Published in Proc Natl Acad Sci U S A on October 13, 2009
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature (2011) 5.50
Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. Nat Neurosci (2012) 2.93
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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Cohesin mediates chromatin interactions that regulate mammalian β-globin expression. J Biol Chem (2011) 1.29
RNA polymerase II transcription elongation control. Chem Rev (2013) 1.27
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Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation. J Biol Chem (2012) 1.25
Fast transcription rates of RNA polymerase II in human cells. EMBO Rep (2011) 1.24
A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection. EMBO J (2012) 1.21
TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J (2012) 1.21
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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 role for intragenic DNA methylation in alternative pre-mRNA splicing. Transcription (2012) 1.07
Counting on co-transcriptional splicing. F1000Prime Rep (2013) 1.06
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p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-κB complexes. Elife (2014) 1.03
Fixing the model for transcription: the DNA moves, not the polymerase. Transcription (2012) 1.00
Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate. Genome Res (2014) 0.98
Where splicing joins chromatin. Nucleus (2011) 0.98
Mechanism of glycyrrhizic acid inhibition of Kaposi's sarcoma-associated herpesvirus: disruption of CTCF-cohesin-mediated RNA polymerase II pausing and sister chromatid cohesion. J Virol (2011) 0.93
Dynamic cross-talk analysis among TNF-R, TLR-4 and IL-1R signalings in TNFalpha-induced inflammatory responses. BMC Med Genomics (2010) 0.93
A comparison of herpes simplex virus type 1 and varicella-zoster virus latency and reactivation. J Gen Virol (2015) 0.93
Dynamic reconfiguration of long human genes during one transcription cycle. Mol Cell Biol (2012) 0.92
Transcript processing and export kinetics are rate-limiting steps in expressing vertebrate segmentation clock genes. Proc Natl Acad Sci U S A (2013) 0.91
Occupancy of chromatin organizers in the Epstein-Barr virus genome. Virology (2011) 0.91
CTCF regulates Kaposi's sarcoma-associated herpesvirus latency transcription by nucleosome displacement and RNA polymerase programming. J Virol (2012) 0.90
SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample. PLoS One (2014) 0.90
Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus. Nucleic Acids Res (2014) 0.88
Space exploration by the promoter of a long human gene during one transcription cycle. Nucleic Acids Res (2013) 0.87
TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing. EMBO J (2015) 0.87
Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories. Nucleic Acids Res (2015) 0.86
Direct evidence for pitavastatin induced chromatin structure change in the KLF4 gene in endothelial cells. PLoS One (2014) 0.84
TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biol (2014) 0.83
Splicing of many human genes involves sites embedded within introns. Nucleic Acids Res (2015) 0.81
CTCF-mediated chromatin loops enclose inducible gene regulatory domains. BMC Genomics (2016) 0.81
Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data. PLoS Comput Biol (2014) 0.80
Distribution of histone3 lysine 4 trimethylation at T3-responsive loci in the heart during reversible changes in gene expression. Gene Expr (2012) 0.79
Mathematical model of the Tat-Rev regulation of HIV-1 replication in an activated cell predicts the existence of oscillatory dynamics in the synthesis of viral components. BMC Genomics (2014) 0.79
Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription. BMC Genomics (2015) 0.79
Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites. J Cell Sci (2013) 0.79
RNA Polymerase II cluster dynamics predict mRNA output in living cells. Elife (2016) 0.79
On the right track: following the nucleo-cytoplasmic path of an mRNA. Nucleus (2010) 0.78
Uncovering transcription factor modules using one- and three-dimensional analyses. J Biol Chem (2012) 0.78
Pol II caught speeding by single gene imaging. EMBO Rep (2011) 0.77
Measuring the kinetics of mRNA transcription in single living cells. J Vis Exp (2011) 0.77
Regulation of mRNA export by the PI3 kinase/AKT signal transduction pathway. Mol Biol Cell (2013) 0.77
Splicing of designer exons informs a biophysical model for exon definition. RNA (2014) 0.76
Super-resolution measurement of distance between transcription sites using RNA FISH with intronic probes. Methods (2015) 0.76
CTCF regulates NELF, DSIF and P-TEFb recruitment during transcription. Transcription (2015) 0.76
Transcription and splicing: when the twain meet. Transcription (2012) 0.76
Cutting a Long Intron Short: Recursive Splicing and Its Implications. Front Physiol (2016) 0.76
Are genes switched on when they kiss? Nucleus (2014) 0.76
Utilization of the Eμ-Myc mouse to model heterogeneity of therapeutic response. Mol Cancer Ther (2014) 0.75
A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing. PLoS One (2015) 0.75
