PMID- 21103382
OWN - NLM
STAT- MEDLINE
DCOM- 20110427
LR  - 20211020
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 5
IP  - 11
DP  - 2010 Nov 16
TI  - A complete set of nascent transcription rates for yeast genes.
PG  - e15442
LID - 10.1371/journal.pone.0015442 [doi]
LID - e15442
AB  - 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.
FAU - Pelechano, Vicent
AU  - Pelechano V
AD  - Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, 
      Universitat de Valencia, Burjassot, Spain.
FAU - Chavez, Sebastian
AU  - Chavez S
FAU - Perez-Ortin, Jose E
AU  - Perez-Ortin JE
LA  - eng
SI  - GEO/GSE11521
SI  - GEO/GSE13096
SI  - GEO/GSE14060
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20101116
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Chromatin)
RN  - 0 (RNA, Messenger)
RN  - 0 (Saccharomyces cerevisiae Proteins)
RN  - EC 2.7.7.- (RNA Polymerase II)
SB  - IM
EIN - PLoS One. 2014;9(12):e115560
MH  - Chromatin/genetics/metabolism
MH  - *Gene Expression Profiling
MH  - Gene Expression Regulation, Fungal
MH  - Genes, Fungal/genetics
MH  - RNA Polymerase II/genetics/metabolism
MH  - RNA Stability
MH  - RNA, Messenger/genetics/metabolism
MH  - Saccharomyces cerevisiae/*genetics
MH  - Saccharomyces cerevisiae Proteins/*genetics
MH  - Transcription, Genetic/*genetics
PMC - PMC2982843
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2010/11/26 06:00
MHDA- 2011/04/28 06:00
PMCR- 2010/11/16
CRDT- 2010/11/25 06:00
PHST- 2010/08/12 00:00 [received]
PHST- 2010/09/21 00:00 [accepted]
PHST- 2010/11/25 06:00 [entrez]
PHST- 2010/11/26 06:00 [pubmed]
PHST- 2011/04/28 06:00 [medline]
PHST- 2010/11/16 00:00 [pmc-release]
AID - PONE-D-10-00658 [pii]
AID - 10.1371/journal.pone.0015442 [doi]
PST - epublish
SO  - PLoS One. 2010 Nov 16;5(11):e15442. doi: 10.1371/journal.pone.0015442.