Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics

Shukron, Ofir; Seeber, Andrew; Amitai, Assaf; Holcman, David

doi:10.1016/j.tig.2019.06.007

Cited by 38 publications

(36 citation statements)

References 110 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Analysis of the chromatin bound NuRD complex protein molecules in 500 ms exposure trajectories initially revealed two states of chromatin bound CHD4 (Figure 1f): both the slow and fast states were primarily subdiffusive (with an anomalous exponent a of around 0.5), but were characterised by different confinement lengths of 62 ± 12 nm and 110 ± 30 nm and apparent diffusion coefficients of 0.006 ± 0.002 µm " #$ and 0.018 ± 0.006 µm " #$ . These experiments thus reveal for the first time dynamics below the 200-250 nm length scale that had previously been observed 43,47 . By determining similar parameters for fixed dye molecules, we found that the slow-diffusing state was within our precision limit and so represents molecules that are essentially immobile (Extended Data Figure 10).…”

Section: The Holo-nurd Complex Modulates Chromatin Movement At Enhancsupporting

confidence: 69%

“…], is particularly informative: diffusing proteins are characterised by an anomalous exponent close to 1 whereas chromatin bound proteins exhibit a lower anomalous exponent 4,41,42 . In addition, for chromatin bound proteins, lower anomalous exponents represent a more condensed chromatin state 43 and higher values can represent energy-dependent directed motion. The localisation length Lc of chromatin bound proteins is also informative as it reflects the spatial scale that the molecule explores within the nucleus.…”

Section: A Novel Trajectory Segmentation Algorithm For Extracting Nurmentioning

confidence: 99%

See 1 more Smart Citation

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Basu

Shukron²,

Ponjavic³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Enhancer-promoter dynamics are critical for the spatiotemporal control of gene expression, but it remains unclear how these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) complex. Here, we use Hi-C experiments to show that the intact NuRD complex increases CTCF/Cohesin binding and the probability of the interaction of intermediate-range (~1Mb) genomic sequences.To understand how NuRD alters 3D genome structure in this way, we developed an approach to segment and extract key biophysical parameters from trajectories of the NuRD complex determined using live-cell 3D singlemolecule imaging. Unexpectedly, this revealed that the intact NuRD complex decompacts chromatin structure and makes NuRD-bound sequences move faster, thus increasing the overall volume of the nucleus that these sequences explore. Interestingly, we also uncovered a rare fast-diffusing state of chromatin that exhibits directed motion. The intact NuRD complex reduces the amount of time that enhancers/promoters remain in this fastdiffusing state, which we propose would otherwise re-organise enhancer-promoter proximity. Thus, we uncover an intimate connection between a chromatin remodeller and the spatial dynamics of the local region of the genome to which it binds.3D genome organisation is thought to be critical for the spatiotemporal control of gene expression. However, little is known about the multi-scale chromatin dynamics of cis-regulatory elements or how they relate to genome organisation. To probe these dynamics at the single-cell level, one of two complementary methods are typically used: either live-cell imaging 1-4 or single nucleus versions of chromosome conformation capture experiments (such as Hi-C), which reveal the proximity of DNA sequences in different individual fixed cells [5][6][7][8][9][10][11][12][13][14][15][16] . For example, live-cell tracking of enhancers and promoters has revealed fast diffusion (or 'stirring') during transcription 4 , but the mechanisms underlying these changes in enhancer dynamics or how they relate to Hi-C measurements of enhancer-promoter proximity remain unclear.The nucleosome remodelling and deacetylase (NuRD) complex is a highly conserved 1 MDa multisubunit protein complex that we have previously shown clusters in 3D space in the nucleus with active enhancers and promoters 16 . It combines two key enzymatic activities -nucleosome remodelling via its helicasecontaining ATPase (predominantly CHD4 in ES cells) and lysine deacetylation via its HDAC1/2 subunits [16][17][18][19][20][21][22] .These activities are thought to be present in two sub-complexes (Figure 1a). HDAC1/2 associates, along with the histone chaperones RBBP4/7, with the core scaffold proteins MTA1/2/3 (metastasis tumour antigens) to form a stable sub-complex with deacetylase activity 23 . The nucleosome remodeller CHD4 interacts with chromatin by itself and may also form a second sub-complex with GATAD2A/B and DOC1 (CDK2AP1) 23-25 .The methyl-CpG DNA binding domain proteins MBD2/3 ...