Structural maintenance of chromosome complexes and bone development: the beginning of a wonderful relationship? Bonekey Rep (2013) 0.75
Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics (2012) 0.75
Higher frequency of intron loss from the promoter proximally paused genes of Drosophila melanogaster. Fly (Austin) (2014) 0.75
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (2008) 16.48
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature (2008) 12.01
An extensive network of coupling among gene expression machines. Nature (2002) 11.84
Divergent transcription from active promoters. Science (2008) 11.03
Visualization of single RNA transcripts in situ. Science (1998) 10.51
Nuclear organization of the genome and the potential for gene regulation. Nature (2007) 8.22
Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell (2008) 7.80
A unified theory of gene expression. Cell (2002) 7.61
Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev (2006) 7.44
Circuitry of nuclear factor kappaB signaling. Immunol Rev (2006) 6.49
In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol (2007) 6.10
Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science (2008) 5.48
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet (2008) 4.91
Multiple links between transcription and splicing. RNA (2004) 4.90
CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
Cracking the RNA polymerase II CTD code. Trends Genet (2008) 4.00
The molecular basis of eukaryotic transcription. Proc Natl Acad Sci U S A (2007) 3.09
The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nat Genet (1995) 2.76
The transcription cycle of RNA polymerase II in living cells. J Cell Biol (2002) 2.59
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet (2005) 2.36
Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev (2006) 1.98
Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation. Mol Cell (2007) 1.87
A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. Mol Cell (2006) 1.71
The role of specialized transcription factories in chromosome pairing. Biochim Biophys Acta (2008) 1.24
Histone deacetylase inhibitor reduces monocyte adhesion to endothelium through the suppression of vascular cell adhesion molecule-1 expression. Arterioscler Thromb Vasc Biol (2006) 1.14
Show and tell: visualizing gene expression in living cells. J Cell Sci (2007) 1.05
Global variation in copy number in the human genome. Nature (2006) 57.50
Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature (2007) 37.09
International network of cancer genome projects. Nature (2010) 20.35
DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator of innate immune response. Nature (2007) 13.56
Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature (2008) 12.01
Bile acids induce energy expenditure by promoting intracellular thyroid hormone activation. Nature (2006) 9.36
Induction and activation of the transcription factor NFATc1 (NFAT2) integrate RANKL signaling in terminal differentiation of osteoclasts. Dev Cell (2002) 9.10
Copy number variation: new insights in genome diversity. Genome Res (2006) 8.66
Genome assembly comparison identifies structural variants in the human genome. Nat Genet (2006) 6.93
TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab (2009) 6.91
S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature (2003) 6.43
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res (2006) 5.97
Tumour-mediated upregulation of chemoattractants and recruitment of myeloid cells predetermines lung metastasis. Nat Cell Biol (2006) 5.82
Evidence for osteocyte regulation of bone homeostasis through RANKL expression. Nat Med (2011) 5.66
Th17 functions as an osteoclastogenic helper T cell subset that links T cell activation and bone destruction. J Exp Med (2006) 5.63
Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. Genes Dev (2005) 5.50
Specific SIRT1 activation mimics low energy levels and protects against diet-induced metabolic disorders by enhancing fat oxidation. Cell Metab (2008) 5.44
Cohesin relocation from sites of chromosomal loading to places of convergent transcription. Nature (2004) 5.00
Costimulatory signals mediated by the ITAM motif cooperate with RANKL for bone homeostasis. Nature (2004) 4.92
Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet (2013) 4.61
Identification and characterization of lin-28 homolog B (LIN28B) in human hepatocellular carcinoma. Gene (2006) 4.13
Activation of peroxisome proliferator-activated receptor delta induces fatty acid beta-oxidation in skeletal muscle and attenuates metabolic syndrome. Proc Natl Acad Sci U S A (2003) 4.03
Down's syndrome suppression of tumour growth and the role of the calcineurin inhibitor DSCR1. Nature (2009) 3.93
Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues. Genomics (2005) 3.92
Nrf2 redirects glucose and glutamine into anabolic pathways in metabolic reprogramming. Cancer Cell (2012) 3.90
HMGB proteins function as universal sentinels for nucleic-acid-mediated innate immune responses. Nature (2009) 3.86
High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet (2011) 3.86
Postreplicative recruitment of cohesin to double-strand breaks is required for DNA repair. Mol Cell (2004) 3.83
Protein phosphatase 2A protects centromeric sister chromatid cohesion during meiosis I. Nature (2006) 3.81
