Published in Mol Cell on June 01, 2003
Control of stochasticity in eukaryotic gene expression. Science (2004) 12.85
Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell (2009) 8.69
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res (2006) 7.72
Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol (2005) 6.37
Pioneer transcription factors: establishing competence for gene expression. Genes Dev (2011) 6.01
H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet (2009) 5.82
Global nucleosome occupancy in yeast. Genome Biol (2004) 5.49
Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell (2005) 5.36
Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev (2003) 5.13
Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol (2006) 5.01
Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol (2005) 4.48
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
Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol Cell Biol (2004) 4.06
Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol Cell Biol (2005) 3.83
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res (2004) 3.63
Transcriptional activation triggers deposition and removal of the histone variant H3.3. Genes Dev (2005) 3.57
Chromatin decouples promoter threshold from dynamic range. Nature (2008) 3.24
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods (2009) 3.16
The molecular basis of eukaryotic transcription. Proc Natl Acad Sci U S A (2007) 3.09
Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet (2006) 3.08
Chromatin remodeling: insights and intrigue from single-molecule studies. Nat Struct Mol Biol (2007) 2.79
Acetylation of H2AZ Lys 14 is associated with genome-wide gene activity in yeast. Genes Dev (2006) 2.73
Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. EMBO J (2004) 2.63
Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell (2008) 2.47
Chromatin remodeling by nucleosome disassembly in vitro. Proc Natl Acad Sci U S A (2006) 2.41
Sir2 deacetylates histone H3 lysine 56 to regulate telomeric heterochromatin structure in yeast. Mol Cell (2007) 2.38
Nutritional control of growth and development in yeast. Genetics (2012) 2.33
A role for noncoding transcription in activation of the yeast PHO5 gene. Proc Natl Acad Sci U S A (2007) 2.33
Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias. Genes Dev (2005) 2.26
FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter. Mol Cell (2009) 2.19
Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev (2005) 2.06
Centromere-encoded RNAs are integral components of the maize kinetochore. Proc Natl Acad Sci U S A (2004) 1.95
Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level. Nucleic Acids Res (2005) 1.94
Replication-independent core histone dynamics at transcriptionally active loci in vivo. Genes Dev (2005) 1.94
Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res (2009) 1.93
Evidence for histone eviction in trans upon induction of the yeast PHO5 promoter. Mol Cell Biol (2004) 1.92
Domain-wide displacement of histones by activated heat shock factor occurs independently of Swi/Snf and is not correlated with RNA polymerase II density. Mol Cell Biol (2005) 1.89
VP16-dependent association of chromatin-modifying coactivators and underrepresentation of histones at immediate-early gene promoters during herpes simplex virus infection. J Virol (2004) 1.89
A quantitative model of transcription factor-activated gene expression. Nat Struct Mol Biol (2008) 1.86
Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms. J Mol Biol (2007) 1.85
Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. EMBO J (2005) 1.83
Linking stochastic fluctuations in chromatin structure and gene expression. PLoS Biol (2013) 1.81
H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics (2012) 1.73
LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin. PLoS Genet (2009) 1.73
The Swi/Snf complex is important for histone eviction during transcriptional activation and RNA polymerase II elongation in vivo. Mol Cell Biol (2007) 1.72
Spontaneous access to DNA target sites in folded chromatin fibers. J Mol Biol (2008) 1.69
Dynamic epigenetic regulation in neurons: enzymes, stimuli and signaling pathways. Nat Neurosci (2010) 1.68
Structure of a RSC-nucleosome complex and insights into chromatin remodeling. Nat Struct Mol Biol (2008) 1.62
SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol Cell (2010) 1.62
Chromatin and transcription in yeast. Genetics (2012) 1.61
Fine-structure analysis of ribosomal protein gene transcription. Mol Cell Biol (2006) 1.61
Architecture of the SWI/SNF-nucleosome complex. Mol Cell Biol (2008) 1.58
Histone dynamics on the interleukin-2 gene in response to T-cell activation. Mol Cell Biol (2005) 1.57
Recruitment and dissociation of nonhomologous end joining proteins at a DNA double-strand break in Saccharomyces cerevisiae. Genetics (2008) 1.55
Histone deacetylases RPD3 and HOS2 regulate the transcriptional activation of DNA damage-inducible genes. Mol Cell Biol (2007) 1.52
Global turnover of histone post-translational modifications and variants in human cells. Epigenetics Chromatin (2010) 1.49
Coordinated histone modifications are associated with gene expression variation within and between species. Genome Res (2011) 1.49
Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules. Genes Dev (2008) 1.48
Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. PLoS Genet (2006) 1.48
Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation. EMBO J (2004) 1.46
Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators. Mol Cell Biol (2007) 1.44
Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc Natl Acad Sci U S A (2010) 1.37
SWI/SNF displaces SAGA-acetylated nucleosomes. Eukaryot Cell (2006) 1.36
Altered nucleosome occupancy and histone H3K4 methylation in response to 'transcriptional stress'. EMBO J (2005) 1.35
Dynamic histone variant exchange accompanies gene induction in T cells. Mol Cell Biol (2009) 1.31
Regulating the chromatin landscape: structural and mechanistic perspectives. Annu Rev Biochem (2014) 1.29
The spring-loaded genome: nucleosome redistributions are widespread, transient, and DNA-directed. Genome Res (2013) 1.27
Affinity purification of specific chromatin segments from chromosomal loci in yeast. Mol Cell Biol (2003) 1.24
Quantitative analysis of the transcription control mechanism. Mol Syst Biol (2010) 1.22
Human histone chaperone nucleophosmin enhances acetylation-dependent chromatin transcription. Mol Cell Biol (2005) 1.22
Promoter occupancy is a major determinant of chromatin remodeling enzyme requirements. Mol Cell Biol (2005) 1.20
Dynamic regulation of replication independent deposition of histone H3 in fission yeast. Nucleic Acids Res (2005) 1.16
FACT and the proteasome promote promoter chromatin disassembly and transcriptional initiation. J Biol Chem (2009) 1.15
Spt3 and Mot1 cooperate in nucleosome remodeling independently of TBP recruitment. EMBO J (2004) 1.14
Diversity of operation in ATP-dependent chromatin remodelers. Biochim Biophys Acta (2011) 1.14
Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes. BMC Bioinformatics (2005) 1.13
Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast. Proc Natl Acad Sci U S A (2011) 1.12
The Tup1 corepressor directs Htz1 deposition at a specific promoter nucleosome marking the GAL1 gene for rapid activation. Mol Cell Biol (2007) 1.11
Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation. PLoS Genet (2013) 1.09
Splitting of H3-H4 tetramers at transcriptionally active genes undergoing dynamic histone exchange. Proc Natl Acad Sci U S A (2011) 1.09
Direct role for the Rpd3 complex in transcriptional induction of the anaerobic DAN/TIR genes in yeast. Mol Cell Biol (2007) 1.09
Histone modifications: from genome-wide maps to functional insights. Genome Biol (2005) 1.08
Chromatin accessibility: a window into the genome. Epigenetics Chromatin (2014) 1.06
Genome-wide nucleosome mapping of Plasmodium falciparum reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes. BMC Genomics (2009) 1.06
The Histone Database: a comprehensive resource for histones and histone fold-containing proteins. Proteins (2006) 1.05
Histone deacetylation of RB-responsive promoters: requisite for specific gene repression but dispensable for cell cycle inhibition. Mol Cell Biol (2003) 1.04
Mechanism(s) of SWI/SNF-induced nucleosome mobilization. Chembiochem (2010) 1.04
SWI/SNF and Asf1p cooperate to displace histones during induction of the saccharomyces cerevisiae HO promoter. Mol Cell Biol (2009) 1.04
