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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
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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.
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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.
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Contributor(s) |
Steglich C, Futschik M, Lindell D, Rector T, Steen R, Chisholm SW |
Citation missing |
Has this study been published? Please login to update or notify GEO. |
Submission date |
Jul 14, 2009 |
Last update date |
Mar 21, 2012 |
Contact name |
Claudia Steglich |
E-mail(s) |
claudia.steglich@biologie.uni-freiburg.de
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Phone |
0049 761 203 6986
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Fax |
0049 761 203 6996
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Organization name |
University of Freiburg
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Department |
Biology
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Street address |
Schaenzlestr. 1
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City |
Freiburg |
ZIP/Postal code |
79104 |
Country |
Germany |
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Platforms (1) |
GPL8853 |
University of Freiburg - Prochlorococcus microarray - MD4-9313 (MD4-9313a520062) version GC3.0 |
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Samples (20)
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GSM427216 |
cells at T 2.5 min, biological rep1 |
GSM427217 |
cells at T 2.5 min, biological rep2 |
GSM427218 |
cells at T 2.5 min, biological rep3 |
GSM427219 |
cells at T 5 min, biological rep1 |
GSM427220 |
cells at T 5 min, biological rep2 |
GSM427221 |
cells at T 10 min, biological rep1 |
GSM427222 |
cells at T 10 min, biological rep2 |
GSM427223 |
cells at T 10 min, biological rep3 |
GSM427224 |
cells at T 20 min, biological rep1 |
GSM427225 |
cells at T 20 min, biological rep2 |
GSM427226 |
cells at T 20 min, biological rep3 |
GSM427227 |
cells at T 40 min, biological rep1 |
GSM427228 |
cells at T 40 min, biological rep2 |
GSM427229 |
cells at T 40 min, biological rep3 |
GSM427230 |
cells at T 60 min, biological rep1 |
GSM427231 |
cells at T 60 min, biological rep2 |
GSM427232 |
cells at T 60 min, biological rep3 |
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Relations |
BioProject |
PRJNA119815 |
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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