Published in Science on December 04, 2008
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Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature (2013) 3.93
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The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis. EMBO J (2011) 2.97
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Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90
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CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell (2010) 2.86
Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. Biochim Biophys Acta (2010) 2.86
Enhancer transcripts mark active estrogen receptor binding sites. Genome Res (2013) 2.82
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Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat Struct Mol Biol (2011) 2.73
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The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev (2012) 2.55
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X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature (2011) 2.44
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Suppression of the antiviral response by an influenza histone mimic. Nature (2012) 2.18
A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A (2009) 2.18
Transcription initiation activity sets replication origin efficiency in mammalian cells. PLoS Genet (2009) 2.17
The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog (2010) 2.15
A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods (2010) 2.14
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Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures. Nat Struct Mol Biol (2013) 2.09
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
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RNA polymerase is poised for activation across the genome. Nat Genet (2007) 9.57
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet (2007) 9.56
Nucleosome organization in the Drosophila genome. Nature (2008) 8.65
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Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature (2008) 7.18
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New perspectives on connecting messenger RNA 3' end formation to transcription. Curr Opin Cell Biol (2004) 4.04
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NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev (2008) 3.69
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res (2008) 2.62
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Res (2008) 2.01
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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
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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
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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
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Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science (2013) 2.66
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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
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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
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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
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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
Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J Mol Biol (2004) 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
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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
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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
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Interactions between subunits of Drosophila Mediator and activator proteins. Trends Biochem Sci (2005) 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
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Extracting falsifiable predictions from sloppy models. Ann N Y Acad Sci (2007) 1.06
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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
Indirect immunofluorescent labeling of Drosophila polytene chromosomes: visualizing protein interactions with chromatin in vivo. Methods Enzymol (2004) 0.99
Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters. Lab Chip (2009) 0.97
RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II. Cell Rep (2014) 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
Pol II docking and pausing at growth and stress genes in C. elegans. Cell Rep (2014) 0.91
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
A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology. Am J Pathol (2011) 0.87
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
Paused Pol II captures enhancer activity and acts as a potent insulator. Genes Dev (2009) 0.85
Distinct transcriptional responses of RNA polymerases I, II and III to aptamers that bind TBP. Nucleic Acids Res (2005) 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
Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins. G3 (Bethesda) (2012) 0.83
Evolutionary dynamics and population control during in vitro selection and amplification with multiple targets. RNA (2002) 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
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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
Profile of John T. Lis. Interviewed by Kristie Nybo. Biotechniques (2012) 0.75
Corrigendum: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast. Genome Res (2016) 0.75
Variational method for estimating the rate of convergence of Markov-chain Monte Carlo algorithms. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 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