The transcription cycle of RNA polymerase II in living cells.

In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol (2007) 6.10

Global transcription in pluripotent embryonic stem cells. Cell Stem Cell (2008) 5.81

Analysis of binding reactions by fluorescence recovery after photobleaching. Biophys J (2004) 5.12

Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol (2004) 4.41

Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol (2007) 3.82

A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J Cell Biol (2008) 3.39

Nuclear speckles. Cold Spring Harb Perspect Biol (2011) 3.04

Transcription factories: gene expression in unions? Nat Rev Genet (2009) 2.92

The transcriptional cycle of HIV-1 in real-time and live cells. J Cell Biol (2007) 2.69

Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev (2008) 2.41

A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A (2009) 2.18

Dynamic interaction of TTDA with TFIIH is stabilized by nucleotide excision repair in living cells. PLoS Biol (2006) 1.89

Gene regulation and large-scale chromatin organization in the nucleus. Chromosome Res (2006) 1.87

Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins. J Cell Biol (2004) 1.86

Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS One (2008) 1.82

Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on serine2 residues of the C-terminal domain. Mol Biol Cell (2006) 1.77

Imaging transcription in living cells. Annu Rev Biophys (2009) 1.76

FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know? Curr Opin Cell Biol (2010) 1.64

Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations. Genes Dev (2003) 1.64

UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair. Nat Genet (2012) 1.63

Eukaryotic transcriptional dynamics: from single molecules to cell populations. Nat Rev Genet (2013) 1.57

A benchmark for chromatin binding measurements in live cells. Nucleic Acids Res (2012) 1.56

Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Mol Cell (2015) 1.48

Modulation of RNA polymerase assembly dynamics in transcriptional regulation. Mol Cell (2008) 1.47

Entropy-driven genome organization. Biophys J (2006) 1.42

DNA damage stabilizes interaction of CSB with the transcription elongation machinery. J Cell Biol (2004) 1.42

Regulation of TATA-binding protein dynamics in living yeast cells. Proc Natl Acad Sci U S A (2008) 1.38

Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region. PLoS Genet (2008) 1.38

Active RNA polymerases: mobile or immobile molecular machines? PLoS Biol (2010) 1.37

The muscle fiber type-fiber size paradox: hypertrophy or oxidative metabolism? Eur J Appl Physiol (2010) 1.36

Condensed chromatin domains in the mammalian nucleus are accessible to large macromolecules. EMBO Rep (2003) 1.35

Dynamics of transcription and mRNA export. Curr Opin Cell Biol (2005) 1.35

Poised transcription factories prime silent uPA gene prior to activation. PLoS Biol (2010) 1.28

Molecular determinants of NOTCH4 transcription in vascular endothelium. Mol Cell Biol (2005) 1.27

A reaction-diffusion model to study RNA motion by quantitative fluorescence recovery after photobleaching. Biophys J (2007) 1.27

Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to up-regulate gene expression. Genome Res (2009) 1.26

Acetylation-induced transcription is required for active DNA demethylation in methylation-silenced genes. Mol Cell Biol (2007) 1.24

Organization of transcription. Cold Spring Harb Perspect Biol (2010) 1.20

The yin and yang of chromatin spatial organization. Genome Biol (2010) 1.20

Mobility of multi-subunit complexes in the nucleus: accessibility and dynamics of chromatin subcompartments. Histochem Cell Biol (2005) 1.17

Chromatin remodeling complexes interact dynamically with a glucocorticoid receptor-regulated promoter. Mol Biol Cell (2008) 1.16

Connecting variability in global transcription rate to mitochondrial variability. PLoS Biol (2010) 1.13

Transcription-associated breaks in xeroderma pigmentosum group D cells from patients with combined features of xeroderma pigmentosum and Cockayne syndrome. Mol Cell Biol (2005) 1.13

Fibroblast growth factor receptor-1 (FGFR1) nuclear dynamics reveal a novel mechanism in transcription control. Mol Biol Cell (2009) 1.12

Gene expression within a dynamic nuclear landscape. EMBO J (2006) 1.10

Inhibition of transcription at radiation-induced nuclear foci of phosphorylated histone H2AX in mammalian cells. Chromosome Res (2007) 1.08

Actively transcribing RNA polymerase II concentrates on spliced leader genes in the nucleus of Trypanosoma cruzi. Eukaryot Cell (2005) 1.06

