Published in J Mol Biol on December 22, 2004
High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat Struct Mol Biol (2009) 2.74
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The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair. J Cell Biol (2010) 1.80
Chromatin dynamics and the repair of DNA double strand breaks. Cell Cycle (2011) 1.63
Nucleosomal elements that control the topography of the barrier to transcription. Cell (2012) 1.46
Nucleosome disassembly intermediates characterized by single-molecule FRET. Proc Natl Acad Sci U S A (2009) 1.44
SWI/SNF displaces SAGA-acetylated nucleosomes. Eukaryot Cell (2006) 1.36
In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet (2012) 1.28
Histone modifications in Trypanosoma brucei. Mol Biochem Parasitol (2007) 1.27
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Mechanism of transcription through a nucleosome by RNA polymerase II. Biochim Biophys Acta (2012) 1.19
Acetylation of vertebrate H2A.Z and its effect on the structure of the nucleosome. Biochemistry (2009) 1.17
Histone acetyltransferase inhibitor anacardic acid causes changes in global gene expression during in vitro Plasmodium falciparum development. Eukaryot Cell (2008) 1.15
Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II. EMBO Rep (2010) 1.15
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The nucleosome: a transparent, slippery, sticky and yet stable DNA-protein complex. Eur Phys J E Soft Matter (2006) 1.13
Histone structure and nucleosome stability. Expert Rev Proteomics (2005) 1.11
Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss. Nat Commun (2013) 1.07
Histone N-terminal tails interfere with nucleosome traversal by RNA polymerase II. J Biol Chem (2008) 1.06
Chromatin fiber dynamics under tension and torsion. Int J Mol Sci (2010) 1.03
Histone acetylation at the human beta-globin locus changes with developmental age. Blood (2007) 1.03
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Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev (2014) 0.99
CBP mediates NF-κB-dependent histone acetylation and estrogen receptor recruitment to an estrogen response element in the BIRC3 promoter. Mol Cell Biol (2011) 0.98
Efficient and rapid nucleosome traversal by RNA polymerase II depends on a combination of transcript elongation factors. J Biol Chem (2010) 0.97
Magnetic manipulation of nanorods in the nucleus of living cells. Biophys J (2011) 0.97
Clipping of flexible tails of histones H3 and H4 affects the structure and dynamics of the nucleosome. Biophys J (2013) 0.90
Kinetics and thermodynamics of phenotype: unwinding and rewinding the nucleosome. J Mol Biol (2012) 0.90
Human T-lymphotropic virus type 1 transcription and chromatin-remodeling complexes. J Virol (2010) 0.89
Visualizing posttranslational and epigenetic modifications of endogenous proteins in vivo. Histochem Cell Biol (2015) 0.87
NuA4 links methylation of histone H3 lysines 4 and 36 to acetylation of histones H4 and H3. J Biol Chem (2014) 0.87
Opposing roles of H3- and H4-acetylation in the regulation of nucleosome structure––a FRET study. Nucleic Acids Res (2015) 0.87
Interplay among nucleosomal DNA, histone tails, and corepressor CoREST underlies LSD1-mediated H3 demethylation. Proc Natl Acad Sci U S A (2015) 0.86
H2A and H2B tails are essential to properly reconstitute nucleosome core particles. Eur Biophys J (2007) 0.85
Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations. PLoS Comput Biol (2015) 0.85
Charge state of the globular histone core controls stability of the nucleosome. Biophys J (2010) 0.85
Structural dynamics of nucleosomes at single-molecule resolution. Trends Biochem Sci (2012) 0.83
Direct measurement of local chromatin fluidity using optical trap modulation force spectroscopy. Biophys J (2006) 0.83
Unzipping single DNA molecules to study nucleosome structure and dynamics. Methods Enzymol (2012) 0.81
Homebuilt single-molecule scanning confocal fluorescence microscope studies of single DNA/protein interactions. Methods (2007) 0.80
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Deacetylase inhibitors repress STAT5-mediated transcription by interfering with bromodomain and extra-terminal (BET) protein function. Nucleic Acids Res (2015) 0.80
Reciprocal epigenetic modification of histone H2B occurs in chromatin during apoptosis in vitro and in vivo. Cell Death Differ (2010) 0.79
DNA Y structure: a versatile, multidimensional single molecule assay. Nano Lett (2014) 0.79
Pulling the chromatin. Eur Phys J E Soft Matter (2006) 0.78
β-Arrestin1 promotes the progression of chronic myeloid leukaemia by regulating BCR/ABL H4 acetylation. Br J Cancer (2014) 0.78
Activator-independent transcription of Snf1-dependent genes in mutants lacking histone tails. Mol Microbiol (2011) 0.78
Unwinding and rewinding the nucleosome inner turn: force dependence of the kinetic rate constants. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.78
