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Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain.

Zhang L, Radtke K, Zheng L, Cai AQ, Schilling TF, Nie Q - Mol. Syst. Biol. (2012)

Bottom Line: During development of rhombomeres in the zebrafish hindbrain, the morphogen retinoic acid (RA) induces expression of hoxb1a in rhombomere 4 (r4) and krox20 in r3 and r5.Computational analysis of spatial stochastic models shows, surprisingly, that noise in hoxb1a/krox20 expression actually promotes sharpening of boundaries between adjacent segments.This finding suggests a novel noise attenuation mechanism that relies on intracellular noise to induce switching and coordinate cellular decisions during developmental patterning.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics, University of California, Irvine, CA 92697-3875, USA.

ABSTRACT
Morphogens provide positional information for spatial patterns of gene expression during development. However, stochastic effects such as local fluctuations in morphogen concentration and noise in signal transduction make it difficult for cells to respond to their positions accurately enough to generate sharp boundaries between gene expression domains. During development of rhombomeres in the zebrafish hindbrain, the morphogen retinoic acid (RA) induces expression of hoxb1a in rhombomere 4 (r4) and krox20 in r3 and r5. Fluorescent in situ hybridization reveals rough edges around these gene expression domains, in which cells co-express hoxb1a and krox20 on either side of the boundary, and these sharpen within a few hours. Computational analysis of spatial stochastic models shows, surprisingly, that noise in hoxb1a/krox20 expression actually promotes sharpening of boundaries between adjacent segments. In particular, fluctuations in RA initially induce a rough boundary that requires noise in hoxb1a/krox20 expression to sharpen. This finding suggests a novel noise attenuation mechanism that relies on intracellular noise to induce switching and coordinate cellular decisions during developmental patterning.

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Sharpening of gene expression boundaries in the zebrafish hindbrain. (A–F) Single confocal images of fluorescent in situ hybridization (FISH) for krox20 (red) mRNA, dorsal views, anterior to the left, between 10.7 and 12.7 h post fertilization (h.p.f.). (G–I) Fluorescence measurements at different positions along the anterior-posterior axis (X axis) at 11, 11.7, and 12.7 h.p.f. Lines represent four different samples. (J–L) Single confocal images of two-color FISH for hoxb1a (r4, red) and krox20 (r3 and r5, green). Insets show enlargements of cells co-expressing both (yellow). (M–O) Sample distributions of mis-expressing cells along the r4/5 boundary (black lines) between 10.7 and 12 h.p.f., anterior to the top. Cells mis-expressing krox20—green dots, hoxb1a—red dots and co-expressing cells—orange dots.
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f1: Sharpening of gene expression boundaries in the zebrafish hindbrain. (A–F) Single confocal images of fluorescent in situ hybridization (FISH) for krox20 (red) mRNA, dorsal views, anterior to the left, between 10.7 and 12.7 h post fertilization (h.p.f.). (G–I) Fluorescence measurements at different positions along the anterior-posterior axis (X axis) at 11, 11.7, and 12.7 h.p.f. Lines represent four different samples. (J–L) Single confocal images of two-color FISH for hoxb1a (r4, red) and krox20 (r3 and r5, green). Insets show enlargements of cells co-expressing both (yellow). (M–O) Sample distributions of mis-expressing cells along the r4/5 boundary (black lines) between 10.7 and 12 h.p.f., anterior to the top. Cells mis-expressing krox20—green dots, hoxb1a—red dots and co-expressing cells—orange dots.

Mentions: To determine the temporal dynamics of hoxb1a and krox20 expression in the embryonic zebrafish hindbrain, we performed fluorescent in situ hybridization (FISH) analysis. Previous studies showed that initial boundaries of hoxb1a in r4 and krox20 expression in r3 and r5 are rough but become razor sharp between 10 and 14  h post fertilization (h.p.f.) (Figure 1A–F; Cooke and Moens, 2002; Cooke et al, 2005). Cells that find themselves on the wrong side of a boundary (i.e., surrounded by neighbors with a different pattern of gene expression) may go through a transient phase in which they express both genes and subsequently downregulate one or the other to enable sharpening (Schilling et al, 2001; Cooke and Moens, 2002). To quantify sharpness in krox20 expression, confocal stacks were collected for a minimum of 10 embryos at 6 different stages (between 10.7 and 12.7 h.p.f.) (Figure 1A–F) and the fluorescence was measured at different positions along the anterior-posterior (A-P) axis focusing on the r4/5 boundary (Figure 1G–I). This analysis demonstrated quantitatively how krox20 expression sharpens at rhombomere boundaries over time.


Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain.

