Fig. 1

Negative feedback loop established by Her1/7 proteins suppresses uncorrelated transcriptional variability

(A) The sketch of a wild-type zebrafish embryo at the 12-somite stage. The PSM, highlighted in orange, is dissected from the embryo for confocal imaging. Anterior (Ant) is to the right, and posterior (Pos) is to the left.

(B) Her1 and Her7 repress transcription of their own genes, and thereby form a cell-autonomous negative feedback loop.

(C–E) Red stars (∗) mark her1 and her7 genes carrying point mutations causing premature stop codons.

(F–H) The boundaries of somite segments are marked by xirp2 ISH staining in wild-type (F), her1^ci301/+;her7^hu2526/+ (G), and her1^ci301;her7^hu2526 mutants (H). Scale bar is 200 μm. (I-J) Expression of her7 displays kinematic waves and oscillations in wild-type (I) and her1^ci301/+;her7^hu2526/+ (J) mutants.

(K) Expression pattern of her7 is disrupted in double homozygous her1^ci301;her7^hu2526 mutants. Scale bar is 30 μm.

(L) The PSM is divided into single-cell width slices. Red or gray circles represent the cells, which contain higher or lower RNA levels than an arbitrary threshold, respectively. Three oscillatory waves of her7 are visible. The images are divided into two portions as left (top) and right (bottom) halves of the PSM.

(M) her7 RNA counts are plotted along the right half of PSM (posterior-to-anterior). Each dot corresponds to the mean RNA number in a sliced cell population. Error bars are 2 SEM.

(N) The frequency histogram of total her (her1+her7) RNA per cell is plotted in wild-type (dark gray) (n=24, N=2), her1^ci301/+;her7^hu2526/+ (silver) (n=18, N=2), her1^ci301;her7^hu2526 (red) (n=28, N=2) mutant embryos.

(O) Each dot represents her1 (x axis) and her7 (y axis) counts in a single cell. Correlated (green) and uncorrelated (purple) variability of her expression can be quantified in the population.

(P and Q) Correlated (P) and uncorrelated (Q) transcriptional variability of her1 and her7 are plotted based on mean her RNA concentration (mRNA counts normalized by cell volume). Error bars are two standard errors.

(R) Changing the size or frequency of transcriptional bursts affect the variability curve (CV² vs. mean) differently.

(S) Loss of Her proteins results in more uncorrelated transcriptional variability most likely due to increased burst sizes in her1^ci301;her7^hu2526 mutants. n is the number of embryos; N is the number of independent experiments. See also Figure S1.