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List of works by Patrick Cramer

500 years after the first circumnavigation of the world: the efforts, rewards and drawbacks of exploration

scientific article published on 19 December 2019

A Movie of RNA Polymerase II Transcription ⬇️

scientific article published on June 22, 2012

A Tandem SH2 Domain in Transcription Elongation Factor Spt6 Binds the Phosphorylated RNA Polymerase II C-terminal Repeat Domain (CTD)

scientific article

A conformational switch underlies ClpP protease function

scientific article

A conserved GA element in TATA-less RNA polymerase II promoters

scientific article

A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer

scientific article published on 14 February 2005

A cytoplasmic complex mediates specific mRNA recognition and localization in yeast

scientific article

A model for transcription initiation in human mitochondria

scientific article

A movie of the RNA polymerase nucleotide addition cycle.

scientific article published on 27 May 2009

A nano-positioning system for macromolecular structural analysis

scientific article published on 12 October 2008

A novel intermediate in transcription initiation by human mitochondrial RNA polymerase.

scientific article published on 06 January 2014

A structural perspective of CTD function

scientific article

A structural perspective on Mediator function ⬇️

scientific article published on February 15, 2012

A tale of chromatin and transcription in 100 structures

scientific article

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN.

scientific article

Allosteric antibody inhibition of human hepsin protease ⬇️

scientific article published on March 15, 2012

An alternative RNA polymerase I structure reveals a dimer hinge

scientific article

An atypical spinal meningioma with CSF metastasis: fatal progression despite aggressive treatment. Case report

scientific article published in August 2005

An experimentally generated peptide database increases the sensitivity of XL-MS with complex samples

scientific article published on 19 March 2020

An extended winged helix domain in general transcription factor E/IIE alpha

scientific article

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle

scientific article

Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus

scientific article published on 26 October 2007

Architecture and RNA binding of the human negative elongation factor.

scientific article published on 10 June 2016

Architecture of a transcribing-translating expressome

scientific article

Architecture of initiation-competent 12-subunit RNA polymerase II

scientific article (publication date: 10 June 2003)

Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex

scientific article

Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry

scientific article

Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage

scientific article

Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity

scientific article

BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies

scientific article

BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies

Biochemie und Molekulargenetik 2001

Biogenesis of multisubunit RNA polymerases ⬇️

scientific article published on January 17, 2012

CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

scientific article published on 01 August 2020

CDK9-dependent RNA polymerase II pausing controls transcription initiation

scientific article

CPD damage recognition by transcribing RNA polymerase II

scientific article published on 9 February 2007

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

scientific article published on 08 June 2020

CTD Tyrosine Phosphorylation Impairs Termination Factor Recruitment to RNA Polymerase II ⬇️

scientific article published on June 29, 2012

Cap Completion and C-Terminal Repeat Domain Kinase Recruitment Underlie the Initiation-Elongation Transition of RNA Polymerase II ⬇️

scientific article published on July 22, 2013

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

scientific article published on 30 March 2012

Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS

scientific article published on 01 December 2004

Conservation between the RNA polymerase I, II, and III transcription initiation machineries

scientific article

Conserved RNA polymerase II initiation complex structure

scientific article

Conserved architecture of the core RNA polymerase II initiation complex

scientific article published on 10 July 2014

Core Mediator structure at 3.4 Å extends model of transcription initiation complex

scientific article published on 3 May 2017

Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage ⬇️

scientific article published on March 6, 2012

Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by α-amanitin.

scientific article published on 17 March 2018

Crystallization of RNA polymerase I subcomplex A14/A43 by iterative prediction, probing and removal of flexible regions

scientific article published on 24 April 2008

DNA photodamage recognition by RNA polymerase II.

scientific article published on 11 May 2007

Deciphering the RNA polymerase II structure: a personal perspective

scientific article published in December 2006

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

scientific article published on 16 February 2016

Dimeric form of SARS-CoV-2 polymerase

scientific article

Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II

scientific article published on 01 May 2018

Drosophila miR-277 controls branched-chain amino acid catabolism and affects lifespan.