Chromatin loops, gene positioning, and gene expression. Front Genet (2012) 1.03

Self-organization vs Watchmaker: stochastic gene expression and cell differentiation. Dev Genes Evol (2004) 1.02

Nuclear proteins: finding and binding target sites in chromatin. Chromosome Res (2011) 1.01

Establishment and mitotic stability of an extra-chromosomal mammalian replicon. BMC Cell Biol (2007) 1.00

Modelling reveals kinetic advantages of co-transcriptional splicing. PLoS Comput Biol (2011) 0.99

Differentiation driven changes in the dynamic organization of Basal transcription initiation. PLoS Biol (2009) 0.99

Transcription of productive and nonproductive VDJ-recombined alleles after IgH allelic exclusion. EMBO J (2007) 0.98

Transcription factories in the context of the nuclear and genome organization. Nucleic Acids Res (2011) 0.97

Surface mu heavy chain signals down-regulation of the V(D)J-recombinase machinery in the absence of surrogate light chain components. J Exp Med (2004) 0.96

Chinese hamster ORC subunits dynamically associate with chromatin throughout the cell-cycle. Exp Cell Res (2005) 0.95

Transcriptional repression induces a slowly progressive atypical neuronal death associated with changes of YAP isoforms and p73. J Cell Biol (2006) 0.95

Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Res (2003) 0.95

Transcription factories. Front Genet (2012) 0.95

Morphology of nuclear transcription. Histochem Cell Biol (2016) 0.94

Assembly of the transcription machinery: ordered and stable, random and dynamic, or both? Chromosoma (2011) 0.93

Spurious transcription factor binding: non-functional or genetically redundant? Bioessays (2014) 0.92

Complex dynamics of transcription regulation. Biochim Biophys Acta (2012) 0.92

The principles of nuclear structure. Chromosome Res (2003) 0.91

Distribution of different phosphorylated forms of RNA polymerase II in relation to Cajal and PML bodies in human cells: an ultrastructural study. Histochem Cell Biol (2005) 0.90

Visualizing posttranslational and epigenetic modifications of endogenous proteins in vivo. Histochem Cell Biol (2015) 0.87

Transition from initiation to promoter proximal pausing requires the CTD of RNA polymerase II. Nucleic Acids Res (2005) 0.86

Phosphorylation-elicited quaternary changes of GA binding protein in transcriptional activation. Mol Cell Biol (2003) 0.86

Identification of biomolecule mass transport and binding rate parameters in living cells by inverse modeling. Theor Biol Med Model (2006) 0.86

Zooming in on single active genes in living mammalian cells. Histochem Cell Biol (2013) 0.86

Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Mol Biol Cell (2014) 0.85

High mobility of flap endonuclease 1 and DNA polymerase eta associated with replication foci in mammalian S-phase nucleus. Mol Biol Cell (2005) 0.84

3'UTR-mediated gene silencing of the Mixed Lineage Leukemia (MLL) gene. PLoS One (2011) 0.84

Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level. Int J Mol Sci (2013) 0.83

Global variability in gene expression and alternative splicing is modulated by mitochondrial content. Genome Res (2015) 0.83

A finite element model for protein transport in vivo. Biomed Eng Online (2007) 0.82

In vivo assay of presynaptic microtubule cytoskeleton dynamics in Drosophila. J Neurosci Methods (2007) 0.82

A biophysical model for transcription factories. BMC Biophys (2013) 0.79

RNA Polymerase II cluster dynamics predict mRNA output in living cells. Elife (2016) 0.79

Heterogeneous nuclear ribonucleoprotein R cooperates with mediator to facilitate transcription reinitiation on the c-Fos gene. PLoS One (2013) 0.78

Simultaneous measurement of anisotropic solute diffusivity and binding reaction rates in biological tissues by FRAP. Ann Biomed Eng (2010) 0.77

Measuring the kinetics of mRNA transcription in single living cells. J Vis Exp (2011) 0.77

Coactivators and general transcription factors have two distinct dynamic populations dependent on transcription. EMBO J (2017) 0.76

Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains. Biophys J (2017) 0.75

iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function. BMC Biol (2015) 0.75

DNA intercalator stimulates influenza transcription and virus replication. Virol J (2011) 0.75

Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution. Nucleic Acids Res (2016) 0.75

Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement. Biophys J (2017) 0.75

