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  1. Article ; Online: Good reasons for structural biology.

    Cramer, Patrick

    Nature structural & molecular biology

    2024  Volume 31, Issue 3, Page(s) 393–394

    MeSH term(s) Molecular Biology ; Biology
    Language English
    Publishing date 2024-03-01
    Publishing country United States
    Document type Letter
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-024-01232-7
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  2. Article ; Online: AlphaFold2 and the future of structural biology.

    Cramer, Patrick

    Nature structural & molecular biology

    2021  Volume 28, Issue 9, Page(s) 704–705

    MeSH term(s) Algorithms ; Amino Acid Sequence ; Computational Biology/methods ; Deep Learning ; Internet ; Protein Conformation ; Protein Folding ; Sequence Alignment ; Structure-Activity Relationship
    Language English
    Publishing date 2021-08-10
    Publishing country United States
    Document type Letter
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-021-00650-1
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  3. Article ; Online: RNA polymerase II elongation factors use conserved regulatory mechanisms.

    Chen, Ying / Cramer, Patrick

    Current opinion in structural biology

    2024  Volume 84, Page(s) 102766

    Abstract: RNA polymerase II (Pol II) transcription is regulated by many elongation factors. Among these factors, TFIIF, PAF-RTF1, ELL and Elongin stimulate mRNA chain elongation by Pol II. Cryo-EM structures of Pol II complexes with these elongation factors now ... ...

    Abstract RNA polymerase II (Pol II) transcription is regulated by many elongation factors. Among these factors, TFIIF, PAF-RTF1, ELL and Elongin stimulate mRNA chain elongation by Pol II. Cryo-EM structures of Pol II complexes with these elongation factors now reveal some general principles on how elongation factors bind Pol II and how they stimulate transcription. All four elongation factors contact Pol II at domains external 2 and protrusion, whereas TFIIF and ELL additionally bind the Pol II lobe. All factors apparently stabilize cleft-flanking elements, whereas RTF1 and Elongin additionally approach the active site with a latch element and may influence catalysis or translocation. Due to the shared binding sites on Pol II, factor binding is mutually exclusive, and thus it remains to be studied what determines which elongation factors bind at a certain gene and under which condition.
    MeSH term(s) RNA Polymerase II/chemistry ; Elongin/genetics ; Elongin/metabolism ; Peptide Elongation Factors/genetics ; Peptide Elongation Factors/metabolism ; Transcription Factors, TFII/chemistry ; Transcription Factors, TFII/genetics ; Transcription Factors, TFII/metabolism ; Binding Sites ; Transcription, Genetic
    Chemical Substances RNA Polymerase II (EC 2.7.7.-) ; Elongin ; Peptide Elongation Factors ; Transcription Factors, TFII
    Language English
    Publishing date 2024-01-04
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2023.102766
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  4. Article ; Online: Rosalind Franklin and the Advent of Molecular Biology.

    Cramer, Patrick

    Cell

    2020  Volume 182, Issue 4, Page(s) 787–789

    Abstract: Rosalind Franklin provided the key data for deriving the double helix structure of DNA. The English chemist also pioneered structural studies of colloids, viruses, and RNA. To celebrate the ... ...

    Abstract Rosalind Franklin provided the key data for deriving the double helix structure of DNA. The English chemist also pioneered structural studies of colloids, viruses, and RNA. To celebrate the 100
    MeSH term(s) Biographies as Topic ; DNA/chemistry ; History, 20th Century ; Molecular Biology/history ; RNA/chemistry ; Viruses/chemistry ; X-Ray Diffraction
    Chemical Substances RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2020-07-29
    Publishing country United States
    Document type Historical Article ; Journal Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2020.07.028
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  5. Article ; Online: 500 years after the first circumnavigation of the world: the efforts, rewards and drawbacks of exploration.

    Cramer, Patrick

    FEBS letters

    2019  Volume 594, Issue 2, Page(s) 207–208

    MeSH term(s) Earth, Planet ; Geography/history ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Research/history ; Travel/history
    Language English
    Publishing date 2019-12-19
    Publishing country England
    Document type Editorial ; Historical Article
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1002/1873-3468.13714
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  6. Article ; Online: Eukaryotic Transcription Turns 50.