The connectome of a decision-making neural network. Science (2012) 3.70
Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature (2010) 3.55
Interdependence of AMPK and SIRT1 for metabolic adaptation to fasting and exercise in skeletal muscle. Cell Metab (2010) 3.46
Osteoprotection by semaphorin 3A. Nature (2012) 3.40
The S100A8-serum amyloid A3-TLR4 paracrine cascade establishes a pre-metastatic phase. Nat Cell Biol (2008) 3.30
U1 snRNA associates with TFIIH and regulates transcriptional initiation. Nat Struct Biol (2002) 3.25
Phase II study of SMILE chemotherapy for newly diagnosed stage IV, relapsed, or refractory extranodal natural killer (NK)/T-cell lymphoma, nasal type: the NK-Cell Tumor Study Group study. J Clin Oncol (2011) 3.10
HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. Nature (2012) 3.08
G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription. EMBO J (2008) 3.08
Survivin reads phosphorylated histone H3 threonine 3 to activate the mitotic kinase Aurora B. Science (2010) 3.07
DNA damage-dependent acetylation and ubiquitination of H2AX enhances chromatin dynamics. Mol Cell Biol (2007) 3.03
NFAT and Osterix cooperatively regulate bone formation. Nat Med (2005) 2.99
Overexpression of the aldo-keto reductase family protein AKR1B10 is highly correlated with smokers' non-small cell lung carcinomas. Clin Cancer Res (2005) 2.97
Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol (2009) 2.89
Identification of cis-acting sites for condensin loading onto budding yeast chromosomes. Genes Dev (2008) 2.87
Hepatocyte-specific deletion of the keap1 gene activates Nrf2 and confers potent resistance against acute drug toxicity. Biochem Biophys Res Commun (2005) 2.85
CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. BMC Bioinformatics (2006) 2.82
Postreplicative formation of cohesion is required for repair and induced by a single DNA break. Science (2007) 2.82
Glucokinase and IRS-2 are required for compensatory beta cell hyperplasia in response to high-fat diet-induced insulin resistance. J Clin Invest (2007) 2.81
Dynamic behavior of Nuf2-Hec1 complex that localizes to the centrosome and centromere and is essential for mitotic progression in vertebrate cells. J Cell Sci (2003) 2.78
Skeletal muscle FOXO1 (FKHR) transgenic mice have less skeletal muscle mass, down-regulated Type I (slow twitch/red muscle) fiber genes, and impaired glycemic control. J Biol Chem (2004) 2.72
Monopolar attachment of sister kinetochores at meiosis I requires casein kinase 1. Cell (2006) 2.70
Nuclear factor of activated T-cells (NFAT) rescues osteoclastogenesis in precursors lacking c-Fos. J Biol Chem (2004) 2.66
The replication checkpoint protects fork stability by releasing transcribed genes from nuclear pores. Cell (2011) 2.65
Mrc1 and DNA polymerase epsilon function together in linking DNA replication and the S phase checkpoint. Mol Cell (2008) 2.63
The transcription cycle of RNA polymerase II in living cells. J Cell Biol (2002) 2.59
Evidence that loading of cohesin onto chromosomes involves opening of its SMC hinge. Cell (2006) 2.58
Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster. EMBO J (2009) 2.56
Fusion between CIC and DUX4 up-regulates PEA3 family genes in Ewing-like sarcomas with t(4;19)(q35;q13) translocation. Hum Mol Genet (2006) 2.51
Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res (2002) 2.49
Deficiency of cathepsin S reduces atherosclerosis in LDL receptor-deficient mice. J Clin Invest (2003) 2.48
Origin association of Sld3, Sld7, and Cdc45 proteins is a key step for determination of origin-firing timing. Curr Biol (2011) 2.47
Impaired insulin signaling in endothelial cells reduces insulin-induced glucose uptake by skeletal muscle. Cell Metab (2011) 2.42
Crystal structure of the human centromeric nucleosome containing CENP-A. Nature (2011) 2.42
Establishment of sister chromatid cohesion at the S. cerevisiae replication fork. Mol Cell (2006) 2.39
Cytosolic chaperonin prevents polyglutamine toxicity with altering the aggregation state. Nat Cell Biol (2006) 2.37
Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res (2010) 2.36
Differential function of Tie2 at cell-cell contacts and cell-substratum contacts regulated by angiopoietin-1. Nat Cell Biol (2008) 2.35
Identification of soluble NH2-terminal fragment of glypican-3 as a serological marker for early-stage hepatocellular carcinoma. Cancer Res (2004) 2.34
Synergy between LRH-1 and beta-catenin induces G1 cyclin-mediated cell proliferation. Mol Cell (2004) 2.31
The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. PLoS Genet (2010) 2.30
Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast. EMBO J (2007) 2.29
The murine homolog of SALL4, a causative gene in Okihiro syndrome, is essential for embryonic stem cell proliferation, and cooperates with Sall1 in anorectal, heart, brain and kidney development. Development (2006) 2.27
Manipulation of alternative splicing by a newly developed inhibitor of Clks. J Biol Chem (2004) 2.26
Multiple renal cysts, urinary concentration defects, and pulmonary emphysematous changes in mice lacking TAZ. Am J Physiol Renal Physiol (2008) 2.24
An Smc3 acetylation cycle is essential for establishment of sister chromatid cohesion. Mol Cell (2010) 2.23