Key Points
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Transcriptional regulation is highly complex on many timescales.
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The binding of transcription factors to eukaryotic chromosomes is strongly restricted by complex chromatin structures.
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Through the recruitment of chromatin-modifying activities that reorganize local nucleosome structures, transcription factors gain access to regulatory elements.
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Genome-wide methodologies provide extensive data sets on the localization of transcription factors, global histone modifications and regions of accessible chromatin.
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By their nature, these approaches average signals across large cell populations that represent many heterogeneous states at the molecular level and lead to a static view of transcriptional states.
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By contrast, single-cell approaches have shown that many of the molecular factor–template interactions are highly dynamic in living cells.
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These dynamic processes are integrated over the lifetime of the cell cycle to create transcriptional profiles that often fluctuate with time, either in response to external signals or as a direct consequence of the internal molecular networks.
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A rigorous mechanistic understanding of fundamental transcriptional processes must integrate both the large-scale identification of factors and their activities, and the highly dynamic molecular processes that underlie their function.
Abstract
The interaction of regulatory proteins with the complex nucleoprotein structures that are found in mammalian cells involves chromatin reorganization at multiple levels. Mechanisms that support these transitions are complex on many timescales, which range from milliseconds to minutes or hours. In this Review, we discuss emerging concepts regarding the function of regulatory elements in living cells. We also explore the involvement of these dynamic and stochastic processes in the evolution of fluctuating transcriptional activity states that are now commonly reported in eukaryotic systems.
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The authors acknowledge careful reading of the manuscript and numerous suggestions by L. Grontved and D. Pressman, the US National Institutes of Health.
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FURTHER INFORMATION
Glossary
- DNase hypersensitive sites
-
Local regions of nucleosome reorganization that are detected by their increased accessibility to nucleases.
- Fluorescence recovery after photobleaching
-
(FRAP). An optical technique to measure interaction lifetimes of molecular species. It involves labelling a specific cell component with a fluorescent molecule, followed by photobleaching a sharply defined region of the cell. Imaging is used to observe the subsequent rates and patterns of fluorescence recovery.
- Fluorescence lifetime imaging
-
(FLIM). An alternative fluorescence method to measure lifetimes of molecular species.
- Fluorescence correlation spectroscopy
-
(FCS). A fluorescence method to determine the average lifetime of the interaction between two molecular species when they are present within a given volume.
- Single-molecule tracking
-
A method in which the path of a protein that is labelled with a bright chromophore is followed through the cell in real time.
- Tethering
-
The localization of a protein to a specific site on DNA not by direct DNA binding but by interactions with another protein factor that is bound to the DNA; it is usually detected by chromatin immunoprecipitation.
- ATP-dependent remodelling systems
-
Large multisubunit molecular machines that use ATP energy to reorganize nucleosome structures, often by sliding the nucleosome to a new position on the DNA.
- Pioneer proteins
-
Factors that are proposed to have properties which allow them to penetrate local nucleosome structures and thus to pioneer the recruitment of secondary factors.
- DMS footprinting
-
A method that detects regions of DNA resistance to chemical attack by dimethyl sulphoxide (DMS) owing to the presence of an interacting DNA-binding protein.
- UV laser crosslinking
-
A method that uses dense pulses of high-energy ultraviolet (UV) photons to crosslink DNA bound proteins to the template rapidly and with high efficiency.
- Assisted loading
-
A mechanism that proposes the transient recruitment of a transcription factor to the template by dynamic nucleosome remodelling.
- Transcriptional bursting
-
The phenomenon whereby transcripts are sometimes released from activated promoters as rapid short pulses rather than in a continuous mode.
- Hit-and-run model
-
The hypothesis that many transcription factors reside on specific binding sites for brief periods, which is followed by many of these factors returning to template cycles.
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Voss, T., Hager, G. Dynamic regulation of transcriptional states by chromatin and transcription factors. Nat Rev Genet 15, 69–81 (2014). https://doi.org/10.1038/nrg3623
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DOI: https://doi.org/10.1038/nrg3623
