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  1. Article ; Online: Changing structures, changing paradigms: NELF helps regulate paused or elongating RNA polymerase II.

    Richter, William F / Taatjes, Dylan J

    Molecular cell

    2024  Volume 84, Issue 7, Page(s) 1180–1182

    Abstract: Using cryo-EM and biochemical methods, Su and ... ...

    Abstract Using cryo-EM and biochemical methods, Su and Vos
    MeSH term(s) Promoter Regions, Genetic ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic
    Chemical Substances RNA Polymerase II (EC 2.7.7.-) ; Transcription Factors ; NSMF protein, human
    Language English
    Publishing date 2024-02-05
    Publishing country United States
    Document type Journal Article ; News
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2024.03.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5055: Show issues Location:
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  2. Article ; Online: RNA Polymerase II Transcription.

    Taatjes, Dylan J

    Journal of molecular biology

    2021  Volume 433, Issue 14, Page(s) 167037

    MeSH term(s) Gene Expression Regulation ; RNA Polymerase II/metabolism ; Transcription, Genetic
    Chemical Substances RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2021-05-04
    Publishing country Netherlands
    Document type Editorial
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.167037
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  3. Article ; Online: SnapShot: Mediator complex structure.

    Nayak, Shraddha / Taatjes, Dylan J

    Cell

    2022  Volume 185, Issue 18, Page(s) 3458–3458.e1

    Abstract: The Mediator complex controls RNA polymerase II transcription genome-wide. In humans, Mediator consists of 26 subunits; furthermore, a four-subunit "Mediator kinase module" can reversibly associate with the complex. Mediator structure is generally ... ...

    Abstract The Mediator complex controls RNA polymerase II transcription genome-wide. In humans, Mediator consists of 26 subunits; furthermore, a four-subunit "Mediator kinase module" can reversibly associate with the complex. Mediator structure is generally conserved from yeast to humans, although the human complex is larger, more structurally disordered, and contains metazoan-specific subunits. To view this SnapShot, open or download the PDF.
    MeSH term(s) Animals ; Humans ; Mediator Complex/metabolism ; RNA Polymerase II/metabolism ; Yeasts
    Chemical Substances Mediator Complex ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2022-09-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2022.07.011
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    Zs.A 1167: Show issues Location:
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  4. Article ; Online: Chemical inhibitors of transcription-associated kinases.

    Clopper, Kevin C / Taatjes, Dylan J

    Current opinion in chemical biology

    2022  Volume 70, Page(s) 102186

    Abstract: Transcription by RNA polymerase II (pol II) is regulated by kinases. In recent years, many selective and potent inhibitors of pol II transcription-associated kinases have been developed, and these molecules have advanced understanding of kinase function ... ...

    Abstract Transcription by RNA polymerase II (pol II) is regulated by kinases. In recent years, many selective and potent inhibitors of pol II transcription-associated kinases have been developed, and these molecules have advanced understanding of kinase function in mammalian cells. Here, we focus on chemical inhibitors of the transcription-associated kinases CDK7, CDK8, CDK9, CDK12, CDK13, and CDK19. We provide a brief overview of the function of these kinases and common activation mechanisms. We then highlight the advantages of kinase inhibitors compared with other basic research methods, and describe the caveats associated with non-selective compounds (e.g. flavopiridol). We conclude with strategies and recommendations for implementation of chemical inhibitors for experimental analysis of transcription-associated kinases.
    MeSH term(s) Animals ; Cyclin-Dependent Kinases/genetics ; Cyclin-Dependent Kinases/metabolism ; Mammals ; Phosphorylation ; RNA Polymerase II
    Chemical Substances Cyclin-Dependent Kinases (EC 2.7.11.22) ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2022-08-01
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1439176-4
    ISSN 1879-0402 ; 1367-5931
    ISSN (online) 1879-0402
    ISSN 1367-5931
    DOI 10.1016/j.cbpa.2022.102186
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4986: Show issues Location:
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  5. Article: The Mediator kinase module: an interface between cell signaling and transcription.

    Luyties, Olivia / Taatjes, Dylan J

    Trends in biochemical sciences

    2022  Volume 47, Issue 4, Page(s) 314–327

    Abstract: The Mediator complex controls RNA polymerase II (pol II) activity by coordinating the assembly of pol II regulatory factors at transcription start sites and by mediating interactions between enhancer-bound transcription factors (TFs) and the pol II ... ...

    Abstract The Mediator complex controls RNA polymerase II (pol II) activity by coordinating the assembly of pol II regulatory factors at transcription start sites and by mediating interactions between enhancer-bound transcription factors (TFs) and the pol II enzyme. Mediator structure and function is completely altered upon binding the Mediator kinase module, a multi-subunit complex that contains CDK8 or its vertebrate-specific paralog CDK19. Here, we review the mechanisms by which the Mediator kinase module controls pol II transcription, emphasizing its impact on TF activity, pol II elongation, enhancer function, and chromatin architecture. We also highlight how the Mediator kinase module integrates signaling pathways with transcription to enable rapid, stimulus-specific responses, as well as its links to human disease.
    MeSH term(s) Cyclin-Dependent Kinase 8/genetics ; Cyclin-Dependent Kinase 8/metabolism ; Cyclin-Dependent Kinases/metabolism ; Humans ; Mediator Complex/genetics ; Mediator Complex/metabolism ; RNA Polymerase II/metabolism ; Signal Transduction ; Transcription, Genetic
    Chemical Substances Mediator Complex ; CDK19 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinase 8 (EC 2.7.11.22) ; Cyclin-Dependent Kinases (EC 2.7.11.22) ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2022-02-19
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2022.01.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1207: Show issues Location:
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  6. Article ; Online: Everything at once: cryo-EM yields remarkable insights into human RNA polymerase II transcription.