Close encounters with DNA. J Phys Condens Matter (2014) 0.77
Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal. PLoS One (2013) 0.77
DNA looping mediates nucleosome transfer. Nat Commun (2016) 0.77
Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability. Sci Rep (2016) 0.76
Tension-Dependent Free Energies of Nucleosome Unwrapping. ACS Cent Sci (2016) 0.76
Effects of orally applied butyrate bolus on histone acetylation and cytochrome P450 enzyme activity in the liver of chicken - a randomized controlled trial. Nutr Metab (Lond) (2013) 0.76
High mobility group protein 1: A collaborator in nucleosome dynamics and estrogen-responsive gene expression. World J Biol Chem (2016) 0.75
The effect of epigenetic modifications on the secondary structures and possible binding positions of the N-terminal tail of histone H3 in the nucleosome: a computational study. J Mol Model (2017) 0.75
The Eaf3/5/7 Subcomplex Stimulates NuA4 Interaction with Methylated Histone H3 Lys-36 and RNA Polymerase II. J Biol Chem (2016) 0.75
Data on force-dependent structural changes of chromatin fibers measured with magnetic tweezers. Data Brief (2014) 0.75
Biocompatible and High Stiffness Nanophotonic Trap Array for Precise and Versatile Manipulation. Nano Lett (2016) 0.75
Capitalizing on disaster: Establishing chromatin specificity behind the replication fork. Bioessays (2017) 0.75
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (2008) 16.48
Breaking barriers to transcription elongation. Nat Rev Mol Cell Biol (2006) 8.18
PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell (2002) 5.59
Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science (2008) 5.48
The PARP side of the nucleus: molecular actions, physiological outcomes, and clinical targets. Mol Cell (2010) 5.06
Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell (2008) 4.81
Poly(ADP-ribosyl)ation by PARP-1: 'PAR-laying' NAD+ into a nuclear signal. Genes Dev (2005) 4.61
A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell (2011) 4.42
Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet (2012) 4.37
Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature (2009) 4.31
NAD+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1. Cell (2004) 4.21
Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock. Mol Cell Biol (2003) 3.65
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev (2011) 3.55
Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc Natl Acad Sci U S A (2002) 3.52
New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs. Nat Rev Mol Cell Biol (2012) 3.45
Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes. Science (2008) 3.45
Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes. Mol Cell (2004) 3.26
Tracking FACT and the RNA polymerase II elongation complex through chromatin in vivo. Science (2003) 3.22
PARP goes transcription. Cell (2003) 3.16
Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell (2007) 3.09
Enhancer transcripts mark active estrogen receptor binding sites. Genome Res (2013) 2.82
On PAR with PARP: cellular stress signaling through poly(ADP-ribose) and PARP-1. Genes Dev (2012) 2.82
The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature (2002) 2.77
High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat Struct Mol Biol (2009) 2.74
Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol Cell (2005) 2.68
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science (2013) 2.66
Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proc Natl Acad Sci U S A (2002) 2.53
CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes Dev (2010) 2.52
Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science (2013) 2.51
Divergent transcription: a new feature of active promoters. Cell Cycle (2009) 2.50
Dynamics of heat shock factor association with native gene loci in living cells. Nature (2006) 2.45
X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature (2011) 2.44
Regulation of coactivator complex assembly and function by protein arginine methylation and demethylimination. Proc Natl Acad Sci U S A (2005) 2.40
Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol (2007) 2.33
A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell (2004) 2.27
Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules. Phys Rev Lett (2008) 2.17
Drosophila Paf1 modulates chromatin structure at actively transcribed genes. Mol Cell Biol (2006) 2.16
Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell (2013) 2.13
PARP-1 regulates chromatin structure and transcription through a KDM5B-dependent pathway. Mol Cell (2010) 2.06
Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J Mol Biol (2004) 1.92
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Defining the status of RNA polymerase at promoters. Cell Rep (2012) 1.91
Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation. Mol Cell (2007) 1.87
The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing. Genes Dev (2009) 1.82
Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet (2010) 1.82
The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription. Mol Cell Biol (2007) 1.82
P-TEFb is critical for the maturation of RNA polymerase II into productive elongation in vivo. Mol Cell Biol (2007) 1.81
The Drosophila BRM complex facilitates global transcription by RNA polymerase II. EMBO J (2002) 1.78
Spt6 enhances the elongation rate of RNA polymerase II in vivo. EMBO J (2009) 1.77
Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Mol Cell Biol (2010) 1.75
Acetylation of estrogen receptor alpha by p300 at lysines 266 and 268 enhances the deoxyribonucleic acid binding and transactivation activities of the receptor. Mol Endocrinol (2006) 1.73
Tracking rates of transcription and splicing in vivo. Nat Struct Mol Biol (2009) 1.73
Enzymes in the NAD+ salvage pathway regulate SIRT1 activity at target gene promoters. J Biol Chem (2009) 1.70
A global view of transcriptional regulation by nuclear receptors: gene expression, factor localization, and DNA sequence analysis. Nucl Recept Signal (2008) 1.62
Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection. Nat Methods (2007) 1.61
Postrecruitment regulation of RNA polymerase II directs rapid signaling responses at the promoters of estrogen target genes. Mol Cell Biol (2008) 1.60
Probing protein-DNA interactions by unzipping a single DNA double helix. Biophys J (2002) 1.59
Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nat Struct Mol Biol (2006) 1.58
Optical torque wrench: angular trapping, rotation, and torque detection of quartz microparticles. Phys Rev Lett (2004) 1.57
Estrogen-regulated gene networks in human breast cancer cells: involvement of E2F1 in the regulation of cell proliferation. Mol Endocrinol (2007) 1.55
Transcription under torsion. Science (2013) 1.54
Poly(ADP-ribose) polymerase 1 is inhibited by a histone H2A variant, MacroH2A, and contributes to silencing of the inactive X chromosome. J Biol Chem (2007) 1.53
Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. Elife (2013) 1.51
Recruitment timing and dynamics of transcription factors at the Hsp70 loci in living cells. Mol Cell (2010) 1.50
Molecular mechanism of transcription inhibition by peptide antibiotic Microcin J25. Mol Cell (2004) 1.49
The Zn3 domain of human poly(ADP-ribose) polymerase-1 (PARP-1) functions in both DNA-dependent poly(ADP-ribose) synthesis activity and chromatin compaction. J Biol Chem (2010) 1.47
Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes. Nat Commun (2011) 1.46
Drosophila Set1 is the major histone H3 lysine 4 trimethyltransferase with role in transcription. EMBO J (2011) 1.44
Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. Genes Dev (2013) 1.43
Synergistic action of RNA polymerases in overcoming the nucleosomal barrier. Nat Struct Mol Biol (2010) 1.43
SIRT1-dependent regulation of chromatin and transcription: linking NAD(+) metabolism and signaling to the control of cellular functions. Biochim Biophys Acta (2009) 1.41
Cdk7 is required for full activation of Drosophila heat shock genes and RNA polymerase II phosphorylation in vivo. Mol Cell Biol (2003) 1.39
Genomic analyses of hormone signaling and gene regulation. Annu Rev Physiol (2010) 1.38
Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet (2013) 1.38
Activator-induced spread of poly(ADP-ribose) polymerase promotes nucleosome loss at Hsp70. Mol Cell (2011) 1.37
Single-molecule analysis of RNA polymerase transcription. Annu Rev Biophys Biomol Struct (2006) 1.37
Peptidylarginine deiminase 2-catalyzed histone H3 arginine 26 citrullination facilitates estrogen receptor α target gene activation. Proc Natl Acad Sci U S A (2012) 1.35
Genome-wide analysis reveals PADI4 cooperates with Elk-1 to activate c-Fos expression in breast cancer cells. PLoS Genet (2011) 1.33
Global analysis of transcriptional regulation by poly(ADP-ribose) polymerase-1 and poly(ADP-ribose) glycohydrolase in MCF-7 human breast cancer cells. J Biol Chem (2009) 1.32
Smads orchestrate specific histone modifications and chromatin remodeling to activate transcription. EMBO J (2006) 1.30
Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors. Phys Rev Lett (2011) 1.30
Mechanochemical kinetics of transcription elongation. Phys Rev Lett (2007) 1.25
Multiple facets of the unique histone variant macroH2A: from genomics to cell biology. Cell Cycle (2010) 1.25
Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA. Phys Rev Lett (2003) 1.25
Overcoming the nucleosome barrier during transcript elongation. Trends Genet (2012) 1.19
Specific SR protein-dependent splicing substrates identified through genomic SELEX. Nucleic Acids Res (2003) 1.18
Clickable NAD analogues for labeling substrate proteins of poly(ADP-ribose) polymerases. J Am Chem Soc (2010) 1.18
ATP-induced helicase slippage reveals highly coordinated subunits. Nature (2011) 1.16
A single-molecule technique to study sequence-dependent transcription pausing. Biophys J (2004) 1.15