Published in Methods Enzymol on January 01, 2004
Transcriptional activation triggers deposition and removal of the histone variant H3.3. Genes Dev (2005) 3.57
CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes Dev (2010) 2.52
Polytene chromosome squash methods for studying transcription and epigenetic chromatin modification in Drosophila using antibodies. Methods (2009) 1.45
Polycomb group targeting through different binding partners of RING1B C-terminal domain. Structure (2010) 1.19
Signal Transduction Pathways Leading to Heat Shock Transcription. Sign Transduct Insights (2010) 1.04
A key role for Chd1 in histone H3 dynamics at the 3' ends of long genes in yeast. PLoS Genet (2012) 1.02
Imaging transcription dynamics at endogenous genes in living Drosophila tissues. Methods (2008) 0.99
An RNA aptamer perturbs heat shock transcription factor activity in Drosophila melanogaster. Nucleic Acids Res (2011) 0.89
The metazoan-specific mediator subunit 26 (Med26) is essential for viability and is found at both active genes and pericentric heterochromatin in Drosophila melanogaster. Mol Cell Biol (2014) 0.83
Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain is required for efficient transcription of heat shock genes. Mol Cell Biol (2012) 0.83
Visualization of the Genomic Loci That Are Bound by Specific Multiprotein Complexes by Bimolecular Fluorescence Complementation Analysis on Drosophila Polytene Chromosomes. Methods Enzymol (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
Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell (2008) 4.81
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
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
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
A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell (2004) 2.27
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
Control of transcriptional elongation. Annu Rev Genet (2013) 1.92
Defining the status of RNA polymerase at promoters. Cell Rep (2012) 1.91
Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J Mol Biol (2004) 1.87
Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation. Mol Cell (2007) 1.87
Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet (2010) 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
Tracking rates of transcription and splicing in vivo. Nat Struct Mol Biol (2009) 1.73
Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nat Struct Mol Biol (2006) 1.58
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
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
Cdk7 is required for full activation of Drosophila heat shock genes and RNA polymerase II phosphorylation in vivo. Mol Cell Biol (2003) 1.39
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
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
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
Transcription through chromatin: understanding a complex FACT. Biochim Biophys Acta (2004) 1.15
Minichromosome maintenance helicase paralog MCM9 is dispensible for DNA replication but functions in germ-line stem cells and tumor suppression. Proc Natl Acad Sci U S A (2011) 1.12
RNA aptamers directed to discrete functional sites on a single protein structural domain. Proc Natl Acad Sci U S A (2007) 1.10
Interactions between subunits of Drosophila Mediator and activator proteins. Trends Biochem Sci (2005) 1.10
Accurate prediction of inducible transcription factor binding intensities in vivo. PLoS Genet (2012) 1.10
An RNA aptamer that interferes with the DNA binding of the HSF transcription activator. Nucleic Acids Res (2006) 1.10
Probing TBP interactions in transcription initiation and reinitiation with RNA aptamers that act in distinct modes. Proc Natl Acad Sci U S A (2004) 1.09
Mechanisms by which transcription factors gain access to target sequence elements in chromatin. Curr Opin Genet Dev (2012) 1.09
Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A (2009) 1.04
The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo. Mol Cell (2011) 1.02
Imaging transcription dynamics at endogenous genes in living Drosophila tissues. Methods (2008) 0.99
Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters. Lab Chip (2009) 0.97
Kinetics of promoter Pol II on Hsp70 reveal stable pausing and key insights into its regulation. Genes Dev (2014) 0.94
RNA aptamers that functionally interact with green fluorescent protein and its derivatives. Nucleic Acids Res (2011) 0.92
Multiplexed microcolumn-based process for efficient selection of RNA aptamers. Anal Chem (2013) 0.89
An RNA aptamer perturbs heat shock transcription factor activity in Drosophila melanogaster. Nucleic Acids Res (2011) 0.89
Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection. Nucleic Acids Res (2013) 0.89
The Drosophila 7SK snRNP and the essential role of dHEXIM in development. Nucleic Acids Res (2012) 0.88
Comparison of femtosecond laser and continuous wave UV sources for protein-nucleic acid crosslinking. Photochem Photobiol (2007) 0.87
Knocking down gene function with an RNA aptamer expressed as part of an intron. Nucleic Acids Res (2010) 0.86
TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages. Nucleic Acids Res (2008) 0.86
Distinct transcriptional responses of RNA polymerases I, II and III to aptamers that bind TBP. Nucleic Acids Res (2005) 0.85
Paused Pol II captures enhancer activity and acts as a potent insulator. Genes Dev (2009) 0.85
The metazoan-specific mediator subunit 26 (Med26) is essential for viability and is found at both active genes and pericentric heterochromatin in Drosophila melanogaster. Mol Cell Biol (2014) 0.83
Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain is required for efficient transcription of heat shock genes. Mol Cell Biol (2012) 0.83
Evolutionary dynamics and population control during in vitro selection and amplification with multiple targets. RNA (2002) 0.83
High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device. Anal Bioanal Chem (2014) 0.80
A systematic study of the features critical for designing a high avidity multivalent aptamer. Nucleic Acid Ther (2013) 0.80
How does Pol II overcome the nucleosome barrier? Mol Cell (2002) 0.78
A universal DNA-based protein detection system. J Am Chem Soc (2013) 0.76
A new player in Pol II pausing. EMBO J (2013) 0.76
Development of temperature-sensitive mutants of the Drosophila melanogaster P-TEFb (Cyclin T/CDK9) heterodimer using yeast two-hybrid screening. Biochem Biophys Res Commun (2013) 0.75
Corrigendum: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast. Genome Res (2016) 0.75
Profile of John T. Lis. Interviewed by Kristie Nybo. Biotechniques (2012) 0.75
Improving slide-based assays by stirring: application of liquid-on-liquid mixing to immunofluorescence staining of polytene chromosomes. J Biochem Biophys Methods (2005) 0.75