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.
Highlights
Gene transcription in eukaryotes is a complex process that starts with the recruitment of an RNA polymerase (RNA pol) complex to the gene promoter and is followed by a set of successive steps, such as initiation, elongation, splicing, termination, mRNA export, and degradation
As the regulation at the mRNA stability level is increasingly recognized to be important in gene regulation [5,6,7,8], the mRNA measurement can no longer be used as a direct estimation of gene transcription
Estimation of transcription rates using improved and corrected GRO values When we first described the GRO method [10], we calculated the TRs for 5886 yeast genes, these being the vast majority of the RNA pol II genes
Summary
Gene transcription in eukaryotes is a complex process that starts with the recruitment of an RNA polymerase (RNA pol) complex to the gene promoter and is followed by a set of successive steps, such as initiation, elongation, splicing, termination, mRNA export, and degradation. The main regulatory step for the gene expression of many genes is the control of their TR, which is assumed to be exercised mainly at the RNA pol recruitment level. The use of this kind of TR dataset has become very popular for yeast since Holstege et al [9] provided a set of TR data as a supplementary material of that paper Those data represent, the indirect calculation of the rate of appearance of mature mRNAs in the cytoplasm, taking into account all possible posttranscriptional processes of the mRNA, and do not represent the actual synthesis of new mRNAs by RNA pol in the genes (i.e. nascent TR)
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