Evidence that the localization of the elongation factor Spt16 across transcribed genes is dependent upon histone H3 integrity in Saccharomyces cerevisiae. Genetics (2007) 1.04
Differential cofactor requirements for histone eviction from two nucleosomes at the yeast PHO84 promoter are determined by intrinsic nucleosome stability. Mol Cell Biol (2009) 1.03
Structure of a bacterial RNA polymerase holoenzyme open promoter complex. Elife (2015) 1.02
Selective removal of promoter nucleosomes by the RSC chromatin-remodeling complex. Nat Struct Mol Biol (2011) 1.02
TEL-AML1 regulation of survivin and apoptosis via miRNA-494 and miRNA-320a. Blood (2010) 1.01
Occlusion of regulatory sequences by promoter nucleosomes in vivo. PLoS One (2011) 1.01
Regulation of histone deposition on the herpes simplex virus type 1 genome during lytic infection. J Virol (2009) 1.00
Exposing the core promoter is sufficient to activate transcription and alter coactivator requirement at RNR3. Proc Natl Acad Sci U S A (2007) 1.00
Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev (2014) 0.99
Structure of a thiol monolayer-protected gold nanoparticle at 1.1 A resolution. Science (2007) 4.73
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell (2006) 4.49
A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3. Proc Natl Acad Sci U S A (2001) 3.87
Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science (2004) 3.46
Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell (2004) 3.34
Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science (2004) 3.08
Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription. Proc Natl Acad Sci U S A (2003) 2.92
Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol Cell (2004) 2.90
Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science (2009) 2.68
The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Mol Cell (2008) 2.62
Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell (2008) 2.47
Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science (2009) 2.43
Chromatin remodeling by nucleosome disassembly in vitro. Proc Natl Acad Sci U S A (2006) 2.41
Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution. Proc Natl Acad Sci U S A (2002) 2.37
Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol Cell (2002) 2.32
A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell (2004) 2.27
Epigenomics: a roadmap, but to where? Science (2008) 1.99
Mediator as a general transcription factor. J Biol Chem (2005) 1.88
A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast. J Biol Chem (2002) 1.84
Head module control of mediator interactions. Mol Cell (2006) 1.72
Structure of a RSC-nucleosome complex and insights into chromatin remodeling. Nat Struct Mol Biol (2008) 1.62
RNA polymerase II/TFIIF structure and conserved organization of the initiation complex. Mol Cell (2003) 1.60
Association of the Mediator complex with enhancers of active genes. Proc Natl Acad Sci U S A (2003) 1.55
Architecture of an RNA polymerase II transcription pre-initiation complex. Science (2013) 1.52
Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proc Natl Acad Sci U S A (2012) 1.51
Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules. Genes Dev (2008) 1.48
Mechanism of chromatin remodeling. Proc Natl Acad Sci U S A (2010) 1.42
Structural basis of eukaryotic gene transcription. FEBS Lett (2005) 1.35
Architecture of the Mediator head module. Nature (2011) 1.30
Structural analysis of the RSC chromatin-remodeling complex. Proc Natl Acad Sci U S A (2002) 1.25
Affinity purification of specific chromatin segments from chromosomal loci in yeast. Mol Cell Biol (2003) 1.24
Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center. Proc Natl Acad Sci U S A (2004) 1.23
Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc Natl Acad Sci U S A (2012) 1.23
Rigid, specific, and discrete gold nanoparticle/antibody conjugates. J Am Chem Soc (2006) 1.22
Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damage. Mol Cell (2005) 1.22
RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription. Proc Natl Acad Sci U S A (2010) 1.17
Initiation complex structure and promoter proofreading. Science (2011) 1.13
Defined DNA/nanoparticle conjugates. Proc Natl Acad Sci U S A (2005) 1.09
TOR-dependent reduction in the expression level of Rrn3p lowers the activity of the yeast RNA Pol I machinery, but does not account for the strong inhibition of rRNA production. Nucleic Acids Res (2010) 1.05
