Transcription factors: from enhancer binding to developmental control (Q38032407)

27 August 2017

title

Transcription factors: from enhancer binding to developmental control (English)

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27 August 2017

François Spitz

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27 August 2017

Eileen E M Furlong

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27 August 2017

publication date

7 August 2012

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27 August 2017

published in

Nature Reviews Genetics

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27 August 2017

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27 August 2017

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27 August 2017

page(s)

613-626

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Emerging properties of animal gene regulatory networks

27 August 2017

cites work

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Conserved enhancer and silencer elements responsible for differential Adh transcription in Drosophila cell lines

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Insulators: exploiting transcriptional and epigenetic mechanisms

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Different core promoters possess distinct regulatory activities in the Drosophila embryo

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Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex

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Expression of a β-globin gene is enhanced by remote SV40 DNA sequences

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Regulation of even-skipped stripe 2 in the Drosophila embryo

31 March 2020

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https://pubmed.ncbi.nlm.nih.gov/22868264

31 March 2020

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors.

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Complexity and organization of DNA-protein interactions in the 5'-regulatory region of an endoderm-specific marker gene in the sea urchin embryo.

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A core transcriptional network for early mesoderm development in Drosophila melanogaster

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Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly

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Regulation of a Segmentation Stripe by Overlapping Activators and Repressors in the Drosophila Embryo

31 March 2020

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Smad proteins act in combination with synergistic and antagonistic regulators to target Dpp responses to the Drosophila mesoderm

31 March 2020

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Nuclear integration of positive Dpp signals, antagonistic Wg inputs and mesodermal competence factors during Drosophila visceral mesoderm induction.

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Control of a genetic regulatory network by a selector gene.

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Master transcription factors determine cell-type-specific responses to TGF-β signaling

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Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration

31 March 2020

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A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development

31 March 2020

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Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network

31 March 2020

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Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

31 March 2020

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A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

31 March 2020

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Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation

31 March 2020

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Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4.

31 March 2020

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Dynamic CRM occupancy reflects a temporal map of developmental progression

31 March 2020

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Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

31 March 2020

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Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.

31 March 2020

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Cell signaling can direct either binary or graded transcriptional responses

31 March 2020

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Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs

31 March 2020

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Interactions between DNA-bound repressors govern regulation by the λ phage repressor

31 March 2020

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Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila

31 March 2020

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Computational models for neurogenic gene expression in the Drosophila embryo.

31 March 2020

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Multiple modes of dorsal-bHLH transcriptional synergy in the Drosophila embryo.

31 March 2020

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Combinatorial patterning mechanisms in the Drosophila embryo

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Robustness: mechanisms and consequences

31 March 2020

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How different eukaryotic transcriptional activators can cooperate promiscuously.

31 March 2020

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Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription

31 March 2020

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Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism

31 March 2020

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Collaborative competition mechanism for gene activation in vivo

31 March 2020

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An Atomic Model of the Interferon-β Enhanceosome

31 March 2020

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Reversal of intrinsic DNA bends in the IFN beta gene enhancer by transcription factors and the architectural protein HMG I(Y)

31 March 2020

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Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.

31 March 2020

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Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites

31 March 2020

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A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos

31 March 2020

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Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins

31 March 2020

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Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

31 March 2020

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The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

31 March 2020

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Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

31 March 2020

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DNase I sensitivity QTLs are a major determinant of human expression variation

31 March 2020

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A chromatin-mediated mechanism for specification of conditional transcription factor targets

31 March 2020

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Accessibility of transcriptionally inactive genes is specifically reduced at homeoprotein-DNA binding sites in Drosophila

31 March 2020

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Interaction of the glucocorticoid receptor with the chromatin landscape

31 March 2020

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Two chromatin remodeling activities cooperate during activation of hormone responsive promoters

31 March 2020

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Mechanisms that specify promoter nucleosome location and identity

31 March 2020

1 reference

Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae

31 March 2020

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Nucleosome core displacement in vitro via a metastable transcription factor-nucleosome complex

31 March 2020

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Nucleosome disruption by transcription factor binding in yeast.

31 March 2020

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High-resolution profiling of histone methylations in the human genome

31 March 2020

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Differential chromatin marking of introns and expressed exons by H3K36me3.

31 March 2020

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

31 March 2020

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Histone modifications at human enhancers reflect global cell-type-specific gene expression

31 March 2020

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Mapping and analysis of chromatin state dynamics in nine human cell types

31 March 2020

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Finding distal regulatory elements in the human genome

31 March 2020

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Enhancer function: new insights into the regulation of tissue-specific gene expression

31 March 2020

1 reference

Histone H3K27ac separates active from poised enhancers and predicts developmental state

31 March 2020

1 reference

A unique chromatin signature uncovers early developmental enhancers in humans

31 March 2020

1 reference

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.

31 March 2020

1 reference

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

31 March 2020

1 reference

The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells

31 March 2020

1 reference

Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages.

31 March 2020

1 reference

Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors.

31 March 2020

1 reference

Gene regulatory logic of dopamine neuron differentiation

31 March 2020

1 reference

Combinatorial binding predicts spatio-temporal cis-regulatory activity

31 March 2020

1 reference

Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers

31 March 2020

1 reference

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development

31 March 2020

1 reference

Genome-wide discovery of human heart enhancers

31 March 2020

1 reference

Immunity regulatory DNAs share common organizational features in Drosophila

31 March 2020

1 reference

Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer

31 March 2020

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Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome

31 March 2020

1 reference

31 March 2020

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Information display by transcriptional enhancers

31 March 2020

1 reference

Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?

