Transcription factors: from enhancer binding to developmental control

@article{Spitz2012TranscriptionFF,
  title={Transcription factors: from enhancer binding to developmental control},
  author={François Spitz and Eileen E. M. Furlong},
  journal={Nature Reviews Genetics},
  year={2012},
  volume={13},
  pages={613-626}
}
Developmental progression is driven by specific spatiotemporal domains of gene expression, which give rise to stereotypically patterned embryos even in the presence of environmental and genetic variation. Views of how transcription factors regulate gene expression are changing owing to recent genome-wide studies of transcription factor binding and RNA expression. Such studies reveal patterns that, at first glance, seem to contrast with the robustness of the developmental processes they encode… Expand
The Genome in Development
TLDR
This chapter considers three major levels at which gene expression is controlled, with respect to their roles in the developmental process, including transcriptional regulation by sequence-specific transcription factors and their interaction with cis -regulatory modules. Expand
Polycomb in Transcriptional Phase Transition of Developmental Genes.
TLDR
The mechanisms of transition between transcriptional status of developmental regulators are summarized, including complex processes for enhancer activation and promoter-enhancer association, and testable models in which Polycomb group factors contribute to promoter- enhancer associations and thus proper gene expression are proposed. Expand
Combinatorial function of transcription factors and cofactors.
TLDR
How TF synergy is mediated at the level of DNA binding and after binding, the role of cofactors and the post-translational modifications they catalyze, and different models of enhancer-core-promoter communication are reviewed. Expand
Transcriptional enhancers: from properties to genome-wide predictions
TLDR
How properties of enhancer sequences and chromatin are used to predict enhancers in genome-wide studies are discussed and recently developed high-throughput methods that allow the direct testing and identification of enhancers on the basis of their activity are covered. Expand
Transcriptional enhancers and their communication with gene promoters.
TLDR
Classic and recent evidence on the regulatory logic of enhancers is synthesised, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. Expand
Enhancer function: mechanistic and genome-wide insights come together.
TLDR
This work integrates whole-genome studies with recent mechanistic studies to illuminate how enhancers physically interact with target genes, how enhancer activity is regulated during development, and the role of noncoding RNAs transcribed from enhancers in their function. Expand
Using synthetic biology to study gene regulatory evolution.
TLDR
Several studies clearly show that synthetic biology can provide a way to reverse-engineer and reengineer transcriptional regulation in animal genomes with enormous potential for understanding evolution. Expand
The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains.
TLDR
The molecular mechanisms that enable and accompany the action of long-range acting elements and the integration of multiple distributed regulatory inputs into the coherent and specific regulatory programs that are key to embryonic development are discussed. Expand
Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution
TLDR
An overview of emerging principles of enhancers function, current models of enhancer architecture, genomic substrates from which enhancers emerge during evolution, and the influence of three-dimensional genome organization on long-range gene regulation are given. Expand
Enhancer and super‐enhancer: Positive regulators in gene transcription
TLDR
The history, importance, advances and challenges on enhancer and super‐enhancer field are reviewed to benefit the understanding of their function mechanism for transcription underlying precise gene expression. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 175 REFERENCES
Enhancer function: new insights into the regulation of tissue-specific gene expression
TLDR
Surprisingly, cohesin and non-coding RNAs are emerging as crucial players responsible for facilitating enhancer–promoter interactions at some genes and may be required not only to facilitate initiation of transcription but also to activate the release of RNA polymerase II from promoter-proximal pausing. Expand
A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development.
TLDR
A global approach revealed three temporal patterns of Mef2 enhancer binding, providing a glimpse of dynamic enhancer use within the context of a developing embryo and suggesting cooperativity with the bHLH protein Twist. Expand
Transcriptional Enhancers in Animal Development and Evolution
  • M. Levine
  • Medicine, Biology
  • Current Biology
  • 2010
TLDR
This review summarizes well-defined examples of enhancers controlling key processes in animal development and discusses the prospects for reconstructing transitions in animal evolution by introducing derived enhancers in basal ancestors. Expand
Program-Specific Distribution of a Transcription Factor Dependent on Partner Transcription Factor and MAPK Signaling
TLDR
Yeast Ste12 transcription factor is bound to distinct program-specific target genes dependent on the developmental condition, which may be a general mechanism by which transcription factors regulate distinct gene expression programs in response to signaling. Expand
Information display by transcriptional enhancers
TLDR
It is shown that a simple, compact enhancer is capable of representing both repressed and activated states at the same time and in the same nucleus, suggesting that closely apposed factor binding sites, situated within compact cis-elements, can be independently interpreted by the transcriptional machinery. Expand
Combinatorial binding predicts spatio-temporal cis-regulatory activity
TLDR
A novel approach to predict spatio-temporal cis-regulatory activity based only on in vivo transcription factor binding and enhancer activity data is used, generating a high-resolution atlas of cis-Regulatory modules describing their temporal and combinatorial occupancy during Drosophila mesoderm development. Expand
Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence.
TLDR
The results suggest that interaction between Dorsal and Zelda drives expression within the presumptive neurogenic ectoderm, but they also demonstrate that regulatory architecture directing expression in this domain is flexible. Expand
Functional and Mechanistic Diversity of Distal Transcription Enhancers
Biological differences among metazoans and between cell types in a given organism arise in large part due to differences in gene expression patterns. Gene-distal enhancers are key contributors toExpand
A core transcriptional network for early mesoderm development in Drosophila melanogaster.
TLDR
It is suggested that Twist binds to almost all mesodermal CRMs to provide the competence to integrate inputs from more specialized transcription factors, and extensive combinatorial binding, feed-forward regulation, and complex logical outputs as prevalent features are revealed. Expand
Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers.
TLDR
It is shown that induction ofFOXA1 expression and its subsequent recruitment to enhancers is associated with DNA demethylation, and histone H3 lysine 4 methylation is induced at these enhancers, which are intrinsic cell-type-specific regulatory regions of which activities have to be potentiated by FOXA1 through induction of an epigenetic switch that includes notably DNA dem methylation. Expand
...
1
2
3
4
5
...