Subunit architecture of general transcription factor TFIIH. Proc Natl Acad Sci U S A (2012) 1.04
Selective removal of promoter nucleosomes by the RSC chromatin-remodeling complex. Nat Struct Mol Biol (2011) 1.02
Thiolate ligands for synthesis of water-soluble gold clusters. J Am Chem Soc (2005) 1.02
Establishment and maintenance of alternative chromatin states at a multicopy gene locus. Cell (2011) 1.02
RNA polymerase II transcription: structure and mechanism. Biochim Biophys Acta (2012) 1.01
Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution. Proc Natl Acad Sci U S A (2009) 1.01
Occlusion of regulatory sequences by promoter nucleosomes in vivo. PLoS One (2011) 1.01
Chromatin remodeling by DNA bending, not twisting. Proc Natl Acad Sci U S A (2005) 1.00
Isolation and assay of the RSC chromatin-remodeling complex from Saccharomyces cerevisiae. Methods Enzymol (2004) 0.97
Revised subunit structure of yeast transcription factor IIH (TFIIH) and reconciliation with human TFIIH. J Biol Chem (2003) 0.96
Formation and fate of a complete 31-protein RNA polymerase II transcription preinitiation complex. J Biol Chem (2013) 0.94
Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S. cerevisiae. Nucleic Acids Res (2012) 0.94
Site specific phosphorylation of yeast RNA polymerase I. Nucleic Acids Res (2007) 0.94
Synthesis and bioconjugation of 2 and 3 nm-diameter gold nanoparticles. Bioconjug Chem (2010) 0.94
An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics. Mol Cell Biol (2009) 0.93
Tfb6, a previously unidentified subunit of the general transcription factor TFIIH, facilitates dissociation of Ssl2 helicase after transcription initiation. Proc Natl Acad Sci U S A (2012) 0.92
Chromatin states at ribosomal DNA loci. Biochim Biophys Acta (2013) 0.92
Lock and key to transcription: σ-DNA interaction. Cell (2011) 0.90
Studies on the assembly characteristics of large subunit ribosomal proteins in S. cerevisae. PLoS One (2013) 0.90
Reduction in ribosomal protein synthesis is sufficient to explain major effects on ribosome production after short-term TOR inactivation in Saccharomyces cerevisiae. Mol Cell Biol (2010) 0.90
Alternative chromatin structures of the 35S rRNA genes in Saccharomyces cerevisiae provide a molecular basis for the selective recruitment of RNA polymerases I and II. Mol Cell Biol (2010) 0.90
RNA polymerase I termination: Where is the end? Biochim Biophys Acta (2012) 0.90
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proc Natl Acad Sci U S A (2014) 0.88
Purification of specific chromatin domains from single-copy gene loci in Saccharomyces cerevisiae. Methods Mol Biol (2014) 0.88
Purification of defined chromosomal domains. Methods Enzymol (2004) 0.88
A bridge to transcription by RNA polymerase. J Biol (2008) 0.87
Synthesis and characterization of Au102(p-MBA)44 nanoparticles. J Am Chem Soc (2011) 0.87
Isolation of an activator-dependent, promoter-specific chromatin remodeling factor. Proc Natl Acad Sci U S A (2011) 0.86
Interrelationships between yeast ribosomal protein assembly events and transient ribosome biogenesis factors interactions in early pre-ribosomes. PLoS One (2012) 0.86
The Reb1-homologue Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast. EMBO J (2012) 0.84
Electronic and vibrational signatures of the Au102(p-MBA)44 cluster. J Am Chem Soc (2011) 0.83
Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic Acids Res (2013) 0.82
Electron microscopic analysis of the RSC chromatin remodeling complex. Methods Enzymol (2004) 0.80
Chromatin structure analysis of single gene molecules by psoralen cross-linking and electron microscopy. Methods Mol Biol (2015) 0.77
Local tertiary structure probing of ribonucleoprotein particles by nuclease fusion proteins. PLoS One (2012) 0.76
UV light-induced DNA lesions cause dissociation of yeast RNA polymerases-I and establishment of a specialized chromatin structure at rRNA genes. Nucleic Acids Res (2013) 0.75
Corrigendum: Double-flow focused liquid injector for efficient serial femtosecond crystallography. Sci Rep (2017) 0.75
An autobiographic conversation with Roger D. Kornberg on his work on transcription regulation. Cell Death Differ (2007) 0.75
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