Fig 1.
Motif mapping as a subsequence matching task.
(A) Images of the early and late stages of Drosophila GBE, a convergence-extension movement that involves repeated cell intercalation events in the form of T1-transitions (red and green) or rosettes (brown). (B,C) Illustrations of optimal matchings (dashed gray lines) between all time points of the templates (top) and subsequences of time points within the candidates (bottom) in a T1-transition (B) and a 5-cell rosette (C). In (B) red and green curves represent the boundary distances between the two nearing (dorso-ventral) and the two parting (antero-posterior) cells, respectively. The transition time points are indicated by asterisks.
Fig 2.
Early candidate rejection using a graph theoretic approach and method pipeline Examples of 4, 5, and 6 cell configurations and their empirical frequencies in imaging data.
(A) All possible 4-cell configurations. The two configurations relevant for T1-transitions account for only 6.66% of the dataset. (B) Examples of 5-cell configurations. Valid configurations account for 4.53% of observed 5-cell connected components. (C) Valid and invalid 6-cell configurations. (D) Summary of the method’s pipeline demonstrated on the search of T1-transitions.
Fig 3.
Visualization of detected motif appearances.
(A,B) Multiple sequence alignment of identified T1-transitions (A) and 5-cell rosettes (B). Snapshots in the rectangle correspond to the time points of cell rearrangement. Left arrows indicate that the sequence was temporally stretched by repeating the previous time point. (C) Left: Quantification of time-dependent frequencies of T1-transitions (red) and rosettes (green, blue) during the first 30 minutes of GBE, expressed as the number of events occurring in a size normalized tissue of 100 cells over a period of 1 minute. Right: a snapshot taken 16 minutes into GBE, showing the identified motifs, corresponding to cell groups at the transition time point. The image includes other cell groups undergoing rearrangements, but they are not at their transition points.
Fig 4.
Dynamics and efficiency of T1-transitions.
(A,B) The first and last snapshots of GBE imaged in the wild-type (A) and bcd nos tsl (B) embryos. Quantification of the average number of T1-transition events within a size normalized tissue of 100 cells throughout GBE shows a significant decrease in their prevalence within the mutant (p = 0.0041). (C) The rates of junction contraction (red) and growth (green) in wild-type embryos. Horizontal axis represents the time before contraction completion and after growth initiation. Vertical dashed lines indicate a time gap of between the two events (1.53±1.48 min, see also Fig 2,3 in S2 File). (D) Same as (C) but for bcd nos tsl embryos (time gap: 1.53±1.7 min). (E) Rose diagrams showing angle distributions of contracting junctions with respect to the ventral midline (i: 91.70±18.30°; p << 0.05 Rayleigh test for circular uniformity), and of growing junctions (ii: 1.20±35.90°; p << 0.05). (F) Same as (E) but in bcd nos tsl embryos (83.90±41.40°; p = 0.011 for contraction; 2.40±41.90°; p = 0.012 for growth). 0° = posterior, 90° = dorsal. (G) Bottom: Manually drawn template for a reversing T1-transition. Middle: An example of an identified reversal. Top: Snapshots of the identified reversal. (H) Probabilities of T1 rearrangements and reversals in the wild-type embryos (based on 539 events). (I) Same as (H) but for bcd nos tsl embryos (based on 60 events).
Fig 5.
(A) Distribution of time difference between contraction of the two disappearing junctions in 5-cell rosettes. (B) Left: Snapshots illustrating synchronous and sequential formation of 5-cell rosettes. Right: schematics of junction dynamics. (C,D) Same as (A,B), respectively, but for growing junctions. (E) The rates of junction contraction (red) and growth (green) during the formation of 5-cell rosettes. The horizontal axis is the time before contraction completion and growth initiation (vertical dashed lines indicate a possible time gap between the two events). Average contraction rate is significantly lower than for T1-transition. (F) Schemes of a rosette (i) and a rosette hub (ii). Top: snapshots throughout the lifetime of the motif. Cell numbering allows relating cells over time. Bottom: a simplified diagram of the exemplified motif. A rosette hub (ii) initiates with the formation of a rosette, followed by an iterative process, whereby at least one cell separates from the rosette (cell #6), followed by the joining of at least one new cell (cell #4), all the while maintaining at least 4 cells surrounding the core vertex (cells #1,2,3,5). As a result, the central vertex serves as a hub for intercalating cells.