ArticlePloS one2010
A complete set of nascent transcription rates for yeast genes.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 99 papers, 1 of them a synthesis that pooled it.
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Who cites it
99 citing papers in PubMed, 1 synthesis or guideline pooled it, 182 citations in OpenAlex.
- The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons.Nucleic acids research · 2016Pooled it
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- Noise robustness and metabolic load determine the principles of central dogma regulation.Science advances · 2024Article
- Homeostasis of mRNA concentrations through coupling transcription, export, and degradation.iScience · 2024Article
- Noise robustness and metabolic load determine the principles of central dogma regulation.bioRxiv : the preprint server for biology · 2024Article
- Noise robustness and metabolic load determine the principles of central dogma regulation.ArXiv · 2024Article
- Interplay of the Tfb1 pleckstrin homology domain with Rad2 and Rad4 in transcription coupled and global genomic nucleotide excision repair.Nucleic acids research · 2024Article
- Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration.Cell reports · 2024Article
- Transcription factor exchange enables prolonged transcriptional bursts.Molecular cell · 2024Article
- Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration.bioRxiv : the preprint server for biology · 2023Article
- Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability.Science advances · 2023Article
- Hydroxyurea and inactivation of checkpoint kinase MEC1 inhibit transcription termination and pre-mRNA cleavage at polyadenylation sites in budding yeast.Scientific reports · 2023Article
- Article
39 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) and the RNA pol ChIP-on-chip methods we generated a new, more accurate nascent transcription rate dataset. By comparing this dataset with the indirect ones obtained from the mRNA stabilities and mRNA amount datasets, we are able to obtain biological information about posttranscriptional regulation processes and a genomic snapshot of the location of the active transcriptional machinery. We have obtained nascent transcription rates for 4,670 yeast genes. The median RNA polymerase II density in the genes is 0.078 molecules/kb, which corresponds to an average of 0.096 molecules/gene. Most genes have transcription rates of between 2 and 30 mRNAs/hour and less than 1% of yeast genes have >1 RNA polymerase molecule/gene. Histone and ribosomal protein genes are the highest transcribed groups of genes and other than these exceptions the transcription of genes is an infrequent phenomenon in a yeast cell.
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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.