Zhang L, Radtke K, Zheng L, Cai AQ, Schilling TF, Nie Q - Mol. Syst. Biol. (2012)

Sharpening of gene expression boundaries in the zebrafish hindbrain. (A–F) Single confocal images of fluorescent in situ hybridization (FISH) for krox20 (red) mRNA, dorsal views, anterior to the left, between 10.7 and 12.7 h post fertilization (h.p.f.). (G–I) Fluorescence measurements at different positions along the anterior-posterior axis (X axis) at 11, 11.7, and 12.7 h.p.f. Lines represent four different samples. (J–L) Single confocal images of two-color FISH for hoxb1a (r4, red) and krox20 (r3 and r5, green). Insets show enlargements of cells co-expressing both (yellow). (M–O) Sample distributions of mis-expressing cells along the r4/5 boundary (black lines) between 10.7 and 12 h.p.f., anterior to the top. Cells mis-expressing krox20—green dots, hoxb1a—red dots and co-expressing cells—orange dots.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472692&req=5

f1: Sharpening of gene expression boundaries in the zebrafish hindbrain. (A–F) Single confocal images of fluorescent in situ hybridization (FISH) for krox20 (red) mRNA, dorsal views, anterior to the left, between 10.7 and 12.7 h post fertilization (h.p.f.). (G–I) Fluorescence measurements at different positions along the anterior-posterior axis (X axis) at 11, 11.7, and 12.7 h.p.f. Lines represent four different samples. (J–L) Single confocal images of two-color FISH for hoxb1a (r4, red) and krox20 (r3 and r5, green). Insets show enlargements of cells co-expressing both (yellow). (M–O) Sample distributions of mis-expressing cells along the r4/5 boundary (black lines) between 10.7 and 12 h.p.f., anterior to the top. Cells mis-expressing krox20—green dots, hoxb1a—red dots and co-expressing cells—orange dots.
Mentions: To determine the temporal dynamics of hoxb1a and krox20 expression in the embryonic zebrafish hindbrain, we performed fluorescent in situ hybridization (FISH) analysis. Previous studies showed that initial boundaries of hoxb1a in r4 and krox20 expression in r3 and r5 are rough but become razor sharp between 10 and 14  h post fertilization (h.p.f.) (Figure 1A–F; Cooke and Moens, 2002; Cooke et al, 2005). Cells that find themselves on the wrong side of a boundary (i.e., surrounded by neighbors with a different pattern of gene expression) may go through a transient phase in which they express both genes and subsequently downregulate one or the other to enable sharpening (Schilling et al, 2001; Cooke and Moens, 2002). To quantify sharpness in krox20 expression, confocal stacks were collected for a minimum of 10 embryos at 6 different stages (between 10.7 and 12.7 h.p.f.) (Figure 1A–F) and the fluorescence was measured at different positions along the anterior-posterior (A-P) axis focusing on the r4/5 boundary (Figure 1G–I). This analysis demonstrated quantitatively how krox20 expression sharpens at rhombomere boundaries over time.

Bottom Line: During development of rhombomeres in the zebrafish hindbrain, the morphogen retinoic acid (RA) induces expression of hoxb1a in rhombomere 4 (r4) and krox20 in r3 and r5.Computational analysis of spatial stochastic models shows, surprisingly, that noise in hoxb1a/krox20 expression actually promotes sharpening of boundaries between adjacent segments.This finding suggests a novel noise attenuation mechanism that relies on intracellular noise to induce switching and coordinate cellular decisions during developmental patterning.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics, University of California, Irvine, CA 92697-3875, USA.

ABSTRACT
Morphogens provide positional information for spatial patterns of gene expression during development. However, stochastic effects such as local fluctuations in morphogen concentration and noise in signal transduction make it difficult for cells to respond to their positions accurately enough to generate sharp boundaries between gene expression domains. During development of rhombomeres in the zebrafish hindbrain, the morphogen retinoic acid (RA) induces expression of hoxb1a in rhombomere 4 (r4) and krox20 in r3 and r5. Fluorescent in situ hybridization reveals rough edges around these gene expression domains, in which cells co-express hoxb1a and krox20 on either side of the boundary, and these sharpen within a few hours. Computational analysis of spatial stochastic models shows, surprisingly, that noise in hoxb1a/krox20 expression actually promotes sharpening of boundaries between adjacent segments. In particular, fluctuations in RA initially induce a rough boundary that requires noise in hoxb1a/krox20 expression to sharpen. This finding suggests a novel noise attenuation mechanism that relies on intracellular noise to induce switching and coordinate cellular decisions during developmental patterning.

Show MeSH
Related in: MedlinePlus