    Cramer, Patrick

    Cell

    2019  Volume 179, Issue 4, Page(s) 808–812

    Abstract: This year we celebrate the ... ...

    Abstract This year we celebrate the 50
    MeSH term(s) DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/history ; Eukaryota/genetics ; History, 20th Century ; Humans ; Transcription Factors/genetics ; Transcription, Genetic
    Chemical Substances Transcription Factors ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2019-10-30
    Publishing country United States
    Document type Historical Article ; Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2019.09.018
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  7. Book ; Thesis: Untersuchung zur Dauer und zu Abbruchgründen der antiretroviaralen Startmedikation bei HIV-infizierten Patienten

    Cramer, Patrick

    2003  

    Author's details vorgelegt von Patrick Cramer
    Language German
    Size 100 S. : graph. Darst.
    Publishing country Germany
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Köln, Univ., Diss., 2003
    HBZ-ID HT013792423
    Database Catalogue ZB MED Medicine, Health

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  8. Article ; Online: Organization and regulation of gene transcription.

    Cramer, Patrick

    Nature

    2019  Volume 573, Issue 7772, Page(s) 45–54

    Abstract: The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy ... ...

    Abstract The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy studies have revealed that transcription involves the condensation of factors in the cell nucleus. A model is emerging for the transcription of protein-coding genes in which distinct transient condensates form at gene promoters and in gene bodies to concentrate the factors required for transcription initiation and elongation, respectively. The transcribing enzyme RNA polymerase II may shuttle between these condensates in a phosphorylation-dependent manner. Molecular principles are being defined that rationalize transcriptional organization and regulation, and that will guide future investigations.
    MeSH term(s) Animals ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/metabolism ; Enhancer Elements, Genetic/genetics ; Gene Expression Regulation ; Humans ; Promoter Regions, Genetic/genetics ; Transcription Elongation, Genetic ; Transcription Factors, General/chemistry ; Transcription Factors, General/metabolism ; Transcription Initiation, Genetic
    Chemical Substances Transcription Factors, General ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2019-08-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-019-1517-4
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  9. Article ; Online: In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization.

    Oberbeckmann, Elisa / Quililan, Kimberly / Cramer, Patrick / Oudelaar, A Marieke

    Nature genetics

    2024  Volume 56, Issue 3, Page(s) 483–492

    Abstract: Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms driving the formation of these domains are difficult to dissect in vivo and remain poorly understood. Here we reconstitute Saccharomyces cerevisiae chromatin in vitro and ... ...

    Abstract Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms driving the formation of these domains are difficult to dissect in vivo and remain poorly understood. Here we reconstitute Saccharomyces cerevisiae chromatin in vitro and determine its 3D organization at subnucleosome resolution by micrococcal nuclease-based chromosome conformation capture and molecular dynamics simulations. We show that regularly spaced and phased nucleosome arrays form chromatin domains in vitro that resemble domains in vivo. This demonstrates that neither loop extrusion nor transcription is required for basic domain formation in yeast. In addition, we find that the boundaries of reconstituted domains correspond to nucleosome-free regions and that insulation strength scales with their width. Finally, we show that domain compaction depends on nucleosome linker length, with longer linkers forming more compact structures. Together, our results demonstrate that regular nucleosome positioning is important for the formation of chromatin domains and provide a proof-of-principle for bottom-up 3D genome studies.
    MeSH term(s) Nucleosomes/genetics ; Chromatin/genetics ; DNA ; Saccharomyces cerevisiae/genetics
    Chemical Substances Nucleosomes ; Chromatin ; DNA (9007-49-2)
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-023-01649-8
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  10. Article ; Online: Three-step mechanism of promoter escape by RNA polymerase II.

    Zhan, Yumeng / Grabbe, Frauke / Oberbeckmann, Elisa / Dienemann, Christian / Cramer, Patrick

    Molecular cell

    2024  

    Abstract: The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation ...

    Abstract The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription.
    Language English
    Publishing date 2024-04-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2024.03.016
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