Initial sequencing and analysis of the human genome. Nature (2001) 212.86

The green fluorescent protein. Annu Rev Biochem (1998) 34.17

Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev (2000) 10.64

Visualization of single RNA transcripts in situ. Science (1998) 10.51

High mobility of proteins in the mammalian cell nucleus. Nature (2000) 9.39

The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature (1997) 8.86

The general transcription factors of RNA polymerase II. Genes Dev (1996) 7.15

Ethidium bromide provides a simple tool for identifying genuine DNA-independent protein associations. Proc Natl Acad Sci U S A (1992) 6.23

Transcription of eukaryotic protein-coding genes. Annu Rev Genet (2000) 6.12

Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J Biol Chem (1996) 5.15

The organization of replication and transcription. Science (1999) 5.08

Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J Cell Biol (2001) 4.96

Transcription complex stability and chromatin dynamics in vivo. Nature (1995) 4.51

Protein dynamics: implications for nuclear architecture and gene expression. Science (2001) 4.38

Postinitiation transcriptional control in Drosophila melanogaster. Mol Cell Biol (1990) 3.83

A transcription reinitiation intermediate that is stabilized by activator. Nature (2000) 3.65

Protein traffic on the heat shock promoter: parking, stalling, and trucking along. Cell (1993) 3.43

A general method for preparing chromatin containing intact DNA. EMBO J (1985) 3.22

The role of stable complexes that repress and activate eucaryotic genes. Cell (1984) 3.08

Action of DNA repair endonuclease ERCC1/XPF in living cells. Science (1999) 3.00

Photobleaching GFP reveals protein dynamics inside live cells. Trends Cell Biol (1999) 2.86

Kinetic modelling approaches to in vivo imaging. Nat Rev Mol Cell Biol (2001) 2.85

RNP particles at splice junction sequences on Drosophila chorion transcripts. Cell (1985) 2.69

Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol Biol Cell (1998) 2.30

Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J (1999) 2.28

RNA polymerase II pauses at the 5' end of the transcriptionally induced Drosophila hsp70 gene. Mol Cell Biol (1991) 2.18

Multiple transcript cleavage precedes polymerase release in termination by RNA polymerase II. Cell (2001) 2.15

Macromolecular dynamics in living cell nuclei revealed by fluorescence redistribution after photobleaching. Histochem Cell Biol (2001) 1.93

Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure. Mol Cell Biol (1999) 1.79

TBP dynamics in living human cells: constitutive association of TBP with mitotic chromosomes. Mol Biol Cell (2002) 1.78

Immunoelectron microscope visualization of nuclear ribonucleoprotein antigens within spread transcription complexes. J Cell Biol (1986) 1.62

The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells. FASEB J (2000) 1.55

Interplay between positive and negative elongation factors: drawing a new view of DRB. Genes Cells (1998) 1.53

Mammalian cell lines expressing functional RNA polymerase II tagged with the green fluorescent protein. J Cell Sci (2000) 1.38

Sarkosyl defines three intermediate steps in transcription initiation by RNA polymerase III: application to stimulation of transcription by E1A. Genes Dev (1990) 1.29

Visualization of nascent RNA transcripts and simultaneous transcription and replication in viral nucleoprotein complexes from adenovirus 2-infected HeLa cells. J Mol Biol (1981) 1.27

Morphology of transcription units in Drosophila melanogaster. Chromosoma (1976) 1.26

Dynamics and mobility of nuclear envelope proteins in interphase and mitotic cells revealed by green fluorescent protein chimeras. Methods (1999) 1.21

Visualization of the major late R strand transcription unit of adenovirus serotype 2. J Mol Biol (1981) 1.17

The nucleolus, chromosomes, and visualization of genetic activity. J Cell Biol (1981) 1.04

Sarkosyl block of transcription reinitiation by RNA polymerase II as visualized by the colliding polymerases reinitiation assay. Nucleic Acids Res (1994) 0.92

The functional organization of mitochondrial genomes in human cells. BMC Biol (2004) 2.20

A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A (2009) 2.18

Similar active genes cluster in specialized transcription factories. J Cell Biol (2008) 2.05

What are the molecular ties that maintain genomic loops? Trends Genet (2007) 1.53

The depletion attraction: an underappreciated force driving cellular organization. J Cell Biol (2006) 1.49

Entropy-driven genome organization. Biophys J (2006) 1.42

Active RNA polymerases: mobile or immobile molecular machines? PLoS Biol (2010) 1.37

RNA polymerase II activity is located on the surface of protein-rich transcription factories. J Cell Sci (2008) 1.33

Transcription factories: genome organization and gene regulation. Chem Rev (2013) 1.28