scientific article published on 30 April 2013

Dynamic Architecture of a Minimal RNA Polymerase II Open Promoter Complex

article by Barbara Treutlein et al published April 2012 in Molecular Cell

Dynamic Architecture of the RNA Polymerase II Open Promoter Complex

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast ⬇️

scientific article published on January 4, 2011

Eukaryotic Transcription Turns 50

scientific article published on 01 October 2019

Evolution of Two Modes of Intrinsic RNA Polymerase Transcript Cleavage ⬇️

scientific article published on March 23, 2011

Extending the message

scientific article published in Nature

Finding the right spot to start transcription

scientific article published on 01 August 2007

Fluorescence detection of nucleic acids and proteins in multi-component crystals

scientific article published on 18 January 2006

Functional architecture of RNA polymerase I

scientific article

Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex.

scientific article

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes.

scientific article published on 6 March 2017

Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels

scientific article

Global donor and acceptor splicing site kinetics in human cells.

scientific article

Heptad-Specific Phosphorylation of RNA Polymerase II CTD.

scientific article published in January 2016

Identification, structure, and functional requirement of the Mediator submodule Med7N/31

scientific article

In-cell architecture of an actively transcribing-translating expressome

scientific article published on 01 July 2020

Inference of gene regulation functions from dynamic transcriptome data.

scientific article

Integrator is a genome-wide attenuator of non-productive transcription

scientific article published on 23 December 2020

Iwr1 directs RNA polymerase II nuclear import.

scientific article

MC EMiNEM maps the interaction landscape of the Mediator

scientific article

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

scientific article published on 27 March 2019

Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA).

scientific article published on 28 January 2012

Mechanism of RNA polymerase II stalling by DNA alkylation.

scientific article

Mechanism of SARS-CoV-2 polymerase stalling by remdesivir

scientific article

Mechanism of Transcription Anti-termination in Human Mitochondria

scientific article published on 7 October 2017

Mechanism of Translesion Transcription by RNA Polymerase II and Its Role in Cellular Resistance to DNA Damage

scientific article

Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis

scholarly article by Florian Kabinger et al published 11 August 2021 in Nature Structural & Molecular Biology

Mechanism of transcriptional stalling at cisplatin-damaged DNA

scientific article

Mechanisms of backtrack recovery by RNA polymerases I and II.

scientific article published on 29 February 2016

Mechanistic studies of the mRNA transcription cycle.

scientific article

Mediator Architecture and RNA Polymerase II Interaction.

scientific article published on 3 February 2016

Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization

scientific article

Mediator phosphorylation prevents stress response transcription during non-stress conditions

scientific article published on 7 November 2012

Model of the Mediator middle module based on protein cross-linking.

scientific article published on 11 August 2013

Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation

scientific article

Molecular Basis of Transcription-Coupled Pre-mRNA Capping

scientific article published on 7 May 2015

Molecular Basis of Transcriptional Mutagenesis at 8-Oxoguanine

scientific article

Molecular basis of RNA polymerase III transcription repression by Maf1

scientific article

Molecular basis of RNA-dependent RNA polymerase II activity

scientific article

Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth

scientific article

Molecular biology. Self-correcting messages

scientific article published in Science

Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites

scientific article published on 17 April 2008

Multisubunit RNA polymerases

scientific article

Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site.

scientific article published on 25 May 2007

Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site.

scientific article published in August 2009

NASC-seq monitors RNA synthesis in single cells

NASC-seq monitors RNA synthesis in single cells

scientific article published on 17 July 2019

Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex

scientific article

Nano-Positioning-System Reveals Structure of the RNA Polymerase II Initially Transcribing Complex (ITC)

Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms

scientific article published on 04 September 2020

Nucleosomal arrangement affects single-molecule transcription dynamics.

scientific article published on 24 October 2016

Nucleosome-CHD4 chromatin remodeller structure maps human disease mutations

scientific article published on 16 June 2020

Nucleosome-Chd1 structure and implications for chromatin remodelling

scientific article

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

scientific article published on 22 April 2020

Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells

scientific article published on 27 May 2022

One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data ⬇️

scientific article published on July 25, 2012

Organization and regulation of gene transcription

scientific article published on 28 August 2019

Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression

scientific article published on 30 January 2014

Permissive epigenomes endow reprogramming competence to transcriptional regulators

scientific article published on 17 August 2020

Preparation and topology of the Mediator middle module

scientific article

Promoter Distortion and Opening in the RNA Polymerase II Cleft

scientific article published on 21 November 2018

Proteins: histones and chromatin.

scientific article

Proteins: how RNA polymerases work.

scientific article

RNA polymerase I contains a TFIIF-related DNA-binding subcomplex

scientific article

RNA polymerase I structure and transcription regulation

scientific article

RNA polymerase I-Rrn3 complex at 4.8 Å resolution.

scientific article

RNA polymerase II clustering through carboxy-terminal domain phase separation

scientific article published on 20 August 2018

RNA polymerase II structure: from core to functional complexes

scientific article published on April 2004

RNA polymerase II termination involves C-terminal-domain tyrosine dephosphorylation by CPF subunit Glc7

scientific article

RNA polymerase II-TFIIB structure and mechanism of transcription initiation

scientific article

RNA polymerase III subunit architecture and implications for open promoter complex formation ⬇️

scientific article published on November 6, 2012

RNA polymerase fidelity and transcriptional proofreading

scientific article

RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history

scientific article published in 2022

RNA velocity of single cells

scientific article published in Nature

RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases.

scientific article

Real-time cryo-electron microscopy data preprocessing with Warp

scientific article published on 07 October 2019

Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors

scientific article

Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II

scientific article

Rosalind Franklin and the Advent of Molecular Biology

scientific article published on 24 July 2020

Rpb4 subunit functions mainly in mRNA synthesis by RNA polymerase II.

scientific article published on 5 May 2014

Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

scientific article published in 2021

Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast.

scientific article published on 20 January 2014

Selective Mediator dependence of cell-type-specifying transcription

scientific article published on 01 June 2020

Single-molecule tracking of mRNA exiting from RNA polymerase II

scientific article

Site specific phosphorylation of yeast RNA polymerase I.

scientific article published on 15 December 2007

Small-molecule inhibitors of human mitochondrial DNA transcription

scientific article published on 04 January 2021

Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif

scientific article

Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation

scientific article published on 18 March 2017

Structural Basis of Mitochondrial Transcription Initiation

scientific article published in November 2017

Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes

scientific article published on 01 December 2019

Structural Basis of Poxvirus Transcription: Vaccinia RNA Polymerase Complexes

scientific article published on 01 December 2019

Structural Basis of RNA Polymerase I Transcription Initiation

scientific article published on March 2017

Structural Biology of RNA Polymerase II Transcription: 20 Years On

scientific article published on 21 August 2020

Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday

scientific article published on 10 May 2017

Structural basis of RNA polymerase II backtracking, arrest and reactivation

scientific article

Structural basis of RNA processing by human mitochondrial RNase P

scientific article published on 06 September 2021

Structural basis of TFIIH activation for nucleotide excision repair

scientific article published on 28 June 2019

Structural basis of initial RNA polymerase II transcription ⬇️

scientific article published on November 4, 2011

Structural basis of mitochondrial transcription

scientific article published on 06 September 2018

Structural basis of nucleosome transcription mediated by Chd1 and FACT

scientific article published on 12 April 2021

Structural basis of transcription elongation ⬇️

scientific article published on September 13, 2012

Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation

scientific article

Structural basis of transcription initiation by RNA polymerase II.

scientific article

Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution

scientific article

Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA

scientific article

Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture

scientific article published on October 2007

Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model

scientific article published on 01 July 2006

Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20.

scientific article

Structure and VP16 binding of the Mediator Med25 activator interaction domain

scientific article

Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription

scientific article

Structure and function of RNA polymerase II.

scientific article published on January 2004

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex ⬇️

scientific article published on November 14, 2012

Structure and in vivo requirement of the yeast Spt6 SH2 domain

scientific article

Structure and mechanism of RNA polymerase II CTD phosphatases

scientific article

Structure determination of transient transcription complexes

scientific article published on August 2016

Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold

scientific article

Structure of GPN-Loop GTPase Npa3 and Implications for RNA Polymerase II Assembly

scientific article published on 28 December 2015

Structure of H3K36-methylated nucleosome-PWWP complex reveals multivalent cross-gyre binding

scientific article published on 09 December 2019

Structure of RNA polymerase I transcribing ribosomal DNA genes.

scientific article published on 14 November 2016

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

scientific article published on 11 March 2020

Structure of a bifunctional DNA primase-polymerase

scientific article

Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp

scientific article published on 11 September 2017

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

scientific article published in Nature

Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs

scientific article published on 11 December 2005

Structure of an archaeal RNA polymerase

scientific article published on 5 September 2007

Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation

scientific article published on 15 June 2020

Structure of human mitochondrial RNA polymerase ⬇️

scientific article published on September 25, 2011

Structure of human mitochondrial RNA polymerase elongation complex

scientific article

Structure of paused transcription complex Pol II-DSIF-NELF

scientific article published in Nature

Structure of replicating SARS-CoV-2 polymerase

scientific article published on 21 May 2020

Structure of replicating SARS-CoV-2 polymerase

scientific article published on 28 April 2020

Structure of the Mediator head module

scientific article

Structure of the mediator subunit cyclin C and its implications for CDK8 function

scientific article published in July 2005

Structure of the super-elongation complex subunit AFF4 C-terminal homology domain reveals requirements for AFF homo- and heterodimerization

scientific article published on 30 May 2019

Structure of the transcription coactivator SAGA

scientific article published on 22 January 2020

Structure of transcribing RNA polymerase II-nucleosome complex

scientific article published in Nature Communications

Structure of transcribing mammalian RNA polymerase II

scientific article

Structure-based prediction of asparagine and aspartate degradation sites in antibody variable regions

scientific article (publication date: 2014)

Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement

scientific article published on 10 December 2007

Structure-function studies of the RNA polymerase II elongation complex

scientific article

Structure-system correlation identifies a gene regulatory Mediator submodule

scientific article

Structures and diseases

scientific article published on 01 February 2008

Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue

scientific article

Structures of complete RNA polymerase II and its subcomplex, Rpb4/7.

scientific article

Struggling to let go: a non-coding RNA directs its own extension and destruction ⬇️

scientific article published on February 22, 2013

TT-seq captures enhancer landscapes immediately after T-cell stimulation.

scientific article published on 7 March 2017

TT-seq maps the human transient transcriptome

scientific article

Template misalignment in multisubunit RNA polymerases and transcription fidelity

scientific article published on October 2006

The APT complex is involved in non-coding RNA transcription and is distinct from CPF.

scientific article published in November 2018

The Implication of Early Chromatin Changes in X Chromosome Inactivation

scientific article published on 27 December 2018

The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome.

scientific article

The RNA polymerase trigger loop functions in all three phases of the transcription cycle.

scientific article published on 3 June 2013

The Structural Basis of Transcription: 10 Years After the Nobel Prize in Chemistry

scientific article

The archaeal RNA polymerase subunit P and the eukaryotic polymerase subunit Rpb12 are interchangeable in vivo and in vitro

scientific article published on 18 December 2008

The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis

scientific article

The chemistry of transcription through damaged DNA and of translesion synthesis at atomic resolution

scientific article published on 01 January 2007

The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA.

scientific article published on 3 April 2017

The dynamic machinery of mRNA elongation

scientific article

The interaction landscape between transcription factors and the nucleosome

scientific article published in Nature

The interaction landscape between transcription factors and the nucleosome

scientific article published on 28 December 2017

The mRNA transcription/processing factor Ssu72 is a potential tyrosine phosphatase

scientific article

The pause-initiation limit restricts transcription activation in human cells

scientific article published on 09 August 2019

The phosphatidylserine receptor from Hydra is a nuclear protein with potential Fe(II) dependent oxygenase activity

scientific article

The spt5 C-terminal region recruits yeast 3' RNA cleavage factor I.

scientific article published on 30 January 2012

The transcription elongation factor Bur1-Bur2 interacts with replication protein A and maintains genome stability during replication stress.

scientific article

Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro

scientific article

Towards molecular systems biology of gene transcription and regulation

scientific article published on July 2010

Transcription activation depends on the length of the RNA polymerase II C-terminal domain

scientific article published on 08 February 2021

Transcriptome Maps of mRNP Biogenesis Factors Define Pre-mRNA Recognition

scholarly article by Carlo Baejen published in September 2014

Transcriptome maps of general eukaryotic RNA degradation factors.

scientific article published on 28 May 2019

Transcriptome surveillance by selective termination of noncoding RNA synthesis.

scientific article

Transitions for regulating early transcription

scientific article published on 01 May 2013

Uniform transitions of the general RNA polymerase II transcription complex

scientific article

Yeast mitochondrial protein Pet111p binds directly to two distinct targets in COX2 mRNA, suggesting a mechanism of translational activation

scientific article published on 25 March 2019

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