Protein motion in the nucleus: from anomalous diffusion to weak interactions

@article{Woringer2018ProteinMI,
  title={Protein motion in the nucleus: from anomalous diffusion to weak interactions},
  author={Maxime Woringer and Xavier Darzacq},
  journal={Biochemical Society Transactions},
  year={2018},
  volume={46},
  pages={945 - 956}
}
Understanding how transcription factors (TFs) regulate mammalian gene expression in space and time is a central topic in biology. To activate a gene, a TF has first to diffuse in the available space of the nucleus until it reaches a target DNA sequence or protein (target site). This eventually results in the recruitment of the whole transcriptional machinery. All these processes take place in the mammalian nucleoplasm, a highly organized and dynamic environment, in which some complexes… 

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References

SHOWING 1-10 OF 133 REFERENCES

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

TLDR
Live-cell single-molecule imaging revealed that TF LCDs interact to form local high-concentration hubs at both synthetic DNA arrays and endogenous genomic loci, suggesting that under physiological conditions, rapid, reversible, and selective multivalent LCD-LCD interactions occur between TFs and the RNA Pol II machinery to activate transcription.

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

TLDR
This work quantitatively analyse the search process in human cells of Tet repressors searching for a multi-array locus with single-molecule tracking and single-cell protein–DNA association measurements, finding that TetRs explore the nucleus and reach their target by 3D diffusion interspersed with transient interactions with non-cognate sites, consistent with the facilitated diffusion model.

Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin

TLDR
It is established that volume exclusion and diffusive hindrance occur in dense nuclear compartments by probing the diffusive behaviour of inert fluorescent tracers in living cells and derived a fractal model of chromatin organization, which explains why the dynamics of soluble nuclear proteins are affected independently of their size.

Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell

TLDR
In a living Escherichia coli cell, specific binding of a lac repressor, labeled with a fluorescent protein, to a chromosomal lac operator is observed and the kinetics of binding and dissociation of the repressor in response to metabolic signals are measured using single-molecule detection techniques.

NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA

TLDR
This finding provides a simple mechanism for accelerating the target search in vivo for the specific site in a sea of nonspecific sites by permitting more effective sampling of available DNA sites as the protein jumps from one segment to another.

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

TLDR
A quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells, suggests that transient crowding of enzymes may aid in rate-limiting steps of gene regulation.

DNA residence time is a regulatory factor of transcription repression

TLDR
Single molecule experiments reveal transcription factor DNA residence time as a regulatory factor controlling transcription repression and establish TALE-DNA binding domains as tools for the temporal dissection of transcription regulation.
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