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Integrating regulatory information via combinatorial control of the transcription cycle

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Shadow enhancers: Frequently asked questions about distributed cis‐regulatory information and enhancer redundancy

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cis‐acting control elements for Krüppel expression in the Drosophila embryo.

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Synergistic enhancement of both initiation and elongation by acidic transcription activation domains.

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A mathematical model for synergistic eukaryotic gene activation 1 1Edited by F. E. Cohen

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Markovian Modeling of Gene-Product Synthesis

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The grammar of transcriptional regulation

inferredcites →https://doi.org/10.1016/0092-8674(94)90058-2openalex-snapshot

Transcriptional elongation by RNA polymerase II is stimulated by transactivators

inferredcites →https://doi.org/10.1016/0092-8674(95)90136-1openalex-snapshot

Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome

inferredcites →https://doi.org/10.1016/0896-6273(91)90256-yopenalex-snapshot

Mechanisms for diversity in gene expression patterns

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Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation

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A primer on thermodynamic-based models for deciphering transcriptional regulatory logic

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The core promoter: At the heart of gene expression

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Mechanism of Transcription Initiation at an Activator-Dependent Promoter Defined by Single-Molecule Observation

inferredcites →https://doi.org/10.1016/j.cell.2014.04.047openalex-snapshot

Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation

inferredcites →https://doi.org/10.1016/j.celrep.2015.08.021openalex-snapshot

Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers

inferredcites →https://doi.org/10.1016/j.cub.2014.07.076openalex-snapshot

Pulsatile Dynamics in the Yeast Proteome

inferredcites →https://doi.org/10.1016/j.gde.2005.02.006openalex-snapshot

Transcriptional regulation by the numbers: applications

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Transcriptional regulation by the numbers: models

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The transition from transcriptional initiation to elongation

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Mammalian synthetic biology: Engineering of sophisticated gene networks

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Function of a Eukaryotic Transcription Activator during the Transcription Cycle

inferredcites →https://doi.org/10.1016/j.molcel.2005.04.005openalex-snapshot

Functional Characterization of Core Promoter Elements: DPE-Specific Transcription Requires the Protein Kinase CK2 and the PC4 Coactivator

inferredcites →https://doi.org/10.1016/j.molcel.2005.04.017openalex-snapshot

Eukaryotic Transcription Activation: Right on Target

inferredcites →https://doi.org/10.1016/j.molcel.2006.10.030openalex-snapshot

The Transition between Transcriptional Initiation and Elongation in E. coli Is Highly Variable and Often Rate Limiting

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Crosstalk between mRNA 3′ End Processing and Transcription Initiation

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In search of the determinants of enhancer–promoter interaction specificity

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Theory in Biology: Figure 1 or Figure 7?

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Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors

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Evolutionary bioscience as regulatory systems biology

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Stochasticity in Transcriptional Regulation: Origins, Consequences, and Mathematical Representations

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Synergism analysis of biochemical systems. I. Conceptual framework

inferredcites →https://doi.org/10.1016/s0092-8674(00)80893-4openalex-snapshot

The Enhanceosome and Transcriptional Synergy

inferredcites →https://doi.org/10.1017/s1464793102006036openalex-snapshot

A sigmoidal transcriptional response: cooperativity, synergy and dosage effects

inferredcites →https://doi.org/10.1038/24550openalex-snapshot

Hsp90 as a capacitor for morphological evolution

inferredcites →https://doi.org/10.1038/345359a0openalex-snapshot

How different eukaryotic transcriptional activators can cooperate promiscuously

inferredcites →https://doi.org/10.1038/345361a0openalex-snapshot

A mechanism for synergistic activation of a mammalian gene by GAL4 derivatives

inferredcites →https://doi.org/10.1038/374657a0openalex-snapshot

Basal promoter elements as a selective determinant of transcriptional activator function

