Nucleosomal elements that control the topography of the barrier to transcription.

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Cell

• Publication date

  2012-11-09

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/j.cell.2012.10.009PMID 23141536PMCID PMC3508686
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

  2012influential reference
• Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study.

  2012influential reference
• Development of a "modular" scheme to describe the kinetics of transcript elongation by RNA polymerase.

  2011influential reference
• Fitting experimental transcription data with a comprehensive template-dependent modular kinetic model.

  2011cited by this paper
• Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II

  2010cited by this paper
• Long-range effects of histone point mutations on DNA remodeling revealed from computational analyses of SIN-mutant nucleosome structures

  2010cited by this paper
• RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones

  2010cited by this paper
• spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes.

  2009influential reference
• Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

  2009influential reference
• Inter-Subunit Coordination in a Homomeric Ring-ATPase

  2009cited by this paper
• Single-molecule tracking of mRNA exiting from RNA polymerase II

  2008cited by this paper
• Histone N-terminal Tails Interfere with Nucleosome Traversal by RNA Polymerase II*

  2008influential reference
• The role of chromatin during transcription.

  2007cited by this paper
• Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner

  2007cited by this paper
• Structural basis for the histone chaperone activity of Asf1.

  2006cited by this paper
• Differential detection of dual traps improves the spatial resolution of optical tweezers.

  2006influential reference
• Effect of force on mononucleosomal dynamics

  2006influential reference
• Deciphering the Roles of the Histone H2B N-Terminal Domain in Genome-Wide Transcription

  2006cited by this paper
• DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC.

  2006cited by this paper
• Thermodynamic and kinetic modeling of transcriptional pausing.

  2006cited by this paper
• Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II.

  2006influential reference
• Rapid spontaneous accessibility of nucleosomal DNA

  2005cited by this paper
• Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes.

  2005cited by this paper
• Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

  2005cited by this paper
• Mechanics of the kinesin step

  2005cited by this paper
• Nature of the nucleosomal barrier to RNA polymerase II.

  2005influential reference
• Sequence-dependent kinetic model for transcription elongation by RNA polymerase.

  2004cited by this paper
• Crystal structures of histone Sin mutant nucleosomes reveal altered protein–DNA interactions

  2004influential reference
• DNA translocation and nucleosome remodeling assays by the RSC chromatin remodeling complex.

  2004cited by this paper
• Measurement of histone-DNA interaction free energy in nucleosomes.

  2004influential reference
• Characterization of a novel RNA polymerase II arrest site which lacks a weak 3' RNA-DNA hybrid.

  2004cited by this paper
• Assays and affinity purification of biotinylated and nonbiotinylated forms of double-tagged core RNA polymerase II from Saccharomyces cerevisiae.

  2003cited by this paper
• The Nonessential H2A N-Terminal Tail Can Function as an Essential Charge Patch on the H2A.Z Variant N-Terminal Tail

  2003cited by this paper
• Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II.

  2001cited by this paper
• Preferential interaction of the core histone tail domains with linker DNA

  2001cited by this paper
• A general model for nucleic acid helicases and their "coupling" within macromolecular machines.

  2001cited by this paper
• Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites.

  2001cited by this paper
• Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin.

  2001cited by this paper
• Acetylation Increases the α-Helical Content of the Histone Tails of the Nucleosome*

  2000cited by this paper
• DNA sequence-dependent contributions of core histone tails to nucleosome stability: differential effects of acetylation and proteolytic tail removal.

  2000cited by this paper
• Effects of Histone Tail Domains on the Rate of Transcriptional Elongation through a Nucleosome

  2000cited by this paper
• ATP-Dependent Chromatin-Remodeling Complexes

  2000cited by this paper
• Transcriptional pause, arrest and termination sites for RNA polymerase II in mammalian N- and c-myc genes.

  1999cited by this paper
• New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning.

  1998cited by this paper
• Translocation and Transcriptional Arrest during Transcript Elongation by RNA Polymerase II*

  1996cited by this paper
• Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription.

  1995cited by this paper
• Core histone hyperacetylation co‐maps with generalized DNase I sensitivity in the chicken beta‐globin chromosomal domain.

  1994cited by this paper
• A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli.

  1991influential reference
• Structure of chromatin containing extensively acetylated H3 and H4.

  1978cited by this paper

• Evolution of promoter-proximal pausing enabled a new layer of transcription control

  2025cites this paper
• A nucleosome switch primes hepatitis B virus infection.

  2025cites this paper
• Chromatin buffers torsional stress during transcription.

