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Genome Biol. 2015 Dec 17;16:282. doi: 10.1186/s13059-015-0848-1.

Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling.

Author information

1
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
2
School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK.
3
Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3BF, UK.
4
Present Address: Institute of Neuroscience and Psychology, University of Glasgow, Glasgow, G12 8QB, UK.
5
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK. jbeggs@ed.ac.uk.
6
Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3BF, UK. sgrannem@staffmail.ed.ac.uk.

Abstract

BACKGROUND:

RNA 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.

RESULTS:

By 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.

CONCLUSIONS:

Our 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.

PMID:
26679539
PMCID:
PMC4699367
DOI:
10.1186/s13059-015-0848-1
[Indexed for MEDLINE]
Free PMC Article

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