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Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo
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10.1063/1.4808157
/content/aip/journal/chaos/23/2/10.1063/1.4808157
http://aip.metastore.ingenta.com/content/aip/journal/chaos/23/2/10.1063/1.4808157

Figures

Image of FIG. 1.
FIG. 1.

Two-domain expression patterns of and . (a) Locally activated Torso signaling induces and through relief of Cic-mediated repression. (b) and (c) Spatial patterns of (b) and (c) mRNAs in wild-type embryos. (d) and (e) Expression patterns of (d) and (e) in embryos that lack Bcd (6). (f) and (g) Expression patterns of (f) and (g) in embryos that lack Trunk (1), which is a ligand for Torso.

Image of FIG. 2.
FIG. 2.

Dose-dependent effects of Bcd and Cic on expression. (a) The Bcd activation gradient works against the inverse transcriptional repression gradient of Cic in activating many of its targets. (b) Quantification of the boundaries of anterior expression. (c) and (d) Quantified boundaries of the anterior in embryos with different levels of Bcd (c) and Cic (d). Averaged boundaries are shown with error bars indicating standard error of the mean (s.e.m). The numbers of embryos used in the analysis are N = 23 (6), N = 95 (6), N = 49 (), N = 42 (4), N = 65 (1), N = 56 (1), and N = 32 (4). (e) These results are consistent with incoherent feedforward mechanism, where Bcd and Torso activate both and an anterior repressor of

Image of FIG. 3.
FIG. 3.

Anterior repression of depends on Hkb and Dl. (a) Quantification of the boundary of anterior (b) and (c) Quantified boundaries of the anterior in embryos with different levels of Bcd (b) and Cic (c). (d) Averaged boundaries are shown with error bars indicating s.e.m. The numbers of embryos used in the analysis are N = 101 (6), N = 64 (6), N = 52 (), N = 67 (4), N = 39 (1), N = 103 (1), and N = 41 (4). (e) Dorsal view of an embryo stained with Hkb protein (green) and transcript (red). The pattern of Hkb closely matches with the repression domain of (e) Pattern of in Hkb mutant embryo. (f) Lateral view of an embryo stained for Dl protein and mRNA. (g) mRNA pattern in an embryo that lacks Dl signaling and Hkb protein.

Image of FIG. 4.
FIG. 4.

Kni is an additional repressor of anterior (a)–(d) Expression pattern of in wild-type embryos (a), embryos that lack Bcd (b), Dl signaling (c), or Cic (d). (e) Expression pattern of in embryos with one copy of (f) A model for the regulation of anterior-ventral stripe pattern of by Bcd, Dl, and Torso signaling. (g) Lateral view of an embryo co-stained for (green) and (red) mRNAs. (h) expression pattern in an embryo that lacks Kni and Hkb.

Image of FIG. 5.
FIG. 5.

Cic-dependent control of posterior domains of and . (a)–(c) Simultaneous detection of Cic protein (a) and (b) and (c) mRNAs in a single embryo using FISH. (d) Quantification of nuclear Cic in the posterior half of the embryo. The boundaries of and are indicated by red and green arrows, respectively. (e) and (f) Normalized spatial gradient of (e) and (f) mRNAs. (g) Bar graph of average intensities of Cic at the boundaries of (red) and (green). Each bar represents an average of 52 data with error bars indicating s.e.m. (h) Changes in the boundaries of and in embryos with different copies of gene (see Sec. II for details on the quantification). Posterior pole is denoted as 0% embryo length, and error bars are s.e.m. The number of embryos in each background are N = 65 (1), N = 56 (1), N = 49 (), and N = 32 (4) for and N = 39 (1), N = 103 (1), N = 52 (), and N = 41 (4) for

Image of FIG. 6.
FIG. 6.

Effect of perturbing the Cic gradient. (a) Simultaneous staining of Cic in wild-type and 1 embryos reveal very low level of Cic this mutant. (b) Quantified nuclear Cic in the posterior half of the wild-type embryo (red, N = 21) and embryos from flies (black, N = 14). Error-bars are s.e.m. (c) Assuming that Cic is downregulated completely at the posterior pole of 1 embryos, we obtained normalized Cic gradient in wild-type embryos (red, N = 21), which show that Cic is degraded to approximately 20% of the maximum at the posterior pole. Similar approach was used to determine normalized gradient from heterozygous embryos (green, N = 33) and embryos with two extra copies of (blue, N = 25). Error bars are s.e.m. (d) Nuclear gradient of Cic in the posterior half of wild-type (red, N = 30) and embryos with two extra copies of (blue, N = 32). Filled yellow and green arrows denote the boundaries of and , respectively, in wild-type embryos while empty arrows represent the two gene expression boundaries in the mutant embryos.

Image of FIG. 7.
FIG. 7.

A model for the regulation of and . (a) A regulatory network of anterior and by the three maternal signals. (b) A regulatory network of posterior and by locally activated Torso. (c)–(e) Spatial distributions of Bcd (c), Cic (d), and nuclear Dl (e) gradients that provide spatially distributed inputs to the models shown in (a) and (b). (f) Bcd, Cic, and nuclear Dl gradients superimposed on the same embryo.

Image of FIG. 8.
FIG. 8.

Sequence-specific analysis of enhancers. (a) Expression patterns of enhancers in vivo; fragments are named in accordance to the original publications. Fragments K2 and P3 reproduce the posterior pattern, fragment AD reproduces the anterior pattern and the fragment P2 reproduces both, the anterior and the posterior patterns. (b) binding patterns of five transcriptional regulators in the locus. (c) Results of sequence analysis: statistical significance of binding site density in the locus. Peaks (see the encircled numbers) correspond to significant clusters of binding sites for transcriptional regulators Bcd, Dl, Zld and Cic. (d) Alignment of DNA fragments corresponding to the identified clusters from seven species of , binding site matches to regulatory motifs are boxed. Shaded areas mark regions highly conserved in evolution. (E) Binding motif logos for binding motifs of the transcriptional regulators used in the sequence analysis.

Image of FIG. 9.
FIG. 9.

Modeling of and expression patterns in the wild-type and mutant embryos. The model successfully predicts pattern of and in multiple mutants corresponding to changes in the levels and spatial distribution of inductive signals and their downstream targets. The spatial distribution of inductive signals is shown as a superposition of theBcd, Cic, and nuclear Dl gradients. Predicted and patterns are presented in the 2nd and 3rd columns, and the corresponding experimental patterns are shown in the last two columns.

Tables

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Table I.

Values of the model constants.

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/content/aip/journal/chaos/23/2/10.1063/1.4808157
2013-06-04
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the <em>Drosophila</em> embryo
http://aip.metastore.ingenta.com/content/aip/journal/chaos/23/2/10.1063/1.4808157
10.1063/1.4808157
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