    Schier, Allison C / Taatjes, Dylan J

    Nature structural & molecular biology

    2021  Volume 28, Issue 7, Page(s) 540–543

    MeSH term(s) Cryoelectron Microscopy ; Humans ; Mediator Complex/genetics ; Mediator Complex/metabolism ; Protein Conformation ; RNA Polymerase II/metabolism ; Transcription Factor TFIID/genetics ; Transcription Factor TFIID/metabolism ; Transcription Initiation Site/physiology ; Transcription Initiation, Genetic/physiology
    Chemical Substances Mediator Complex ; Transcription Factor TFIID ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2021-04-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-021-00613-6
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    Zs.A 4101: Show issues Location:
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  7. Article: A transcription factor (TF) inference method that broadly measures TF activity and identifies mechanistically distinct TF networks.

    Jones, Taylor / Sigauke, Rutendo F / Sanford, Lynn / Taatjes, Dylan J / Allen, Mary A / Dowell, Robin D

    bioRxiv : the preprint server for biology

    2024  

    Abstract: TF profiler is a method of inferring transcription factor regulatory activity, i.e. when a TF is present and actively regulating transcription, directly directly from nascent sequencing assays such as PRO-seq and GRO-seq. Transcription factors ... ...

    Abstract TF profiler is a method of inferring transcription factor regulatory activity, i.e. when a TF is present and actively regulating transcription, directly directly from nascent sequencing assays such as PRO-seq and GRO-seq. Transcription factors orchestrate transcription and play a critical role in cellular maintenance, identity and response to external stimuli. While ChIP assays have measured DNA localization, they fall short of identifying when and where transcription factors are actively regulating transcription. Our method, on the other hand, uses RNA polymerase activity to infer TF activity across hundreds of data sets and transcription factors. Based on these classifications we identify three distinct classes of transcription factors: ubiquitous factors that play roles in cellular homeostasis, driving basal gene programs across tissues and cell types, tissue specific factors that act almost exclusively at enhancers and are themselves regulated at transcription, and stimulus responsive TFs which are regulated post-transcriptionally but act predominantly at enhancers. TF profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.
    Language English
    Publishing date 2024-03-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.15.585303
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription.

    Palacio, Megan / Taatjes, Dylan J

    Journal of molecular biology

    2021  Volume 434, Issue 1, Page(s) 167216

    Abstract: The regulation of RNA polymerase II (pol II) transcription requires a complex and context-specific array of proteins and protein complexes, as well as nucleic acids and metabolites. Every major physiological process requires coordinated transcription of ... ...

    Abstract The regulation of RNA polymerase II (pol II) transcription requires a complex and context-specific array of proteins and protein complexes, as well as nucleic acids and metabolites. Every major physiological process requires coordinated transcription of specific sets of genes at the appropriate time, and a breakdown in this regulation is a hallmark of human disease. A proliferation of recent studies has revealed that many general transcription components, including sequence-specific, DNA-binding transcription factors, Mediator, and pol II itself, are capable of liquid-liquid phase separation, to form condensates that partition these factors away from the bulk aqueous phase. These findings hold great promise for next-level understanding of pol II transcription; however, many mechanistic aspects align with more conventional models, and whether phase separation per se regulates pol II activity in cells remains controversial. In this review, we describe the conventional and condensate-dependent models, and why their similarities and differences are important. We also compare and contrast these models in the context of genome organization and pol II transcription (initiation, elongation, and termination), and highlight the central role of RNA in these processes. Finally, we discuss mutations that disrupt normal partitioning of transcription factors, and how this may contribute to disease.
    MeSH term(s) Biophysical Phenomena ; Cell Nucleus/chemistry ; Cell Nucleus/genetics ; Genome, Human ; Humans ; Mutation ; RNA/chemistry ; RNA/genetics ; RNA/metabolism ; RNA Polymerase II/chemistry ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic
    Chemical Substances Transcription Factors ; RNA (63231-63-0) ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2021-08-30
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.167216
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  9. Article ; Online: Transcription Factor-Mediator Interfaces: Multiple and Multi-Valent.

    Taatjes, Dylan J

    Journal of molecular biology

    2017  Volume 429, Issue 20, Page(s) 2996–2998

    MeSH term(s) Gene Expression Regulation ; Mediator Complex/genetics ; RNA Polymerase II/genetics ; Transcription Factors
    Chemical Substances Mediator Complex ; Transcription Factors ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2017-07-15
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2017.07.006
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  10. Article: SnapShot: Mediator complex structure

    Nayak, Shraddha / Taatjes, Dylan J.

    Cell. 2022 Sept. 01, v. 185, no. 18

    2022  

    Abstract: The Mediator complex controls RNA polymerase II transcription genome-wide. In humans, Mediator consists of 26 subunits; furthermore, a four-subunit "Mediator kinase module" can reversibly associate with the complex. Mediator structure is generally ... ...

    Abstract The Mediator complex controls RNA polymerase II transcription genome-wide. In humans, Mediator consists of 26 subunits; furthermore, a four-subunit "Mediator kinase module" can reversibly associate with the complex. Mediator structure is generally conserved from yeast to humans, although the human complex is larger, more structurally disordered, and contains metazoan-specific subunits. To view this SnapShot, open or download the PDF.
    Keywords DNA-directed RNA polymerase ; humans ; yeasts
    Language English
    Dates of publication 2022-0901
    Size p. 3458-3458.e1.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2022.07.011
    Database NAL-Catalogue (AGRICOLA)

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