  2025cites this paper
• Fragile nucleosomes are essential for RNA Polymerase II to transcribe in eukaryotes

  2025cites this paper
• FACT weakens the nucleosomal barrier to transcription and preserves its integrity by forming a hexasome-like intermediate.

  2025cites this paper
• The role of histone modifications in transcription regulation upon DNA damage

  2025cites this paper
• Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes

  2025cites this paper
• Pause Patrol: Negative Elongation Factor's role in Promoter-Proximal Pausing and beyond.

  2024cites this paper
• Chromatin Buffers Torsional Stress During Transcription

  2024cites this paper
• A nucleosome switch primes Hepatitis B Virus infection

  2024cites this paper
• Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA–histone interactions

  2024cites this paper
• Evolution of promoter-proximal pausing enabled a new layer of transcription control

  2024cites this paper
• Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics

  2024cites this paper
• Biomimetic concentric microgrooved titanium surfaces influence bone marrow-derived mesenchymal stem cell osteogenic differentiation via H3K4 trimethylation epigenetic regulation.

  2024cites this paper
• The dynamics and functional mechanisms of H2B mono-ubiquitination

  2024cites this paper
• Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions

  2024cites this paper
• A hypothetical model: Chromatin remodelers couple with acetyltransferases to trigger the elongation of RNA polymerase II (pol II)

  2024cites this paper
• The Effects of Histone H2B ubiquitylations and H3K79me3 on Transcription Elongation

  2023cites this paper
• Effects of Histone H2B Ubiquitylations and H3K79me3 on Transcription Elongation.

  2023cites this paper
• Methods to investigate nucleosome structure and dynamics with single-molecule FRET.

  2023cites this paper
• Single-molecule studies reveal the off-pathway elemental pause state as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors

  2023cites this paper
• Structural Transition of the Nucleosome during Transcription Elongation

  2023cites this paper
• KDM4-dependent DNA breaks at active promoters facilitate +1 nucleosome eviction

  2023cites this paper
• 激光双光镊在单分子生物物理中的研究进展

  2023cites this paper
• Transcription elongation is finely tuned by dozens of regulatory factors

  2022cites this paper
• PARP1: Liaison of Chromatin Remodeling and Transcription

  2022cites this paper
• The Drosophila BEAF insulator protein interacts with the polybromo subunit of the PBAP chromatin remodeling complex

  2022cites this paper
• The development of single molecule force spectroscopy: from polymer biophysics to molecular machines

  2022cites this paper
• Testis-specific H2BFWT disrupts nucleosome integrity through reductions of DNA-histone interactions

  2022cites this paper
• Structure of a backtracked hexasomal intermediate of nucleosome transcription.

  2022cites this paper
• Nucleosome assembly and disassembly pathways in vitro

  2022cites this paper
• RNA polymerase efficiently transcribes through DNA‐scaffolded, cooperative bacteriophage repressor complexes

  2022cites this paper
• Transcriptional activity is shaped by the chromatin landscapes in Arabidopsis

  2022cites this paper
• Secondary structures in RNA synthesis, splicing and translation

  2022cites this paper
• Transcription disrupts DNA-scaffolded bacteriophage repressor complexes

  2022cites this paper
• Multiscale modelling of chromatin organisation: Resolving nucleosomes at near-atomistic resolution inside genes.

  2022cites this paper
• Mechanical determinants of chromatin topology and gene expression

  2022cites this paper
• Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts

  2022influential citation
• Alternative splicing regulation of membrane trafficking genes during myogenesis

  2022cites this paper
• Dynamics of transcription elongation are finely tuned by dozens of regulatory factors

  2021cites this paper
• Recognition of the inherently unstable H2A nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange.

  2021cites this paper
• Proteins mediating different DNA topologies block RNAP elongation with different efficiency

  2021cites this paper
• Histone Tail Conformations: A Fuzzy Affair with DNA.

  2021cites this paper
• RNA polymerase II speed: a key player in controlling and adapting transcriptome composition

  2021cites this paper
• Collaboration through chromatin: mechanisms of molecular motors at the interface of transcription and chromatin structure.

