Defining mechanisms that regulate RNA polymerase II transcription in vivo

The sequence of the human genome

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Transcriptional Regulatory Networks in <i>Saccharomyces cerevisiae</i>

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Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy

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Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

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A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells

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Transcriptional activation by recruitment

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Controlling the elongation phase of transcription with P-TEFb

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The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I

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A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II

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Divergent transcription from active promoters

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Selective Anchoring of TFIID to Nucleosomes by Trimethylation of Histone H3 Lysine 4

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Structure and Function of a Human TAF II 250 Double Bromodomain Module

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Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation

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RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

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RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

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RNA polymerase is poised for activation across the genome

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Nucleosome organization in the Drosophila genome

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From Silencing to Gene Expression

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The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged

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ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor

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Flavopiridol Inactivates P-TEFb and Blocks Most RNA Polymerase II Transcription in Vivo

Chao, S., & Price, D. H. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m102306200 · Cited by 623 · see citing works

Purification of Proteins Associated with Specific Genomic Loci

Déjardin, J., & Kingston, R. E. (2009) · Cell · doi:10.1016/j.cell.2008.11.045 · Cited by 545 · see citing works

Phosphorylation of Serine 2 within the RNA Polymerase II C-Terminal Domain Couples Transcription and 3′ End Processing

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Breaking barriers to transcription elongation

Saunders, A., Core, L. J., & Lis, J. T. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1981 · Cited by 506 · see citing works

Promoter targeting and chromatin remodeling by the SWI/SNF complex

Peterson, C. L., & Workman, J. L. (2000) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00068-x · Cited by 438 · see citing works

A transcription reinitiation intermediate that is stabilized by activator

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Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

Core, L. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1150843 · Cited by 406 · see citing works

Nucleosomes Unfold Completely at a Transcriptionally Active Promoter

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Histones Are First Hyperacetylated and Then Lose Contact with the Activated PHO5 Promoter

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The RNA polymerase II core promoter — the gateway to transcription

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Distinction and Relationship between Elongation Rate and Processivity of RNA Polymerase II In Vivo

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Regulation of Chromatin Remodeling by Inositol Polyphosphates

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Regulation of PHO4 Nuclear Localization by the PHO80-PHO85 Cyclin-CDK Complex

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Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci

Petesch, S. J., & Lis, J. T. (2008) · Cell · doi:10.1016/j.cell.2008.05.029 · Cited by 319 · see citing works

NELF and DSIF cause promoter proximal pausing on thehsp70promoter inDrosophilaPreprint

Wu, C.-H., Yamaguchi, Y., Benjamin, L. R., Horvat‐Gordon, M., Washinsky, J., Enerly, E., Larsson, J., Lambertsson, A., Handa, H., & Gilmour, D. S. (2003) · Genes & Development · doi:10.1101/gad.1091403 · Cited by 314 · see citing works

P-TEFb kinase recruitment and function at heat shock lociPreprint

Lis, J. T., Mason, P., Peng, J., Price, D. H., & Werner, J. K. (2000) · Genes & Development · doi:10.1101/gad.14.7.792 · Cited by 314 · see citing works

Chromatin Disassembly Mediated by the Histone Chaperone Asf1 Is Essential for Transcriptional Activation of the Yeast PHO5 and PHO8 Genes

Adkins, M. W., Howar, S. R., & Tyler, J. K. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.05.016 · Cited by 294 · see citing works

The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4Preprint

Larschan, E., & Winston, F. (2001) · Genes & Development · doi:10.1101/gad.911501 · Cited by 286 · see citing works

Three Functional Classes of Transcriptional Activation Domains

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Myc Recruits P-TEFb to Mediate the Final Step in the Transcriptional Activation of the cad Promoter

Eberhardy, S. R., & Farnham, P. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m207441200 · Cited by 259 · see citing works

Synchronous and Stochastic Patterns of Gene Activation in the Drosophila Embryo

Boettiger, A. N., & Levine, M. (2009) · Science · doi:10.1126/science.1173976 · Cited by 256 · see citing works

Coordination of Transcription, RNA Processing, and Surveillance by P-TEFb Kinase on Heat Shock Genes

Ni, Z., Schwartz, B. E., Werner, J. K., Suárez, J.-R., & Lis, J. T. (2004) · Molecular Cell · doi:10.1016/s1097-2765(03)00526-4 · Cited by 240 · see citing works

Chromatin decouples promoter threshold from dynamic range

Lam, F. H., Steger, D. J., & O’Shea, E. K. (2008) · Nature · doi:10.1038/nature06867 · Cited by 237 · see citing works

Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing.

