Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Department of Physics, University of California, Berkeley, United States
- Biology Department, Bowdoin College, United States
- Univ Grenoble Alpes CNRS, Grenoble INP, TIMC-IMAG, France
- Biophysics Graduate Group, University of California, Berkeley, United States
- Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratory of Biology and Modeling of the Cell, France
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, United States
Figures
Figure 1
Schematic of homologous chromosome pairing in somatic cells in D. melanogaster.
(A) Over the course of embryonic development, homologous chromosomes pair along their lengths. (B) Button model for homolog pairing in which each chromosome carries a series of sites that have …
Figure 2 with 6 supplements
The homologous button model.
(A) Pairing between homologous chromosomes is assumed to be driven by specific, short-range attractive interactions of strength between certain homologous regions, named buttons. Each 10-kb …
Figure 2—figure supplement 1
Simulated time evolution of distance between homologous loci.
Examples of kymographs of the time evolution of the distances between homologous regions predicted by the model in several simulated stochastic trajectories with different initial distances di for a …
Figure 2—figure supplement 2
Properties of the button model.
(A) Phase diagram of parameter ranges resulting in simulations compatible (white area) and incompatible (gray area) with pairing, starting from favorable initial homologous chromosome configurations …
Figure 2—figure supplement 3
Large-scale correlations in pairing probabilities.
(A) Cross-correlation of the simultaneous pairing status of two loci separated by a given genomic distance computed for different values (ρ = 80%) at different simulated developmental times. This …
Figure 2—figure supplement 4
The combinatorial and large button models.
(A) To investigate the possible nature of buttons, we developed a more general model in which buttons are made of nsite binding sites for specific architectural proteins. Every site is occupied by …
Figure 2—video 1
Polymer simulations of homologous pairing.
Example of a 4-hr numerical simulation of the homologous button model (ρ = 60%, = −1.6 kBT) with frames taken every 30 s. The movie focuses on one pair of homologs (red and blue polymers). Orange …
Figure 2—video 2
Polymer simulations of homologous pairing.
Same as in Figure 2—video 1 but taken from a different simulation run. The two pairs of homologs are highlighted (red/blue for one pair; purple/dark blue). Orange/cyan and pink/light blue parts of …
Figure 3 with 6 supplements
Live imaging of chromosomal loci provides dynamic single-locus spatiotemporal information about somatic homolog pairing.
(A) Schematic of the MS2 and PP7 nascent mRNA labeling scheme for live imaging of homologous loci. Expression of the stem loops is driven by UAS under the control of a GAL4 driver. (B) Snapshots at …
Figure 3—figure supplement 1
Experimental dynamics of inter-homolog distances used in Figure 3.
(A) Examples of individual traces in the unpaired (first row) and paired (third row) control cases, and when homologs are unpaired (second row) or paired (fourth row) for locus 38F. For the unpaired …
Figure 3—figure supplement 2
Homologous chromosome reporters inserted at the 53F genomic location.
(A) Representative traces of the dynamics of the distance between imaged loci for unpaired homologous loci and the negative control. (B) Representative traces of the dynamics of the distance between …
Figure 3—video 1
Representative confocal movie of a live Drosophila embryo (cell cycle 14 to gastrulation) in which MS2 and PP7 loops are integrated at equivalent positions on homologous chromosomes.
Examples of nuclei are highlighted whose loci display characteristic dynamics, including loci that do not pair (‘Unpaired’), loci that are already paired (‘Paired’), and loci that are observed …
Figure 3—video 2
Representative confocal movie of a live Drosophila embryo (roughly 4.5 hr old) in which MS2 and PP7 loops are integrated at equivalent positions on homologous chromosomes.
A greater proportion of nuclei show paired homologs relative to the earlier time point represented in Figure 3—video 1. Image stacks were taken roughly every 30 s and max-projected for 2D viewing.
Figure 3—video 3
Representative confocal movie of a live Drosophila embryo (roughly 5.5 hr old) in which MS2 and PP7 loops are integrated at various positions on homologous chromosomes (MS2 at position 38F and PP7 at position 53F) where we expect no pairing between transgenes.
Image stacks were taken roughly every 30 s and max-projected for 2D viewing.
Figure 3—video 4
Representative confocal movie of a live Drosophila embryo (cell cycle 14) in which MS2 and PP7 loops were interlaced in a single transgene on one chromosome at polytene position 38F to act as a positive control for pairing.
Both GFP and mCherry are co-localized to the same locus in all transcriptional loci. Image stacks were taken roughly every 30 s and max-projected for 2D viewing.
Figure 4 with 3 supplements
The homologous button model recapitulates the observed developmental dynamics of pairing.
(A) Mean and SD of the separation of each pair of transgenes integrated at position 38F imaged in a single embryo over 6 h of development. Each data point represents a single nucleus over a 10-min …
Figure 4—figure supplement 1
Comparison of our pairing data to previous results.
Pairing dynamics measured by live imaging at two chromosomal loci (red and blue points) as presented in Figure 4B. The progression of pairing observed in fixed embryos using DNA-FISH was obtained …
Figure 4—figure supplement 2
Establishing values for initial distance between homologous chromosomes via chromosome painting.
(A) Chromosome painting of chromosome arm 2L (red), carrying transgene location 38F, in an embryo in early cycle 14. Nuclei (blue) are stained with DAPI. Inter-homolog distances were determined by …
Figure 4—figure supplement 3
Inference of developmental pairing dynamics.
(A) Predicted time evolution of the mean pairing dynamics computed over all buttons in the simulation (black dots) for a distribution of initial inter-homolog distances given in Figure 4A and for …
Figure 5 with 3 supplements
The homologous button model predicts individual pairing dynamics.
(A) Examples of simulated (top) and experimental (bottom) pairing trajectories showing rapid transitions from the unpaired to the paired state. Simulations were carried out using ρ = 50% and . See …
Figure 5—figure supplement 1
Experimental individual pairing dynamics.
(A,B) Fast single-locus pairing dynamics illustrated by individual pairing traces detected for the experiments on locus 38F (A, n = 11) and locus 53F (B, n = 3) centered at the time of pairing (time …
Figure 5—figure supplement 2
Impact of and small statistics on individual pairing dynamics.
(A) Median pairing dynamics obtained from individual pairing trajectories detected during our simulations (colored lines) for ρ= 80% and different values of . Traces are centered at the time of …
Figure 5—video 1
Representative distance trajectory of two loci denoted as ‘pairing’ (plotted in the black experimental trace in Figure 5A) showing a rapid transition from large distances at earlier time points to smaller distances at later time points.
The trajectory is shown alongside movies of the nucleus and gastrulating embryo from which the distances were calculated to help visualize the speed at which this pairing occurs. Image stacks were …