inferredcites →https://doi.org/10.1038/386569a0openalex-snapshot

Transcriptional activation by recruitment

inferredcites →https://doi.org/10.1038/msb.2011.20openalex-snapshot

Stimulus‐dependent dynamics of p53 in single cells

inferredcites →https://doi.org/10.1038/nature05099openalex-snapshot

Evolution of alternative transcriptional circuits with identical logic

inferredcites →https://doi.org/10.1038/nature07292openalex-snapshot

Frequency-modulated nuclear localization bursts coordinate gene regulation

inferredcites →https://doi.org/10.1038/nature07521openalex-snapshot

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

inferredcites →https://doi.org/10.1038/nature08449openalex-snapshot

Defining mechanisms that regulate RNA polymerase II transcription in vivo

inferredcites →https://doi.org/10.1038/nature09158openalex-snapshot

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

inferredcites →https://doi.org/10.1038/nature13714openalex-snapshot

Regulation of RNA polymerase II activation by histone acetylation in single living cells

inferredcites →https://doi.org/10.1038/nature13994openalex-snapshot

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

inferredcites →https://doi.org/10.1038/nature15545openalex-snapshot

Transcriptional regulators form diverse groups with context-dependent regulatory functions

inferredcites →https://doi.org/10.1038/nature15710openalex-snapshot

Combinatorial gene regulation by modulation of relative pulse timing

inferredcites →https://doi.org/10.1038/nbt.2136openalex-snapshot

Massively parallel functional dissection of mammalian enhancers in vivo

inferredcites →https://doi.org/10.1038/nbt.2205openalex-snapshot

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

inferredcites →https://doi.org/10.1038/ng.2007.26openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ng.2713openalex-snapshot

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

inferredcites →https://doi.org/10.1038/ng1293openalex-snapshot

Dynamics of the p53-Mdm2 feedback loop in individual cells

inferredcites →https://doi.org/10.1038/nrg3207openalex-snapshot

Transcription factors: from enhancer binding to developmental control

inferredcites →https://doi.org/10.1038/nrg3293openalex-snapshot

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

inferredcites →https://doi.org/10.1038/nrg3484openalex-snapshot

Eukaryotic transcriptional dynamics: from single molecules to cell populations

inferredcites →https://doi.org/10.1038/nrmicro787openalex-snapshot

The regulation of bacterial transcription initiation

inferredcites →https://doi.org/10.1038/nsmb.2192openalex-snapshot

Signal-dependent dynamics of transcription factor translocation controls gene expression

inferredcites →https://doi.org/10.1038/nsmb763openalex-snapshot

Structure and mechanism of the RNA polymerase II transcription machinery

inferredcites →https://doi.org/10.1073/pnas.0409624102openalex-snapshot

Logic functions of the genomic cis-regulatory code

inferredcites →https://doi.org/10.1073/pnas.0707904105openalex-snapshot

Transcriptional control of noise in gene expression

inferredcites →https://doi.org/10.1073/pnas.0802406105openalex-snapshot

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

inferredcites →https://doi.org/10.1073/pnas.0930314100openalex-snapshot

On schemes of combinatorial transcription logic

inferredcites →https://doi.org/10.1073/pnas.1015616108openalex-snapshot

Quantitative dissection of the simple repression input–output function

inferredcites →https://doi.org/10.1073/pnas.1109873108openalex-snapshot

Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo

inferredcites →https://doi.org/10.1073/pnas.1413877112openalex-snapshot

Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo

inferredcites →https://doi.org/10.1073/pnas.94.15.8036openalex-snapshot

Synergistic and promoter-selective activation of transcription by recruitment of transcription factors TFIID and TFIIB

inferredcites →https://doi.org/10.1074/jbc.m305995200openalex-snapshot

Kinetics of Transcription Initiation at lacP1

inferredcites →https://doi.org/10.1091/mbc.e03-10-0729openalex-snapshot

Two Functionally Identical Modular Enhancers inDrosophilaTroponin T Gene Establish the Correct Protein Levels in Different Muscle Types

inferredcites →https://doi.org/10.1093/emboj/17.11.3146openalex-snapshot

Transcriptional activation domains stimulate initiation and elongation at different times and via different residues

inferredcites →https://doi.org/10.1093/emboj/17.20.5998openalex-snapshot

Cooperative DNA‐binding by Bicoid provides a mechanism for threshold‐dependent gene activation in the Drosophila embryo

inferredcites →https://doi.org/10.1101/gad.1698108openalex-snapshot

Caudal, a key developmental regulator, is a DPE-specific transcriptional factor

inferredcites →https://doi.org/10.1101/gad.7.2.173openalex-snapshot

Synergism in transcriptional activation: a kinetic view.

