Target prediction for small, noncoding RNAs in bacteria (2006)
Tjaden, Brian, Goodwin, Sarah S., Opdyke, Jason A., Guillier, Maude, Fu, Daniel X., Gottesman, Susan, ...
Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a...
Target prediction for small, noncoding RNAs in bacteria (2006)
Tjaden, Brian, Goodwin, Sarah S., Opdyke, Jason A., Guillier, Maude, Fu, Daniel X., Gottesman, Susan, ...
Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a...
Modulating the outer membrane with small RNAs (2006)
Guillier, Maude, Gottesman, Susan, Storz, Gisela
MicF, one of the first chromosomally encoded regulatory small RNAs (sRNAs) to be discovered, was found to modulate the expression of OmpF, an abundant outer membrane protein. Several recent papers...
An antibody-based microarray assay for small RNA detection (2006)
Hu, Zonglin, Zhang, Aixia, Storz, Gisela, Gottesman, Susan, Leppla, Stephen H.
Detection of RNAs on microarrays is rapidly becoming a standard approach for molecular biologists. However, current methods frequently discriminate against structured and/or small RNA species. Here...
Kawano, Mitsuoki, Storz, Gisela, Rao, B. Sridhar, Rosner, Judah L., Martin, Robert G.
The search for promoters has largely been confined to sequences upstream of open reading frames (ORFs) or stable RNA genes. Here we used a cloning approach to discover other potential promoters in...
Kawano, Mitsuoki, Reynolds, April A., Miranda-Rios, Juan, Storz, Gisela
Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of ∼60 small RNA genes in Escherichia...
Exploiting Thiol Modifications (2004)
Patricia J. Kiley, Gisela Storz
Molecular oxygen may be necessary for life but with its beneficial properties comes formation of potentially toxic reactive oxygen species. One of the ways in which bacteria protect themselves is...
Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli (2001)
Ming Zheng, Xunde Wang, Bernard Doan, Karen A. Lewis, Thomas D. Schneider, Gisela Storz
A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted OxyR binding sites upstream of dsbG, encoding a...
Identification of novel small RNAs using comparative genomics and microarrays (2001)
Wassarman, Karen M., Repoila, Francis, Rosenow, Carsten, Storz, Gisela, Gottesman, Susan
Genomic expression programs in the response of yeast cells to environmental changes (2000)
Audrey P. Gasch, Paul T. Spellman, Camilla M. Kao, Orna Carmel-harel, Michael B. Eisen, Gisela Storz, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Genomic Expression Programs in the Response of Yeast Cells to Environmental ChangesD⃞
Gasch, Audrey P., Spellman, Paul T., Kao, Camilla M., Carmel-Harel, Orna, Eisen, Michael B., Storz, Gisela, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Åslund, Fredrik, Zheng, Ming, Beckwith, Jon, Storz, Gisela
The Escherichia coli transcription factor OxyR is activated by the formation of an intramolecular disulfide bond and subsequently is deactivated by enzymatic reduction of the disulfide bond. Here we...
Zheng, Ming, Wang, Xunde, Templeton, Lori J., Smulski, Dana R., LaRossa, Robert A., Storz, Gisela
The genome-wide transcription profile of Escherichia coli cells treated with hydrogen peroxide was examined with a DNA microarray composed of 4,169 E. coli open reading frames. By measuring gene...
Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli
Zheng, Ming, Wang, Xunde, Doan, Bernard, Lewis, Karen A., Schneider, Thomas D., Storz, Gisela
A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted OxyR binding sites upstream of dsbG, encoding a...
OxyR and SoxRS Regulation of fur
Zheng, Ming, Doan, Bernard, Schneider, Thomas D., Storz, Gisela
The cytotoxic effects of reactive oxygen species are largely mediated by iron. Hydrogen peroxide reacts with iron to form the extremely reactive and damaging hydroxyl radical via the Fenton reaction....
Mukhopadhyay, Partha, Zheng, Ming, Bedzyk, Laura A., LaRossa, Robert A., Storz, Gisela
We examined the genomewide transcriptional responses of Escherichia coli treated with nitrosylated glutathione or the nitric oxide (NO)-generator acidified sodium nitrite (NaNO2) during aerobic...
MicC, a Second Small-RNA Regulator of Omp Protein Expression in Escherichia coli
Chen, Shuo, Zhang, Aixia, Blyn, Lawrence B., Storz, Gisela
In a previous bioinformatics-based search for novel small-RNA genes encoded by the Escherichia coli genome, we identified a region, IS063, located between the ompN and ydbK genes, that encodes an...
GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli
Opdyke, Jason A., Kang, Ju-Gyeong, Storz, Gisela
A previous bioinformatics-based search for small RNAs in Escherichia coli identified a novel RNA named IS183. The gene encoding this small RNA is located between and on the opposite strand of genes...
Exploiting Thiol Modifications
Kiley, Patricia J, Storz, Gisela
Molecular oxygen may be necessary for life but with its beneficial properties comes formation of potentially toxic reactive oxygen species. One of the ways in which bacteria protect themselves is...
Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli
Kawano, Mitsuoki, Reynolds, April A., Miranda-Rios, Juan, Storz, Gisela
Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of ∼60 small RNA genes in Escherichia...
Detection of low-level promoter activity within open reading frame sequences of Escherichia coli
Kawano, Mitsuoki, Storz, Gisela, Rao, B. Sridhar, Rosner, Judah L., Martin, Robert G.
The search for promoters has largely been confined to sequences upstream of open reading frames (ORFs) or stable RNA genes. Here we used a cloning approach to discover other potential promoters in...