Different populations of RNA polymerase II in living mammalian cells. Chromosome Res (2005) 1.24

The role of specialized transcription factories in chromosome pairing. Biochim Biophys Acta (2008) 1.24

Transcription factories. Biochem Soc Trans (2008) 1.22

TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J (2012) 1.21

Multiscale spatial organization of RNA polymerase in Escherichia coli. Biophys J (2013) 1.20

Molecular cross-talk between the transcription, translation, and nonsense-mediated decay machineries. J Cell Sci (2004) 1.17

Specialized transcription factories. Biochem Soc Symp (2006) 1.11

The proteomes of transcription factories containing RNA polymerases I, II or III. Nat Methods (2011) 1.10

Many expressed genes in bacteria and yeast are transcribed only once per cell cycle. FASEB J (2006) 1.07

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization. Proc Natl Acad Sci U S A (2013) 1.07

A conserved organization of transcription during embryonic stem cell differentiation and in cells with high C value. Mol Biol Cell (2006) 1.06

Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin (2012) 1.05

Genome architecture and the role of transcription. Curr Opin Cell Biol (2010) 1.04

Fixing the model for transcription: the DNA moves, not the polymerase. Transcription (2012) 1.00

Analysis of alpha- and beta-tubulin genes of Bombyx mori using an EST database. Insect Biochem Mol Biol (2003) 0.95

The case for nuclear translation. J Cell Sci (2004) 0.93

Phosphorylation-dependent migration of retinoblastoma protein into the nucleolus triggered by binding to nucleophosmin/B23. Exp Cell Res (2002) 0.93

Dynamic reconfiguration of long human genes during one transcription cycle. Mol Cell Biol (2012) 0.92

Transcription factories, chromatin loops, and the dysregulation of gene expression in malignancy. Semin Cancer Biol (2012) 0.91

Confocal fluorescence imaging of photosensitized DNA denaturation in cell nuclei. Photochem Photobiol (2005) 0.91

Modeling a self-avoiding chromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context. Structure (2006) 0.91

Influence of irofulven, a transcription-coupled repair-specific antitumor agent, on RNA polymerase activity, stability and dynamics in living mammalian cells. J Cell Sci (2008) 0.91

Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes. Chromosome Res (2011) 0.88

Space exploration by the promoter of a long human gene during one transcription cycle. Nucleic Acids Res (2013) 0.87

The interdependence of nuclear structure and function. Curr Opin Cell Biol (2002) 0.84

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biol (2014) 0.83

Maximum precision closed-form solution for localizing diffraction-limited spots in noisy images. Opt Express (2012) 0.83

Characterization of cells expressing RNA polymerase II tagged with green fluorescent protein: effect of ionizing irradiation on RNA synthesis. Int J Radiat Biol (2008) 0.81

Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites. J Cell Sci (2013) 0.79

Photobleaching reveals complex effects of inhibitors on transcribing RNA polymerase II in living cells. Exp Cell Res (2007) 0.79

Effects of low-dose heavy ions on the postnatal development of mice and the yield of white spots in the mid-ventrum and tail-tips. J Radiat Res (2011) 0.77

Dynamics of DNA replication: an ultrastructural study. J Struct Biol (2004) 0.77

Analyzing DNA Replication I: Labeling Animals, Tissues, and Cells with Bromodeoxyuridine (BrdU). CSH Protoc (2008) 0.76

"Dark matter" worlds of unstable RNA and protein. Nucleus (2014) 0.76

Applying microscopy to the analysis of nuclear structure and function. Methods (2003) 0.76

Measuring histone and polymerase dynamics in living cells. Methods Enzymol (2004) 0.76

Analyzing DNA Replication III: Antibody Labeling of Incorporated Bromodeoxyuridine (BrdU) in Tissues and Cells. CSH Protoc (2008) 0.76

Effects of low-dose heavy ions on embryonic development in mice and on melanocyte differentiation in the epidermis and hair bulb. J Radiat Res (2012) 0.75

T7 RNA polymerase functions in vitro without clustering. PLoS One (2012) 0.75

Analyzing DNA Replication II: Fixation and Processing of Tissues and Cells Labeled with Bromodeoxyuridine (BrdU). CSH Protoc (2008) 0.75

Effects of low-dose γ-rays on the embryonic development of mouse melanoblasts and melanocytes in the epidermis and hair bulbs. Zoolog Sci (2011) 0.75

Approaches for monitoring nuclear translation. Methods Mol Biol (2004) 0.75