inferredcites →https://doi.org/10.1101/gad.924301openalex-snapshot

Enhancer–promoter specificity mediated by DPE or TATA core promoter motifs

inferredcites →https://doi.org/10.1101/sqb.1998.63.141openalex-snapshot

The Functional and Regulatory Roles of Sigma Factors in Transcription

inferredcites →https://doi.org/10.1126/science.1152398openalex-snapshot

Evolution of Eukaryotic Transcription Circuits

inferredcites →https://doi.org/10.1128/mcb.00586-07openalex-snapshot

Differential Regulation of NF-κB by Elongation Factors Is Determined by Core Promoter Type

inferredcites →https://doi.org/10.1128/mcb.15.11.5906openalex-snapshot

Core Promoter Specificities of the Sp1 and VP16 Transcriptional Activation Domains

inferredcites →https://doi.org/10.1128/mcb.15.3.1405openalex-snapshot

Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative

inferredcites →https://doi.org/10.1128/mcb.16.5.2044openalex-snapshot

Three Functional Classes of Transcriptional Activation Domains

inferredcites →https://doi.org/10.1128/mcb.25.13.5626-5638.2005openalex-snapshot

Simultaneous Recruitment of Coactivators by Gcn4p Stimulates Multiple Steps of Transcription In Vivo

inferredcites →https://doi.org/10.1146/annurev-biophys-083012-130401openalex-snapshot

Regulation of Noise in Gene Expression

inferredcites →https://doi.org/10.1146/annurev.bi.54.070185.001131openalex-snapshot

MECHANISM AND CONTROL OF TRANSCRIPTION INITIATION IN PROKARYOTES

inferredcites →https://doi.org/10.1186/1741-7007-12-29openalex-snapshot

Models in biology: ‘accurate descriptions of our pathetic thinking’

inferredcites →https://doi.org/10.1186/gb-2002-3-12-research0087openalex-snapshot

Computational analysis of core promoters in the Drosophila genome

inferredcites →https://doi.org/10.1242/dev.035493openalex-snapshot

Promoting developmental transcription

inferredcites →https://doi.org/10.1242/dev.069146openalex-snapshot

Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

inferredcites →https://doi.org/10.1371/journal.pbio.0030076openalex-snapshot

A New Paradigm in Eukaryotic Biology: HIV Tat and the Control of Transcriptional Elongation

inferredcites →https://doi.org/10.1371/journal.pbio.0030093openalex-snapshot

Functional Evolution of a cis-Regulatory Module

inferredcites →https://doi.org/10.1371/journal.pcbi.1000935openalex-snapshot

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

inferredcites →https://doi.org/10.1371/journal.pcbi.1001100openalex-snapshot

Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression

inferredcites →https://doi.org/10.1371/journal.pcbi.1002407openalex-snapshot

Thermodynamic State Ensemble Models of cis-Regulation

inferredcites →https://doi.org/10.1371/journal.pcbi.1002811openalex-snapshot

Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

inferredcites →https://doi.org/10.1371/journal.pcbi.1004345openalex-snapshot

Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules

inferredcites →https://doi.org/10.1371/journal.pone.0034439openalex-snapshot

Versatility of Cooperative Transcriptional Activation: A Thermodynamical Modeling Analysis for Greater-Than-Additive and Less-Than-Additive Effects

inferredcites →https://doi.org/10.15252/msb.20156257openalex-snapshot

Structure of silent transcription intervals and noise characteristics of mammalian genes

inferredcites →https://doi.org/10.4161/nucl.29838openalex-snapshot

The core promoter composition establishes a new dimension in developmental gene networks

inferredcites →https://doi.org/10.7554/elife.02407openalex-snapshot

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

inferredcites →https://doi.org/10.7554/elife.07956openalex-snapshot

Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/bies.201600032openalex-snapshot

Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription

inferred← citeshttps://doi.org/10.1016/j.cels.2017.01.012openalex-snapshot

Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms

inferred← citeshttps://doi.org/10.1073/pnas.1621150114openalex-snapshot

Systematic dissection of genomic features determining transcription factor binding and enhancer function

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