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  1. Article ; Online: Transcription-Translation Coupling in Bacteria.

    Blaha, Gregor M / Wade, Joseph T

    Annual review of genetics

    2022  Volume 56, Page(s) 187–205

    Abstract: In bacteria, transcription and translation take place in the same cellular compartment. Therefore, a messenger RNA can be translated as it is being transcribed, a process known as transcription-translation coupling. This process was already recognized at ...

    Abstract In bacteria, transcription and translation take place in the same cellular compartment. Therefore, a messenger RNA can be translated as it is being transcribed, a process known as transcription-translation coupling. This process was already recognized at the dawn of molecular biology, yet the interplay between the two key players, the RNA polymerase and ribosome, remains elusive. Genetic data indicate that an RNA sequence can be translated shortly after it has been transcribed. The closer both processes are in time, the less accessible the RNA sequence is between the RNA polymerase and ribosome. This temporal coupling has important consequences for gene regulation. Biochemical and structural studies have detailed several complexes between the RNA polymerase and ribosome. The in vivo relevance of this physical coupling has not been formally demonstrated. We discuss how both temporal and physical coupling may mesh to produce the phenomenon we know as transcription-translation coupling.
    MeSH term(s) Bacteria/genetics ; Ribosomes/genetics ; RNA, Messenger/genetics
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2022-09-02
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 207928-8
    ISSN 1545-2948 ; 0066-4170 ; 0066-4197
    ISSN (online) 1545-2948
    ISSN 0066-4170 ; 0066-4197
    DOI 10.1146/annurev-genet-072220-033342
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1109: Show issues Location:
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  2. Article ; Online: High-throughput determination of in vivo DNA sequence preferences for Cas protein binding using Library-ChIP.

    Wade, Joseph T

    Methods in enzymology

    2018  Volume 616, Page(s) 117–132

    Abstract: The specificity of CRISPR-Cas systems for nucleic acid targets is determined by a combination of binding and cleavage. Understanding the mechanisms by which Cas proteins specifically select their targets is critical for the development of CRISPR-Cas ... ...

    Abstract The specificity of CRISPR-Cas systems for nucleic acid targets is determined by a combination of binding and cleavage. Understanding the mechanisms by which Cas proteins specifically select their targets is critical for the development of CRISPR-Cas systems for biotechnology applications. Moreover, the specificity of CRISPR-Cas systems plays an important role in prokaryote evolution due to its role in distinguishing self from nonself. Here, I describe Library-ChIP, a high-throughput method for measuring Cas protein occupancy at many DNA sequence variants in a native prokaryotic host. Library-ChIP can be used to identify the determinants of specificity for Cas protein binding to nucleic acid targets.
    MeSH term(s) CRISPR-Associated Proteins/genetics ; CRISPR-Associated Proteins/metabolism ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Protein Binding
    Chemical Substances CRISPR-Associated Proteins ; Escherichia coli Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2018-12-17
    Publishing country United States
    Document type Journal Article
    ISSN 1557-7988 ; 0076-6879
    ISSN (online) 1557-7988
    ISSN 0076-6879
    DOI 10.1016/bs.mie.2018.10.019
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  3. Article ; Online: Direct and indirect control of Rho-dependent transcription termination by the

    Ghosh, Tithi / Jahangirnejad, Shirin / Chauvier, Adrien / Stringer, Anne M / Korepanov, Alexey P / Côté, Jean Phillippe / Wade, Joseph T / Lafontaine, Daniel A

    RNA (New York, N.Y.)

    2024  Volume 30, Issue 4, Page(s) 381–391

    Abstract: Bacterial riboswitches are molecular structures that play a crucial role in controlling gene expression to maintain cellular balance. ... ...

    Abstract Bacterial riboswitches are molecular structures that play a crucial role in controlling gene expression to maintain cellular balance. The
    MeSH term(s) Riboswitch/genetics ; Base Sequence ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Transcription, Genetic ; Bacteria/genetics ; Gene Expression Regulation, Bacterial ; RNA, Bacterial/metabolism
    Chemical Substances Riboswitch ; RNA, Bacterial
    Language English
    Publishing date 2024-03-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.079779.123
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    In stock of ZB MED Cologne/Königswinter

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  4. Article ; Online: Concerns about "Stress-Induced MazF-Mediated Proteins in Escherichia coli".

    Wade, Joseph T / Laub, Michael T

    mBio

    2019  Volume 10, Issue 3

    MeSH term(s) DNA-Binding Proteins ; Endoribonucleases ; Escherichia coli ; Escherichia coli Proteins
    Chemical Substances DNA-Binding Proteins ; Escherichia coli Proteins ; MazF protein, E coli ; Endoribonucleases (EC 3.1.-)
    Language English
    Publishing date 2019-06-04
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.00825-19
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  5. Article ; Online: Reply to: Intraosseous Versus Intravenous Resuscitation During In-Hospital Cardiac Arrest.