show abstract

Section: The Holo-nurd Complex Modulates Chromatin Movement At Enhancsupporting

confidence: 69%

Section: A Novel Trajectory Segmentation Algorithm For Extracting Nurmentioning

confidence: 99%

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Basu

Shukron²,

Ponjavic³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…2d ), the value of each parameter was poorly dependent of their position, suggesting that loci properties do not change significantly during the cell cycle. Ori2 foci had a low value of α (0.16), whereas Ter4 showed a slightly higher α (0.2, p = 3.8 × 10 −13 ), suggesting that the local condensation is slightly higher in ori than in ter , according to the RCL model 32 – 34 . The length of confinement for both loci was small (0.084 and 0.081 μm for Ori2 and Ter4, respectively), revealing loci are confined in small regions, which size depends slightly on chromosomal or cellular location.…”

Section: Resultsmentioning

confidence: 95%

Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP

et al. 2020

View full text Add to dashboard Cite

The ter region of the bacterial chromosome, where replication terminates, is the last to be segregated before cell division in Escherichia coli . Delayed segregation is controlled by the MatP protein, which binds to specific sites ( matS ) within ter, and interacts with other proteins such as ZapB. Here, we investigate the role of MatP by combining short-time mobility analyses of the ter locus with biochemical approaches. We find that ter mobility is similar to that of a non ter locus, except when sister ter loci are paired after replication. This effect depends on MatP, the persistence of catenanes, and ZapB. We characterise MatP/DNA complexes and conclude that MatP binds DNA as a tetramer, but bridging matS sites in a DNA-rich environment remains infrequent. We propose that tetramerisation of MatP links matS sites with ZapB and/or with non-specific DNA to promote optimal pairing of sister ter regions until cell division.

show abstract

“…2d), the value of each parameter was poorly dependent of their position, suggesting that loci properties do not change significantly during the cell cycle. Ori2 foci had a low value of α (0.16), whereas Ter4 showed a slightly higher α (0.2, p=3.8.10 -13 ), suggesting that the local condensation is slightly higher in ori than in ter, according to the RCL model [33][34][35] . The length of confinement for both loci was small (0.084 and 0.081μm for Ori2 and Ter4, respectively), revealing loci are confined in small regions, which size depends slightly on chromosomal or cellular location.…”

Section: Fl and Fh Show Different Dynamicsmentioning

confidence: 94%

Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP

Crozat

Tardin

Salhi

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Regions of the chromosome where replication terminates host specific activities in all organisms. In Escherichia coli, this region, named ter, is also the last segregated before cell division. Delayed segregation is controlled by the MatP protein, binding specific matS sites along ter. We investigated the fate of the E. coli ter region and the role of MatP by combining a detailed in vivo analysis of the mobility of a ter locus at short time scales with in vitro biochemical approaches. We found that ter dynamics differs only slightly from that of a control locus located close to the replication origin, except when sister ter loci are paired following their replication. MatP thus mainly acts in maintaining sister ter paired, but only plays a faint role in absence of pairing. This effect depends on MatP, its 20 C-terminal residues and ZapB to different levels, implying a role for all known MatP activities. We char-acterised MatP/DNA complexes and conclude that while MatP binds DNA as a tetramer, it barely forms specific DNA loops by bridging matS sites in a DNA rich environment. We propose that te-tramerisation of MatP links matS sites with ZapB and/or with non-specific DNA to promote optimal pairing of sister ter regions until cell division.

show abstract

Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics

Cited by 38 publications

References 110 publications

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP

Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP

Contact Info

Product

Resources

About