxiv : the preprint server for biology · 2023Article
- The fission yeast methyl phosphate capping enzyme Bmc1 guides 2'-O-methylation of the U6 snRNA.Nucleic acids research · 2023Article
- Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells.Molecular cell · 2023Article
- Editorial: RNA machines.Frontiers in genetics · 2023Article
- Sequences and proteins that influence mRNA processing in Trypanosoma brucei: Evolutionary conservation of SR-domain and PTB protein functions.PLoS neglected tropical diseases · 2022Article
- Transcript-specific determinants of pre-mRNA splicing revealed through in vivo kinetic analyses of the 1Molecular cell · 2022Article
- Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment.BMC bioinformatics · 2022Article
- Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil.Methods in molecular biology (Clifton, N.J.) · 2022Article
- SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.BMC bioinformatics · 2021Article
- Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates.Genome research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundRNA levels detected at steady state are the consequence of multiple dynamic processes within the cell. In addition to synthesis and decay, transcripts undergo processing. Metabolic tagging with a nucleotide analog is one way of determining the relative contributions of synthesis, decay and conversion processes globally.
resultsBy improving 4-thiouracil labeling of RNA in Saccharomyces cerevisiae we were able to isolate RNA produced during as little as 1 minute, allowing the detection of nascent pervasive transcription. Nascent RNA labeled for 1.5, 2.5 or 5 minutes was isolated and analyzed by reverse transcriptase-quantitative polymerase chain reaction and RNA sequencing. High kinetic resolution enabled detection and analysis of short-lived non-coding RNAs as well as intron-containing pre-mRNAs in wild-type yeast. From these data we measured the relative stability of pre-mRNA species with different high turnover rates and investigated potential correlations with sequence features.
conclusionsOur analysis of non-coding RNAs reveals a highly significant association between non-coding RNA stability, transcript length and predicted secondary structure. Our quantitative analysis of the kinetics of pre-mRNA splicing in yeast reveals that ribosomal protein transcripts are more efficiently spliced if they contain intron secondary structures that are predicted to be less stable. These data, in combination with previous results, indicate that there is an optimal range of stability of intron secondary structures that allows for rapid splicing.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.