    Schwalbach, Kevin T / Chad Wade, R / Barney, Joseph

    Resuscitation

    2021  Volume 169, Page(s) 203–204

    MeSH term(s) Administration, Intravenous ; Hospitals ; Humans ; Infusions, Intraosseous ; Out-of-Hospital Cardiac Arrest/drug therapy
    Language English
    Publishing date 2021-10-08
    Publishing country Ireland
    Document type Letter ; Comment
    ZDB-ID 189901-6
    ISSN 1873-1570 ; 0300-9572
    ISSN (online) 1873-1570
    ISSN 0300-9572
    DOI 10.1016/j.resuscitation.2021.09.036
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    In stock of ZB MED Cologne/Königswinter

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  6. Article: Genome-wide mapping of the

    Fitzgerald, Devon / Stringer, Anne / Smith, Carol / Lapierre, Pascal / Wade, Joseph T

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the : Importance! ...

    Abstract Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the
    Importance: Recent studies have revealed large numbers of transcription factor binding sites within the genes of bacteria. The function, if any, of the vast majority of these binding sites has not been investigated. Here, we map the binding of the transcription factor PhoB across the
    Language English
    Publishing date 2023-02-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.07.527549
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  7. Article ; Online: Genome-Wide Mapping of the Escherichia coli PhoB Regulon Reveals Many Transcriptionally Inert, Intragenic Binding Sites.

    Fitzgerald, Devon M / Stringer, Anne M / Smith, Carol / Lapierre, Pascal / Wade, Joseph T

    mBio

    2023  Volume 14, Issue 3, Page(s) e0253522

    Abstract: Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of, genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia ... ...

    Abstract Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of, genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert and hence are tolerated as genomic "noise."
    MeSH term(s) Escherichia coli/genetics ; Escherichia coli/metabolism ; Regulon ; Bacterial Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Binding Sites ; Phosphates/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism
    Chemical Substances Bacterial Proteins ; Transcription Factors ; Phosphates ; PhoB protein, E coli ; Escherichia coli Proteins
    Language English
    Publishing date 2023-04-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.02535-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq.

    Wade, Joseph T

    Advances in experimental medicine and biology

    2015  Volume 883, Page(s) 119–134

    Abstract: Bacterial genomes encode numerous transcription factors, DNA-binding proteins that regulate transcription initiation. Identifying the regulatory targets of transcription factors is a major challenge of systems biology. Here I describe the use of two ... ...

    Abstract Bacterial genomes encode numerous transcription factors, DNA-binding proteins that regulate transcription initiation. Identifying the regulatory targets of transcription factors is a major challenge of systems biology. Here I describe the use of two genome-scale approaches, ChIP-seq and RNA-seq, that are used to map transcription factor regulons. ChIP-seq maps the association of transcription factors with DNA, and RNA-seq determines changes in RNA levels associated with transcription factor perturbation. I discuss the strengths and weaknesses of these and related approaches, and I describe how ChIP-seq and RNA-seq can be combined to map individual transcription factor regulons and entire regulatory networks.
    MeSH term(s) Base Sequence ; Chromatin Immunoprecipitation/methods ; DNA Barcoding, Taxonomic ; Gene Regulatory Networks ; Molecular Sequence Data ; Sequence Analysis, RNA
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    DOI 10.1007/978-3-319-23603-2_7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Identification of novel translated small ORFs in

    Stringer, Anne / Smith, Carol / Mangano, Kyle / Wade, Joseph T

    Journal of bacteriology

    2021  Volume 204, Issue 1, Page(s) JB0035221

    Abstract: Small proteins of <51 amino acids are abundant across all domains of life but are often overlooked because their small size makes them difficult to predict computationally, and they are refractory to standard proteomic approaches. Ribosome profiling has ... ...

    Abstract Small proteins of <51 amino acids are abundant across all domains of life but are often overlooked because their small size makes them difficult to predict computationally, and they are refractory to standard proteomic approaches. Ribosome profiling has been used to infer the existence of small proteins by detecting the translation of the corresponding open reading frames (ORFs). Detection of translated short ORFs by ribosome profiling can be improved by treating cells with drugs that stall ribosomes at specific codons. Here, we combine the analysis of ribosome profiling data for
    MeSH term(s) Open Reading Frames ; Ribosome Profiling ; Proteomics ; Codon, Terminator ; Escherichia coli/genetics ; Amino Acids/genetics ; Protein Biosynthesis
    Chemical Substances Codon, Terminator ; Amino Acids
    Language English
    Publishing date 2021-10-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.00352-21
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  10. Article ; Online: Where to begin? Mapping transcription start sites genome-wide in Escherichia coli.

    Wade, Joseph T

    Journal of bacteriology

    2014  Volume 197, Issue 1, Page(s) 4–6

    Abstract: Recent genome-wide studies of bacterial transcription have revealed large numbers of promoters located inside genes. In this issue of the Journal of Bacteriology, Thomason and colleagues (J. Bacteriol. 197:18-28, 2015, doi:10.1128/JB.02096-14) map ... ...

    Abstract Recent genome-wide studies of bacterial transcription have revealed large numbers of promoters located inside genes. In this issue of the Journal of Bacteriology, Thomason and colleagues (J. Bacteriol. 197:18-28, 2015, doi:10.1128/JB.02096-14) map transcription start sites in Escherichia coli on an unprecedented scale. This work provides important insights into the regulation of transcripts that initiate inside genes and sources of variability between studies aimed at identifying these RNAs.
    MeSH term(s) Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial/physiology ; RNA, Antisense/metabolism ; RNA, Bacterial/metabolism ; Transcription Initiation Site/physiology
    Chemical Substances RNA, Antisense ; RNA, Bacterial
    Language English
    Publishing date 2014-10-20
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.02410-14
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