  2021influential citation
• Single-Molecule Techniques to Study Chromatin

  2021cites this paper
• Timing RNA polymerase pausing with TV-PRO-seq

  2021cites this paper
• Transcription shapes genome-wide histone acetylation patterns

  2021cites this paper
• Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging

  2021influential citation
• Nucleosome Dynamics during Transcription Elongation

  2020cites this paper
• Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions

  2020cites this paper
• The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

  2020cites this paper
• The potential underlying mechanism of the leukemia caused by MLL‐fusion and potential treatments

  2020cites this paper
• Estudos biofísicos e in vivo de moléculas ligantes de nucleossomo

  2020cites this paper
• The INO80 ATP-dependent chromatin remodelling complex alleviates stalled Polymerase II to promote non-coding RNA transcription termination

  2020cites this paper
• Histone Variants: The Nexus of Developmental Decisions and Epigenetic Memory.

  2020cites this paper
• Interactions With Histone H3 & Tools to Study Them

  2020cites this paper
• Single-Molecule Analysis and Engineering of DNA Motors.

  2020cites this paper
• Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility

  2020cites this paper
• JMJD5 couples with CDK9 to release the paused RNA polymerase II

  2020cites this paper
• Nucleosome unwrapping and unstacking.

  2020cites this paper
• Protein hyperacylation links mitochondrial dysfunction with nuclear organization

  2020cites this paper
• Advances in visualizing transcription factor-DNA interactions.

  2020cites this paper
• Small-angle neutron scattering (SANS) and spin-echo SANS measurements reveal the logarithmic fractal structure of the large-scale chromatin organization in HeLa nuclei

  2019cites this paper
• Using genetic and genomic approaches to understand haematopoietic cellular biology and dysregulation in disease

  2019cites this paper
• Single-Molecule Studies of Exonucleases: Following Cleavage Actions One Step at a Time

  2019cites this paper
• PRC2 bridges non-adjacent nucleosomes to establish heterochromatin

  2019cites this paper
• Transcription through the nucleosome.

  2019cites this paper
• H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity

  2019cites this paper
• Steps toward cell-like systems: spatio-temporal control of shared molecular resources for cell-free gene expression

  2019cites this paper
• Structural insight into nucleosome transcription by RNA polymerase II with elongation factors

  2019cites this paper
• Molecular Mechanism of Spontaneous Nucleosome Unraveling.

  2019cites this paper
• Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II.

  2019cites this paper
• TFS and Spt4/5 accelerate transcription through archaeal histone‐based chromatin

  2019cites this paper
• RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome

  2019cites this paper
• Biophysics of Chromatin Dynamics.

  2019cites this paper
• Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling

  2019cites this paper
• The Role of Archaeal Chromatin in Transcription.

  2019cites this paper
• DNA sequence is a major determinant of tetrasome dynamics

  2019cites this paper
• High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier

  2019cites this paper
• The epigenetic mechanisms of nanotopography-guided osteogenic differentiation of mesenchymal stem cells via high-throughput transcriptome sequencing

  2018cites this paper
• Dissection of structural dynamics of chromatin fibers by single-molecule magnetic tweezers

  2018cites this paper
• New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.

  2018cites this paper
• Molecular Traffic Jams on DNA

  2018influential citation
• Nucleosomes Exhibit Non‐uniform Unwrapping Along Native Chromatin Fibers with Increasing Salt Concentration as Revealed by Direct Imaging in a Microfluidic Channel

  2018cites this paper
• Cooke-Triplet tweezers: more compact, robust, and efficient optical tweezers.

  2018cites this paper
• Timing Polymerase Pausing with TV-PRO-seq

  2018cites this paper
• The role of RNA Polymerase II-dependent transcription elongation in the cross-talk between mRNA synthesis and decay.

  2018cites this paper
• NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes

  2018cites this paper
• Transcriptomics and Functional Analysis of Graphene-Guided Osteogenic Differentiation of Mesenchymal Stem Cells.

  2018cites this paper
• Single‐molecule nucleosome remodeling by INO80 and effects of histone tails

  2018cites this paper
• Modifying Chromatin by Histone Tail Clipping.

  2018cites this paper
• Molecular Highways-Navigating Collisions of DNA Motor Proteins.

  2018cites this paper
• The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome

  2017influential citation
• Cell fate regulation by chromatin ADP-ribosylation.

  2017cites this paper
• The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression

  2017cites this paper
• Cdk9 and Brd4 regulate eukaryotic transcription

  2017cites this paper
• Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b.

  2017cites this paper
• Variation in DNA Methylation Is Not Consistently Reflected by Sociality in Hymenoptera

  2017cites this paper
• The interplay between polymerase organization and nucleosome occupancy along DNA : How dynamic roadblocks on the DNA induce the formation of RNA polymerase pelotons

  2017cites this paper