31 March 2020

1 reference

Functional architecture and evolution of transcriptional elements that drive gene coexpression

31 March 2020

1 reference

Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence

31 March 2020

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A transcription factor collective defines cardiac cell fate and reflects lineage history

31 March 2020

1 reference

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

31 March 2020

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Predicting functionality of protein-DNA interactions by integrating diverse evidence

31 March 2020

1 reference

Direct response to Notch activation: signaling crosstalk and incoherent logic.

31 March 2020

1 reference

Pioneer transcription factors: establishing competence for gene expression

31 March 2020

1 reference

Transcriptional and nontranscriptional functions of E2F1 in response to DNA damage

31 March 2020

1 reference

Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function

31 March 2020

1 reference

Epigenetic silencing of the c-fms locus during B-lymphopoiesis occurs in discrete steps and is reversible.

31 March 2020

1 reference

A two-step, PU.1-dependent mechanism for developmentally regulated chromatin remodeling and transcription of the c-fms gene.

31 March 2020

1 reference

Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements.

31 March 2020

1 reference

Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding

31 March 2020

1 reference

MyoD targets chromatin remodeling complexes to the myogenin locus prior to forming a stable DNA-bound complex

31 March 2020

1 reference

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription

31 March 2020

1 reference

Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis.

31 March 2020

1 reference

Epigenetic priming of a pre-B cell-specific enhancer through binding of Sox2 and Foxd3 at the ESC stage.

31 March 2020

1 reference

Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells

31 March 2020

1 reference

Early chromatin unfolding by RUNX1: a molecular explanation for differential requirements during specification versus maintenance of the hematopoietic gene expression program

31 March 2020

1 reference

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

31 March 2020

1 reference

Temporal coordination of gene networks by Zelda in the early Drosophila embryo.

31 March 2020

1 reference

Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition

31 March 2020

1 reference

Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer

31 March 2020

1 reference

Determinants and dynamics of genome accessibility

31 March 2020

1 reference

Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells

31 March 2020

1 reference

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

31 March 2020

1 reference

DNA-binding factors shape the mouse methylome at distal regulatory regions

31 March 2020

1 reference

SOX genes and neural progenitor identity

31 March 2020

1 reference

bHLH factors in muscle development: dead lines and commitments, what to leave in and what to leave out

31 March 2020

1 reference

Sequentially acting Sox transcription factors in neural lineage development

31 March 2020

1 reference

Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation

31 March 2020

1 reference

Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development

31 March 2020

1 reference

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

31 March 2020

1 reference

Shadow enhancers as a source of evolutionary novelty

31 March 2020

1 reference

Shadow enhancers: frequently asked questions about distributed cis-regulatory information and enhancer redundancy

31 March 2020

1 reference

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

31 March 2020

1 reference

Shadow enhancers foster robustness of Drosophila gastrulation

31 March 2020

1 reference

hairy mediates dominant repression in the Drosophila embryo

31 March 2020

1 reference

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

31 March 2020

1 reference

Multiple modular promoter elements drive graded brinker expression in response to the Dpp morphogen gradient

31 March 2020

1 reference

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

31 March 2020

1 reference

A global control region defines a chromosomal regulatory landscape containing the HoxD cluster

31 March 2020

1 reference

Transgenic analysis of Hoxd gene regulation during digit development.

31 March 2020

1 reference

A regulatory archipelago controls Hox genes transcription in digits

31 March 2020

1 reference

Mammalian genes are transcribed with widely different bursting kinetics

31 March 2020

1 reference

Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription.

31 March 2020

1 reference

A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers.

31 March 2020

1 reference

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells

31 March 2020

1 reference

Deletion of long-range regulatory elements upstream of SOX9 causes campomelic dysplasia

31 March 2020

1 reference

Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb.

31 March 2020

1 reference

Genomic views of distant-acting enhancers

31 March 2020

1 reference

The complex transcription regulatory landscape of our genome: control in three dimensions

31 March 2020

1 reference

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

31 March 2020

1 reference

Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression

31 March 2020

1 reference

Bystander gene activation by a locus control region

31 March 2020

1 reference

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

31 March 2020

1 reference

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

31 March 2020

1 reference

A microduplication of the long range SHH limb regulator (ZRS) is associated with triphalangeal thumb-polysyndactyly syndrome.

31 March 2020

1 reference

Duplications of noncoding elements 5' of SOX9 are associated with brachydactyly-anonychia.

31 March 2020

1 reference

Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2.

31 March 2020

1 reference

Conservation of enhancer location in divergent insects

31 March 2020

1 reference

Long-range regulation is a major driving force in maintaining genome integrity

31 March 2020

1 reference

Genomic regulatory blocks underlie extensive microsynteny conservation in insects

31 March 2020

1 reference

Topological domains in mammalian genomes identified by analysis of chromatin interactions

31 March 2020

1 reference

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

31 March 2020

1 reference

Spatial partitioning of the regulatory landscape of the X-inactivation centre

31 March 2020

1 reference

Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness

31 March 2020

1 reference

Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.

31 March 2020

1 reference

Disperse versus compact elements for the regulation of runt stripes in Drosophila.

31 March 2020

1 reference

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

31 March 2020

1 reference

A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development

31 March 2020

1 reference

Epistatic relationships reveal the functional organization of yeast transcription factors

31 March 2020

1 reference

Structure and regulation of a complex locus: the cut gene of Drosophila.

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22868264

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The bicoid and dorsal morphogens use a similar strategy to make stripes in the Drosophila embryo

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22868264

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG3207

1 reference

Dimensions Publication ID

27 August 2017

1049531859

0 references

1 reference