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Series GSE17075 Query DataSets for GSE17075
Status Public on Dec 31, 2009
Title Expression data from RNA half-life experiments in Prochlorococcus
Platform organisms Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. MIT 9313; Prochlorococcus phage P-SSM4; Tiamatvirus PSSP7
Sample organism Prochlorococcus marinus subsp. pastoris str. CCMP1986
Experiment type Expression profiling by array
Summary RNA decay was measured in Prochlorococcus after inhibition of transcription by rifampicin using customized Affymetrix gene expression arrays.
RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, a relatively slow-growing marine cyanobacterium doubling approximately once a day, which is extremely abundant in the oceans. Using a combination of microarrays, quantitative RT-PCR and a new algorithm for determining RNA decay rates, we found a median half-life of 2.4 min and a median decay rate of 2.6 min for expressed genes – two-fold faster than that reported for any organism. The shortest transcript half-life (33 seconds) was for a gene of unknown function, while some of the longest (ca. 18 min) were for highly expressed genes. Genes organized in operons displayed intriguing mRNA decay patterns, such as increased stability, and delayed onset of decay with greater distance from the transcriptional start site. The same phenomenon was observed on a single probe resolution for genes greater than 2 kb. We hypothesize that the fast turnover relative to generation time in Prochlorococcus may enable a swift response to environmental changes through rapid recycling of nucleotides, which could be advantageous in nutrient poor oceans. Our growing understanding of RNA half-lives will inform on the modelling of cell processes and help interpret the growing bank of metatranscriptomic studies of wild populations of Prochlorococcus. The surprisingly complex decay patterns of large transcripts reported here, and the method developed to describe them, will open new avenues for the investigation and understanding of RNA decay for all organisms.
 
Overall design Prochlorococcus cells were treated with rifampicin, which prevents initiation of new transcripts. Cells were harvested at 0 min (before rifampicin addition), 2.5 min, 5 min, 10 min, 20 min, 40 min and 60 min after rifampicin addition.
 
Contributor(s) Steglich C, Futschik M, Lindell D, Rector T, Steen R, Chisholm SW
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Submission date Jul 14, 2009
Last update date Mar 21, 2012
Contact name Claudia Steglich
E-mail(s) claudia.steglich@biologie.uni-freiburg.de
Phone 0049 761 203 6986
Fax 0049 761 203 6996
Organization name University of Freiburg
Department Biology
Street address Schaenzlestr. 1
City Freiburg
ZIP/Postal code 79104
Country Germany
 
Platforms (1)
GPL8853 University of Freiburg - Prochlorococcus microarray - MD4-9313 (MD4-9313a520062) version GC3.0
Samples (20)
GSM427213 cells at T 0 min, biological rep1
GSM427214 cells at T 0 min, biological rep2
GSM427215 cells at T 0 min, biological rep3
Relations
BioProject PRJNA119815

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Supplementary file Size Download File type/resource
GSE17075_RAW.tar 28.5 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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