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NELF and GAGA Factor Are Linked to Promoter-Proximal Pausing at Many Genes in Drosophila

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Transcription Factor and Polymerase Recruitment, Modification, and Movement on dhsp70 In Vivo in the Minutes following Heat Shock

Boehm, A. K., Saunders, A., Werner, J. K., & Lis, J. T. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.21.7628-7637.2003 · Cited by 212 · see citing works

In vivo target of a transcriptional activator revealed by fluorescence resonance energy transferPreprint

Bhaumik, S. R., Raha, T., Aiello, D. P., & Green, M. R. (2004) · Genes & Development · doi:10.1101/gad.1148404 · Cited by 198 · see citing works

A Highly Purified RNA Polymerase II Elongation Control System

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Dynamics of heat shock factor association with native gene loci in living cells

Yao, J., Munson, K. M., Webb, W. W., & Lis, J. T. (2006) · Nature · doi:10.1038/nature05025 · Cited by 192 · see citing works

Synergism in transcriptional activation: a kinetic view.

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Two Cyclin-Dependent Kinases Promote RNA Polymerase II Transcription and Formation of the Scaffold Complex

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DNA sequence requirements for generating paused polymerase at the start of hsp70.Preprint

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A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome

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The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex

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RelA Ser 276 Phosphorylation Is Required for Activation of a Subset of NF-κB-Dependent Genes by Recruiting Cyclin-Dependent Kinase 9/Cyclin T1 Complexes

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Promoter-associated Pausing in Promoter Architecture and Postinitiation Transcriptional RegulationPreprint

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Mediator-Dependent Recruitment of TFIIH Modules in Preinitiation Complex

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A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genomePreprint

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Transcription factors vs nucleosomes: regulation of the PH05 promoter in yeast

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Efficient Release from Promoter-Proximal Stall Sites Requires Transcript Cleavage Factor TFIIS

Adelman, K., Marr, M. T., Werner, J. K., Saunders, A., Ni, Z., Andrulis, E. D., & Lis, J. T. (2005) · Molecular Cell · doi:10.1016/j.molcel.2004.11.028 · Cited by 168 · see citing works

Spt6 enhances the elongation rate of RNA polymerase II in vivo

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P-TEFb Is Critical for the Maturation of RNA Polymerase II into Productive Elongation In Vivo

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Selective photolabeling of proteins using photoactivatable GFP

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RNA aptamers as effective protein antagonists in a multicellular organism

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Mechanisms of transcriptional activation in vivo: two steps forward

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The transactivation domain of Pho4 is required for nucleosome disruption at the PHO5 promoter.

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The Histone Chaperone Asf1 Increases the Rate of Histone Eviction at the Yeast PHO5 and PHO8 Promoters

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Redundancy of Chromatin Remodeling Pathways for the Induction of the Yeast PHO5 Promoter in Vivo

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CIITA regulates transcription onset via Ser5‐phosphorylation of RNA Pol II

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The breast cell growth inhibitor, estrogen down regulated gene 1, modulates a novel functional interaction between estrogen receptor alpha and transcriptional elongation factor cyclin T1

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Cooperative Pho2-Pho4 Interactions at the PHO5 Promoter Are Critical for Binding of Pho4 to UASp1 and for Efficient Transactivation by Pho4 at UASp2

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Cdk7 Is Required for Full Activation of Drosophila Heat Shock Genes and RNA Polymerase II Phosphorylation In Vivo

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Molecular characterization of Drosophila NELF

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Functional Connections between Mediator Components and General Transcription Factors of Saccharomyces cerevisiae

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Identification In Vivo of Different Rate-Limiting Steps Associated with Transcriptional Activators in the Presence and Absence of a GAGA Element

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Mapping of RNA polymerase on mammalian genes in cells and nuclei.

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Transcriptional architecture of the mammalian circadian clock

Takahashi, J. S. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.150 · Cited by 2,639 · see citing works

Histone methylation: a dynamic mark in health, disease and inheritance

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Transcriptional Regulation and Its Misregulation in Disease

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Transcriptional architecture and chromatin landscape of the core circadian clock in mammals

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Molecular architecture of the mammalian circadian clock

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c-Myc Regulates Transcriptional Pause Release

Rahl, P. B., Lin, C. Y., Seila, A. C., Flynn, R. A., McCuine, S., Burge, C. B., Sharp, P. A., & Young, R. A. (2010) · Cell · doi:10.1016/j.cell.2010.03.030 · Cited by 1,279 · see citing works

Control of the Embryonic Stem Cell State

Young, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.01.032 · Cited by 1,189 · see citing works

Molecular regulation of stem cell quiescence

Cheung, T. H., & Rando, T. A. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3591 · Cited by 1,148 · see citing works

Mammalian genes are transcribed with widely different bursting kinetics

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Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

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Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma

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Organization and regulation of gene transcription

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Occupying Chromatin: Polycomb Mechanisms for Getting to Genomic Targets, Stopping Transcriptional Traffic, and Staying Put

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Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

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Protein–RNA interactions: new genomic technologies and perspectives

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The cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

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Response to Hyperosmotic Stress

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Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

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Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

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Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

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For better or for worse: the role of Pim oncogenes in tumorigenesis

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The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

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Transcriptional Enhancers in Animal Development and Evolution

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