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Correlations of three-dimensional motion of chromosomal loci in yeast revealed by the double-helix point spread function microscope.

Backlund MP, Joyner R, Weis K, Moerner WE - Mol. Biol. Cell (2014)

Bottom Line: As controls, we tracked pairs of loci along the same chromosome at various separations, as well as transcriptionally orthogonal genes on different chromosomes.This relative increase has potentially important biological implications, as it might suggest coupling via shared silencing factors or association with decoupled machinery upon activation.We also found that on the time scale studied (∼0.1-30 s), the loci moved with significantly higher subdiffusive mean square displacement exponents than previously reported, which has implications for the application of polymer theory to chromatin motion in eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Stanford University, Stanford, CA 94305.

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Data from two example track pairs. (A–C) Velocity trajectories of a highly correlated example from the DLDC-dextrose case in each dimension, for δ = 5 s. Green lines correspond to the track from the green fluorescence channel, and red lines to the track from the red fluorescence channel. (D) The time-average velocity cross-correlation of the same track pair as in A–C. (E–G) Same as in A–C but for a different track pair from the DLDC-galactose case, which exhibits low correlations. (H) Same as in D but for the track pair addressed in E–G. (I) The 3D position trajectories of loci from E–H, color coded in time.
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Figure 5: Data from two example track pairs. (A–C) Velocity trajectories of a highly correlated example from the DLDC-dextrose case in each dimension, for δ = 5 s. Green lines correspond to the track from the green fluorescence channel, and red lines to the track from the red fluorescence channel. (D) The time-average velocity cross-correlation of the same track pair as in A–C. (E–G) Same as in A–C but for a different track pair from the DLDC-galactose case, which exhibits low correlations. (H) Same as in D but for the track pair addressed in E–G. (I) The 3D position trajectories of loci from E–H, color coded in time.

Mentions: During the course of our analysis, we observed individual instances of fascinating behavior between distinct chromosomal loci. Of importance, our single-particle tracking approach allows us to highlight prominent track pairs that exhibit either high or low . Supplemental Movies S1–S4 show four such example track pairs that exhibit the range of correlations. Data from one such highly correlated DLDC-dextrose example are shown in Figure 5, A–D. Figure 5, A–C, shows the x-, y-, and z-projections of the velocity trajectories in the green and red channels as calculated for δ = 5 s. The x- and z-projections of both loci appear to exhibit notable pseudo-oscillatory behavior (Pliss et al., 2013). Of interest, however, there seems to be a phase lag between the pseudo-oscillations of the loci, as in this particular case the red-tagged locus leads the green-tagged locus. This fact is further demonstrated by calculating the TAVCC, which is plotted in Figure 5D. Here we see a large peak (>0.5) centered near τ = 2 s, indicating ∼2-s response time between the leading red locus and the lagging green locus. Of course, there is no biological reason why the red should always lead the green, and so the ensemble contains track pairs that show the reverse relation just as often, giving rise to the symmetric T-EAVCC shown in Figure 4, A and B. An example from the DLDC case that shows a significant positive peak for τ < 0 is given in Supplemental Figure S14.


Correlations of three-dimensional motion of chromosomal loci in yeast revealed by the double-helix point spread function microscope.

Backlund MP, Joyner R, Weis K, Moerner WE - Mol. Biol. Cell (2014)

Data from two example track pairs. (A–C) Velocity trajectories of a highly correlated example from the DLDC-dextrose case in each dimension, for δ = 5 s. Green lines correspond to the track from the green fluorescence channel, and red lines to the track from the red fluorescence channel. (D) The time-average velocity cross-correlation of the same track pair as in A–C. (E–G) Same as in A–C but for a different track pair from the DLDC-galactose case, which exhibits low correlations. (H) Same as in D but for the track pair addressed in E–G. (I) The 3D position trajectories of loci from E–H, color coded in time.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4230621&req=5

Figure 5: Data from two example track pairs. (A–C) Velocity trajectories of a highly correlated example from the DLDC-dextrose case in each dimension, for δ = 5 s. Green lines correspond to the track from the green fluorescence channel, and red lines to the track from the red fluorescence channel. (D) The time-average velocity cross-correlation of the same track pair as in A–C. (E–G) Same as in A–C but for a different track pair from the DLDC-galactose case, which exhibits low correlations. (H) Same as in D but for the track pair addressed in E–G. (I) The 3D position trajectories of loci from E–H, color coded in time.
Mentions: During the course of our analysis, we observed individual instances of fascinating behavior between distinct chromosomal loci. Of importance, our single-particle tracking approach allows us to highlight prominent track pairs that exhibit either high or low . Supplemental Movies S1–S4 show four such example track pairs that exhibit the range of correlations. Data from one such highly correlated DLDC-dextrose example are shown in Figure 5, A–D. Figure 5, A–C, shows the x-, y-, and z-projections of the velocity trajectories in the green and red channels as calculated for δ = 5 s. The x- and z-projections of both loci appear to exhibit notable pseudo-oscillatory behavior (Pliss et al., 2013). Of interest, however, there seems to be a phase lag between the pseudo-oscillations of the loci, as in this particular case the red-tagged locus leads the green-tagged locus. This fact is further demonstrated by calculating the TAVCC, which is plotted in Figure 5D. Here we see a large peak (>0.5) centered near τ = 2 s, indicating ∼2-s response time between the leading red locus and the lagging green locus. Of course, there is no biological reason why the red should always lead the green, and so the ensemble contains track pairs that show the reverse relation just as often, giving rise to the symmetric T-EAVCC shown in Figure 4, A and B. An example from the DLDC case that shows a significant positive peak for τ < 0 is given in Supplemental Figure S14.

Bottom Line: As controls, we tracked pairs of loci along the same chromosome at various separations, as well as transcriptionally orthogonal genes on different chromosomes.This relative increase has potentially important biological implications, as it might suggest coupling via shared silencing factors or association with decoupled machinery upon activation.We also found that on the time scale studied (∼0.1-30 s), the loci moved with significantly higher subdiffusive mean square displacement exponents than previously reported, which has implications for the application of polymer theory to chromatin motion in eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Stanford University, Stanford, CA 94305.

Show MeSH
Related in: MedlinePlus