DOI: 10.1101/gr.912603. Global RNA Half-Life Analysis in<i>Escherichia coli</i>Reveals Positional Patterns of Transcript Degradation

Global RNA Half-Life Analysis inEscherichia coliReveals Positional Patterns of Transcript Degradation

10.1101/gr.912603

Crossref journal-article

Cold Spring Harbor Laboratory

Genome Research (246)

Abstract

Subgenic-resolution oligonucleotide microarrays were used to study global RNA degradation in wild-typeEscherichia coliMG1655. RNA chemical half-lives were measured for 1036 open reading frames (ORFs) and for 329 known and predicted operons. The half-life of total mRNA was 6.8 min under the conditions tested. We also observed significant relationships between gene functional assignments and transcript stability. Unexpectedly, transcription of a single operon (tdcABCDEFG) was relatively rifampicin-insensitive and showed significant increases 2.5 min after rifampicin addition. This supports a novel mechanism of transcription for thetdcoperon, whose promoter lacks any recognizable ς binding sites. Probe by probe analysis of all known and predicted operons showed that the 5′ ends of operons degrade, on average, more quickly than the rest of the transcript, with stability increasing in a 3′ direction, supporting and further generalizing the current model of a net 5′ to 3′ directionality of degradation. Hierarchical clustering analysis of operon degradation patterns revealed that this pattern predominates but is not exclusive. We found a weak but highly significant correlation between the degradation of adjacent operon regions, suggesting that stability is determined by a combination of local and operon-wide stability determinants. The 16 ORFdcwgene cluster, which has a complex promoter structure and a partially characterized degradation pattern, was studied at high resolution, allowing a detailed and integrated description of its abundance and degradation. We discuss the application of subgenic resolution DNA microarray analysis to study global mechanisms of RNA transcription and processing.

Bibliography

Selinger, D. W., Saxena, R. M., Cheung, K. J., Church, G. M., & Rosenow, C. (2003). Global RNA Half-Life Analysis inEscherichia coliReveals Positional Patterns of Transcript Degradation. Genome Research, 13(2), 216â223.

Authors 5

Douglas W. Selinger (first)
Rini Mukherjee Saxena (additional)
Kevin J. Cheung (additional)
George M. Church (additional)
Carsten Rosenow (additional)

References 35 Referenced 309

10.1101/gr.10.4.431
10.1073/pnas.112318199
10.1126/science.277.5331.1453
10.1093/nar/24.15.3065
10.1016/S0092-8674(01)00286-0
10.1038/79896
10.1016/S0300-9084(00)01212-8
10.1111/j.1574-6968.2000.tb09127.x
10.1073/pnas.95.25.14863
10.1101/gad.6.1.135
10.1046/j.1365-2958.1997.4001762.x
10.1046/j.1365-2958.1998.01064.x
10.1046/j.1365-2958.1996.363898.x
10.1146/annurev.genet.33.1.193
10.1126/science.1068597
10.1186/gb-2001-2-10-research0041 / Genome Biol. / Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol. by Lam (2001)
10.1186/gb-2001-2-8-research0032 / Genome Biol. / Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application. by Li (2001)
10.1038/nbt1296-1675
10.1128/JB.180.17.4406-4412.1998 / J. Bacteriol. / Contribution of the Pmra promoter to expression of genes in the Escherichia coli mra cluster of cell envelope biosynthesis and cell division genes. by Mengin-Lecreulx (1998)
10.1046/j.1365-2958.1999.01673.x
10.1038/312075a0
10.1111/j.1574-6976.1999.tb00404.x
10.1002/(SICI)1521-1878(200003)22:3<235::AID-BIES5>3.0.CO;2-2
10.1093/nar/29.22.e112 / Nucleic Acids Res. / Prokaryotic RNA preparation methods useful for high density array analysis: Comparison of two approaches. by Rosenow (2001)
10.1093/nar/29.1.72
10.1146/annurev.biochem.66.1.173
10.1111/j.1365-2958.2001.02316.x
10.1038/82367
10.1038/35057141
10.1038/10343
10.1093/bioinformatics/18.suppl_1.S337 / Bioinformatics (Suppl.) / Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis. by Tjaden (2002)
10.1007/s000180050158
10.1073/pnas.092538799
10.1016/S0014-5793(98)01449-5
10.1007/BF00290409

Dates

Type	When
Created	22 years, 7 months ago (Feb. 3, 2003, 4:06 p.m.)
Deposited	8 months, 3 weeks ago (Dec. 11, 2024, 2:10 p.m.)
Indexed	3 weeks, 2 days ago (Aug. 12, 2025, 5:58 p.m.)
Issued	22 years, 7 months ago (Jan. 14, 2003)
Published	22 years, 7 months ago (Jan. 14, 2003)
Published Online	22 years, 7 months ago (Jan. 14, 2003)
Published Print	22 years, 7 months ago (Feb. 1, 2003)

Funders 0

None

BibTeX

@article{Selinger_2003, title={Global RNA Half-Life Analysis inEscherichia coliReveals Positional Patterns of Transcript Degradation}, volume={13}, ISSN={1549-5469}, url={http://dx.doi.org/10.1101/gr.912603}, DOI={10.1101/gr.912603}, number={2}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Selinger, Douglas W. and Saxena, Rini Mukherjee and Cheung, Kevin J. and Church, George M. and Rosenow, Carsten}, year={2003}, month=jan, pages={216–223} }

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