|
| Status |
Public on Mar 07, 2006 |
| Title |
Global analysis of mRNA decay and abundance in Escherichia coli |
| Organism |
Escherichia coli |
| Experiment type |
Expression profiling by array
|
| Summary |
Abstract: Much of the information available about factors that affect mRNA decay in Escherichia coli, and by inference in other bacteria, has been gleaned from study of less than 25 of the approximately 4,300 predicted E. coli messages. To investigate these factors more broadly, we examined the half-lives and steady-state abundance of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. An rRNA-based strategy for normalization of microarray data was developed to permit quantitation of mRNA decay after transcriptional arrest by rifampicin. We found that globally, mRNA half-lives were similar in nutrient-rich media and defined media in which the generation time was approximately tripled. A wide range of stabilities was observed for individual mRNAs of E. coli, although approximately 80% of all mRNAs had half-lives between 3 and 8 min. Genes having biologically related metabolic functions were commonly observed to have similar stabilities. Whereas the half-lives of a limited number of mRNAs correlated positively with their abundance, we found that overall, increased mRNA stability is not predictive of increased abundance. Neither the density of putative sites of cleavage by RNase E, which is believed to initiate mRNA decay in E. coli, nor the free energy of folding of 5' or 3' untranslated region sequences was predictive of mRNA half-life. Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability.
This SuperSeries is composed of the SubSeries listed below.
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| |
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| Overall design |
Refer to individual Series
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| Citation(s) |
12119387 |
| |
| Submission date |
Mar 06, 2006 |
| Last update date |
Dec 28, 2012 |
| Organization |
Stanford Microarray Database (SMD) |
| E-mail(s) |
array@genome.stanford.edu
|
| Phone |
650-498-6012
|
| URL |
http://genome-www5.stanford.edu/
|
| Department |
Stanford University, School of Medicine
|
| Street address |
300 Pasteur Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platforms (2) |
|
| Samples (16)
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| GSM73563 |
Transcript Abundance in LB at 30 degrees OD600=0.8 Trial A |
| GSM73564 |
Transcript Abundance in M9 at 30 degrees OD600=0.8 Trial A |
| GSM73565 |
Transcript Abundance in LB at 30 degrees OD600=0.8 Trial B |
| GSM73566 |
Transcript Abundance in M9 at 30 degrees OD600=0.8 Trial B |
| GSM73567 |
2' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A |
| GSM73568 |
4' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A |
| GSM73569 |
2' RNA Decay of MG1655 (Repaired NCM 3416) in LB at 30 C |
| GSM73570 |
4' RNA Decay of MG1655 (Repaired NCM 3416) in LB at 30 C |
| GSM73571 |
6' RNA Decay of MG1655 (Repaired NCM 3416) in LB at 30 C |
| GSM73572 |
2' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B |
| GSM73573 |
4' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B |
| GSM73574 |
6' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B |
| GSM73575 |
6' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A |
| GSM73576 |
8' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B |
| GSM73577 |
8' RNA Decay of MG1655 (Repaired NCM 3416) in LB at 30 C |
| GSM73578 |
8' RNA Decay of MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose Trial A |
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| This SuperSeries is composed of the following SubSeries: |
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| Relations |
| BioProject |
PRJNA94837 |
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