Identification of novel small RNAs using comparative genomics and microarrays
Wassarman, Karen M., Repoila, Francis, Rosenow, Carsten, Storz, Gisela, Gottesman, Susan
A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence...
An antibody-based microarray assay for small RNA detection
Hu, Zonglin, Zhang, Aixia, Storz, Gisela, Gottesman, Susan, Leppla, Stephen H.
Detection of RNAs on microarrays is rapidly becoming a standard approach for molecular biologists. However, current methods frequently discriminate against structured and/or small RNA species. Here...
Target prediction for small, noncoding RNAs in bacteria
Tjaden, Brian, Goodwin, Sarah S., Opdyke, Jason A., Guillier, Maude, Fu, Daniel X., Gottesman, Susan, ...
Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a...
Genomic Expression Programs in the Response of Yeast Cells to Environmental ChangesD⃞
Gasch, Audrey P., Spellman, Paul T., Kao, Camilla M., Carmel-Harel, Orna, Eisen, Michael B., Storz, Gisela, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Åslund, Fredrik, Zheng, Ming, Beckwith, Jon, Storz, Gisela
The Escherichia coli transcription factor OxyR is activated by the formation of an intramolecular disulfide bond and subsequently is deactivated by enzymatic reduction of the disulfide bond. Here we...
Zheng, Ming, Wang, Xunde, Templeton, Lori J., Smulski, Dana R., LaRossa, Robert A., Storz, Gisela
The genome-wide transcription profile of Escherichia coli cells treated with hydrogen peroxide was examined with a DNA microarray composed of 4,169 E. coli open reading frames. By measuring gene...
Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli
Zheng, Ming, Wang, Xunde, Doan, Bernard, Lewis, Karen A., Schneider, Thomas D., Storz, Gisela
A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted OxyR binding sites upstream of dsbG, encoding a...
OxyR and SoxRS Regulation of fur
Zheng, Ming, Doan, Bernard, Schneider, Thomas D., Storz, Gisela
The cytotoxic effects of reactive oxygen species are largely mediated by iron. Hydrogen peroxide reacts with iron to form the extremely reactive and damaging hydroxyl radical via the Fenton reaction....
Identification of novel small RNAs using comparative genomics and microarrays
Wassarman, Karen M., Repoila, Francis, Rosenow, Carsten, Storz, Gisela, Gottesman, Susan
A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence...
Mukhopadhyay, Partha, Zheng, Ming, Bedzyk, Laura A., LaRossa, Robert A., Storz, Gisela
We examined the genomewide transcriptional responses of Escherichia coli treated with nitrosylated glutathione or the nitric oxide (NO)-generator acidified sodium nitrite (NaNO2) during aerobic...
MicC, a Second Small-RNA Regulator of Omp Protein Expression in Escherichia coli
Chen, Shuo, Zhang, Aixia, Blyn, Lawrence B., Storz, Gisela
In a previous bioinformatics-based search for novel small-RNA genes encoded by the Escherichia coli genome, we identified a region, IS063, located between the ompN and ydbK genes, that encodes an...
GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli
Opdyke, Jason A., Kang, Ju-Gyeong, Storz, Gisela
A previous bioinformatics-based search for small RNAs in Escherichia coli identified a novel RNA named IS183. The gene encoding this small RNA is located between and on the opposite strand of genes...
Exploiting Thiol Modifications
Kiley, Patricia J, Storz, Gisela
Molecular oxygen may be necessary for life but with its beneficial properties comes formation of potentially toxic reactive oxygen species. One of the ways in which bacteria protect themselves is...
Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli
Kawano, Mitsuoki, Reynolds, April A., Miranda-Rios, Juan, Storz, Gisela
Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of ∼60 small RNA genes in Escherichia...
Detection of low-level promoter activity within open reading frame sequences of Escherichia coli
Kawano, Mitsuoki, Storz, Gisela, Rao, B. Sridhar, Rosner, Judah L., Martin, Robert G.
The search for promoters has largely been confined to sequences upstream of open reading frames (ORFs) or stable RNA genes. Here we used a cloning approach to discover other potential promoters in...
An antibody-based microarray assay for small RNA detection
Hu, Zonglin, Zhang, Aixia, Storz, Gisela, Gottesman, Susan, Leppla, Stephen H.
Detection of RNAs on microarrays is rapidly becoming a standard approach for molecular biologists. However, current methods frequently discriminate against structured and/or small RNA species. Here...
Target prediction for small, noncoding RNAs in bacteria
Tjaden, Brian, Goodwin, Sarah S., Opdyke, Jason A., Guillier, Maude, Fu, Daniel X., Gottesman, Susan, ...
Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a...
Wang, Xunde, Mukhopadhyay, Partha, Wood, Matthew J., Outten, F. Wayne, Opdyke, Jason A., Storz, Gisela
The OxyR transcription factor is a key regulator of the Escherichia coli response to oxidative stress. Previous studies showed that OxyR binding to a target promoter enhances RNA polymerase binding...
An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin
Kawano, Mitsuoki, Aravind, L, Storz, Gisela
Only few small, regulatory RNAs encoded opposite another gene have been identified in bacteria. Here, we report the characterization of a locus where a small RNA (SymR) is encoded in cis to an...
Discovery of Fur binding site clusters in Escherichia coli by information theory models
Chen, Zehua, Lewis, Karen A., Shultzaberger, Ryan K., Lyakhov, Ilya G., Zheng, Ming, Doan, Bernard, ...
Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur...