Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

(2014) Christopher M. Weber et al.   MOLECULAR CELL

RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement

(2014) Pyae P Hein et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

(2014) M. H. Larson et al.   SCIENCE

Interactions between RNA polymerase and the "core recognition element" counteract pausing

(2014) I. O. Vvedenskaya et al.   SCIENCE

Transcription-replication encounters, consequences and genomic instability

(2013) Anne Helmrich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

C o F old : an RNA secondary structure prediction method that takes co-transcriptional folding into account

(2013) Jeff R. Proctor et al.   NUCLEIC ACIDS RESEARCH

Intermittent Transcription Dynamics for the Rapid Production of Long Transcripts of High Fidelity

(2013) Martin Depken et al.   Cell Reports

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

(2012) Lacramioara Bintu et al.   CELL

RNA Polymerase Backtracking in Gene Regulation and Genome Instability

(2012) Evgeny Nudler   CELL

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

(2012) B. Zamft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Unified Model of Transcription Elongation: What Have We Learned from Single-Molecule Experiments?

(2011) Dáibhid Ó Maoiléidigh et al.   BIOPHYSICAL JOURNAL

Linking RNA Polymerase Backtracking to Genome Instability in E. coli

(2011) Dipak Dutta et al.   CELL

Structural basis of RNA polymerase II backtracking, arrest and reactivation

(2011) Alan C. M. Cheung et al.   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Splicing-Dependent RNA Polymerase Pausing in Yeast

(2010) Ross D. Alexander et al.   MOLECULAR CELL

Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes

(2010) Norman E. Watkins et al.   NUCLEIC ACIDS RESEARCH

The Origin of Short Transcriptional Pauses

(2009) Martin Depken et al.   BIOPHYSICAL JOURNAL

RNA polymerase fidelity and transcriptional proofreading

(2009) Jasmin F Sydow et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural Basis of Transcription: Mismatch-Specific Fidelity Mechanisms and Paused RNA Polymerase II with Frayed RNA

(2009) Jasmin F. Sydow et al.   MOLECULAR CELL

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH