CTCF and cohesin regulate chromatin loop stability with distinct dynamics

Hansen, Anders S.; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier

doi:10.7554/elife.25776

Cited by 521 publications

(656 citation statements)

References 83 publications

Supporting

Mentioning

593

Contrasting

Unclassified

Order By: Relevance

“…Previous single-molecule studies of TFs have consistently found two populations in the survival probability distributions: a short-lived population with RTs on the order of hundreds of milliseconds and a longer-lived population with RTs on the order of tens of seconds to minutes (Chen et al 2014b;Normanno et al 2015;Hansen et al 2017). These two populations have often been shown to be the nonspecific and specific binding populations, respectively.…”

Section: Single-molecule Imaging In Living Drosophila Embryos Using Llsmmentioning

confidence: 98%

“…To further validate our observation that the RT of the long-lived population of BCD is highly transient compared with the 10-60 sec typically observed for other sequence-specific DNA-binding TFs using single-molecule tracking (Chen et al 2014b;Hansen et al 2017), we performed fluorescence recovery after photobleaching (FRAP) experiments on BCD in the embryo (Fig. 1D), which revealed halftimes of BCD recovery on the order of hundreds of milliseconds (Supplemental Fig.…”

Section: Single-molecule Imaging In Living Drosophila Embryos Using Llsmmentioning

confidence: 99%

See 1 more Smart Citation

Dense Bicoid hubs accentuate binding along the morphogen gradient

et al. 2017

Self Cite

View full text Add to dashboard Cite

Morphogen gradients direct the spatial patterning of developing embryos; however, the mechanisms by which these gradients are interpreted remain elusive. Here we used lattice light-sheet microscopy to perform in vivo singlemolecule imaging in early Drosophila melanogaster embryos of the transcription factor Bicoid that forms a gradient and initiates patterning along the anteroposterior axis. In contrast to canonical models, we observed that Bicoid binds to DNA with a rapid off rate throughout the embryo such that its average occupancy at target loci is on-ratedependent. We further observed Bicoid forming transient "hubs" of locally high density that facilitate binding as factor levels drop, including in the posterior, where we observed Bicoid binding despite vanishingly low protein levels. We propose that localized modulation of transcription factor on rates via clustering provides a general mechanism to facilitate binding to low-affinity targets and that this may be a prevalent feature of other developmental transcription factors.

show abstract

Section: Single-molecule Imaging In Living Drosophila Embryos Using Llsmmentioning

confidence: 98%

Section: Single-molecule Imaging In Living Drosophila Embryos Using Llsmmentioning

confidence: 99%

Dense Bicoid hubs accentuate binding along the morphogen gradient

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…We see a similar ~5-10% difference between Spot-On (4 1223 jumps) and Spot-On (all) on the experimental spaSPT data shown in Figure 4. As we have 1224 discussed previously (Hansen et al, 2017), restricting JumpsToConsider to 4 is a way one can 1225 compensate for all the many acquisition biases (such as motion-blur) that generally cause 1226 undercounting for fast-diffusing molecules and which cannot readily be taken into account in 1227 simulations. While the optimal value will depend on the trajectory length distribution 1228 (JumpsToConsider should not take a value much smaller than the mean trajectory length), we 1229…”

mentioning

confidence: 99%

“…While on simulated data, using a subset of the trajectories is always 945 slightly less accurate than using the entire trajectory since it slightly underestimates the bound 946 fraction, we previously (Hansen et al, 2017) used this as an empirical way of compensating 947 for all the other experimental biases that cause undercounting of freely diffusing molecules 948 that cannot fully be taken into account in simulations. We therefore also tested this approach 949 in the simulations.…”

mentioning

confidence: 99%

Spot-On: robust model-based analysis of single-particle tracking experiments

Hansen

Woringer

Grimm

et al. 2017

Preprint

Self Cite

115

View full text Add to dashboard Cite

2 ABSTRACT 27Single-particle tracking (SPT) has become an important method to bridge 28 biochemistry and cell biology since it allows direct observation of protein binding and 29 diffusion dynamics in live cells. However, accurately inferring information from SPT studies 30 is challenging due to biases in both data analysis and experimental design. To address analysis 31 bias, we introduce "Spot-On", an intuitive web-interface. Spot-On implements a kinetic 32 modeling framework that accounts for known biases, including molecules moving out-of-33 focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule 34 trajectories. To minimize inherent experimental biases, we implement and validate 35 stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking 36 errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On 37 outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian 38 cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently 39 and robustly infers subpopulation fractions and diffusion constants. 40

show abstract

“…Most DNA-binding proteins interact both non-specifically and transiently [1] with many chromatin sites as well as specifically and more stably with cognate binding sites. These interactions and chromatin structure are important in governing protein dynamics [2,3]. However, the effect of these transient interactions on protein motion and distribution has yet been shown from a first principle.…”

mentioning

confidence: 99%

Chromatin configuration affects the dynamics and distribution of a transiently interacting protein

Amitai

2018

Preprint

View full text Add to dashboard Cite

We present a theoretical study of the interaction between a protein (diffusing particle) with chromatin (polymer chain). Each monomer is a trap where a particle can transiently bind. We derive novel formulas for the transition rate between monomer sites, given a specific polymer configuration, and find that a particle is likely to rapidly rebind many times to its release site, before moving to another. The reattachment probability is larger when the local density around the release site is smaller. Interestingly, for an equilibrated polymer, the transition probability decays as a power-law for close monomer-to-monomer distances and reaches an asymptotic value for faraway ones. By computing the transition rate between monomers, we show that the problem of facilitated search by a protein can be mapped to a continuous time Markov chain, which we solve. Our findings suggest that proteins may be locally trapped for a time much longer than their dissociation time, while their overall motion is ergodic. Our results are corroborated by Brownian simulations.The interaction of proteins with chromatin regulates many cellular functions. Most DNA-binding proteins interact both non-specifically and transiently [1] with many chromatin sites as well as specifically and more stably with cognate binding sites. These interactions and chromatin structure are important in governing protein dynamics [2,3]. However, the effect of these transient interactions on protein motion and distribution has yet been shown from a first principle.Some aspects of protein interactions with DNA have been studied in the context of the search of a gene promoter site by a transcription factor (TF) [4]. It was first noted [5] that the search for a promoter site by a TF would be faster if it involves 3d excursions, as well as sliding of the protein along DNA [6], as was shown in prokaryotes [7]. These different types of motion were observed experimentally, leading to massive interest in models of facilitated diffusion [8][9][10][11][12][13][14][15], and in the impact of a regulating site's position on transcription [16,17]. In current microscopy experiments, it is impossible to examine the search process to its fullest [18]. Thus, we concentrate here on modeling the experimentally observed dynamics of the protein as a diffusing and interacting particle.We will show that proteins are likely to stay in the proximity of a site for a time much longer than their dissociation time from DNA due to reattachment. Moreover, we find that reattachment depends on the local density around the release site and that the precise configuration of the polymer impacts the interacting particle's dynamics. We further find the rates associated with the transition between different monomer sites. Finally, we show that the process as a whole is ergodic; it has no long-time power law distribution of the residence time at a site as has been previously suggested [20]. We consider a point particle (protein) placed at a distance a from monomer n (locus), part of a long flexi- The part...

show abstract

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

Cited by 521 publications

References 83 publications

Dense Bicoid hubs accentuate binding along the morphogen gradient

Dense Bicoid hubs accentuate binding along the morphogen gradient

Spot-On: robust model-based analysis of single-particle tracking experiments

Chromatin configuration affects the dynamics and distribution of a transiently interacting protein

Contact Info

Product

Resources

About