Journal articles: 'Bicoid-Hunchback'

1

Janody, F., J. Reischl, and N. Dostatni. "Persistence of Hunchback in the terminal region of the Drosophila blastoderm embryo impairs anterior development." Development 127, no. 8 (April 15, 2000): 1573–82. http://dx.doi.org/10.1242/dev.127.8.1573.

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Anterior terminal development is controlled by several zygotic genes that are positively regulated at the anterior pole of Drosophila blastoderm embryos by the anterior (bicoid) and the terminal (torso) maternal determinants. Most Bicoid target genes, however, are first expressed at syncitial blastoderm as anterior caps, which retract from the anterior pole upon activation of Torso. To better understand the interaction between Bicoid and Torso, a derivative of the Gal4/UAS system was used to selectively express the best characterised Bicoid target gene, hunchback, at the anterior pole when its expression should be repressed by Torso. Persistence of hunchback at the pole mimics most of the torso phenotype and leads to repression at early stages of a labral (cap'n'collar) and two foregut (wingless and hedgehog) determinants that are positively controlled by bicoid and torso. These results uncovered an antagonism between hunchback and bicoid at the anterior pole, whereas the two genes are known to act in concert for most anterior segmented development. They suggest that the repression of hunchback by torso is required to prevent this antagonism and to promote anterior terminal development, depending mostly on bicoid activity.

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Wolff, C., R. Schroder, C. Schulz, D. Tautz, and M. Klingler. "Regulation of the Tribolium homologues of caudal and hunchback in Drosophila: evidence for maternal gradient systems in a short germ embryo." Development 125, no. 18 (September 15, 1998): 3645–54. http://dx.doi.org/10.1242/dev.125.18.3645.

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In short germ embryos, the germ rudiment forms at the posterior ventral side of the egg, while the anterior-dorsal region becomes the extra-embryonic serosa. It is difficult to see how an anterior gradient like that of bicoid in Drosophila could in these embryos be directly involved in patterning of the germ rudiment. Moreover, since it has not yet been possible to recover a bicoid homologue from any species outside the diptera, it has been speculated that the anterior bicoid gradient could be a late addition during insect evolution. We addressed this question by analysing the regulation of potential target genes of bicoid in the short germ embryo of Tribolium castaneum. We demonstrate that homologues of caudal and hunchback from Tribolium are regulated by Drosophila bicoid. In Drosophila, maternal caudal RNA is translationally repressed by bicoid. We find that Tribolium caudal RNA is also translationally repressed by bicoid, when it is transferred into Drosophila embryos under a maternal promoter. This strongly suggests that a functional bicoid homologue must exist in Tribolium. The second target gene, hunchback, is transcriptionally activated by bicoid in Drosophila. Transfer of the regulatory region of Tribolium hunchback into Drosophila also results in regulation by early maternal factors, including bicoid, but in a pattern that is more reminiscent of Tribolium hunchback expression, namely in two early blastoderm domains. Using enhancer mapping constructs and footprinting, we show that caudal activates the posterior of these domains via a specific promoter. Our experiments suggest that a major event in the evolutionary transition from short to long germ embryogenesis was the switch from activation of the hunchback gap domain by caudal to direct activation by bicoid. This regulatory switch can explain how this domain shifted from a posterior location in short germ embryos to its anterior position in long germ insects, and it also suggest how an anterior gradient can pattern the germ rudiment in short germ embryos, i.e. by regulating the expression of caudal.

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Ma, X., D. Yuan, K. Diepold, T. Scarborough, and J. Ma. "The Drosophila morphogenetic protein Bicoid binds DNA cooperatively." Development 122, no. 4 (April 1, 1996): 1195–206. http://dx.doi.org/10.1242/dev.122.4.1195.

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The Drosophila morphogenetic protein Bicoid, encoded by the maternal gene bicoid, is required for the development of the anterior structures in the embryo. Bicoid, a transcriptional activator containing a homeodomain, is distributed in an anterior-to-posterior gradient in the embryo. In response to this gradient, the zygotic gene hunchback is expressed uniformly in the anterior half of the embryo in a nearly all-or-none manner. In this report we demonstrate that a recombinant Bicoid protein binds cooperatively to its sites within a hunchback enhancer element. A less than 4-fold increase in Bicoid concentration is sufficient to achieve an unbound/bound transition in DNA binding. Using various biochemical and genetic methods we further demonstrate that Bicoid molecules can interact with each other. Our results are consistent with previous studies performed in the embryo, and they suggest that one mechanism to achieve a sharp on/off switch of gene expression in response to a morphogenetic gradient is cooperative DNA binding facilitated by protein-protein interaction.

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Schulz, C., and D. Tautz. "Autonomous concentration-dependent activation and repression of Kruppel by hunchback in the Drosophila embryo." Development 120, no. 10 (October 1, 1994): 3043–49. http://dx.doi.org/10.1242/dev.120.10.3043.

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The subdivision of the anterior-posterior axis in Drosophila is achieved by a cascade of spatially regulated transcription factors which form short-range gradients at the syncytial blastoderm stage. These factors are assumed to have concentration-dependent regulatory effects on their target genes. However, there is so far little direct in vivo evidence that a single factor can autonomously activate and repress a given target gene. We have analysed here the regulatory capabilities of the gap gene hunchback by creating an artificial gradient of hunchback in the early embryo. This was achieved by providing the maternally expressed mRNA of hunchback with the anterior localization signal of the bicoid RNA. The effects of this artificial hunchback gradient were then studied in different types of mutant background. We show that under these conditions hb is autonomously capable of activating the target gene Kruppel at low concentrations and repressing it at high concentrations. In addition, we show that the artificially created hunchback gradient can organize a large part of the segment pattern, although it is expressed at a different position and in a different shape than the wild-type gradient of hunchback.

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5

Gaul, U., and H. Jackle. "Analysis of maternal effect mutant combinations elucidates regulation and function of the overlap of hunchback and Kruppel gene expression in the Drosophila blastoderm embryo." Development 107, no. 3 (November 1, 1989): 651–62. http://dx.doi.org/10.1242/dev.107.3.651.

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The metameric organisation of the Drosophila embryo is generated early during development, due to the action of maternal effect and zygotic segmentation and homeotic genes. The gap genes participate in the complex process of pattern formation by providing a link between the maternal and the zygotic gene activities. Under the influence of maternal gene products they become expressed in distinct domains along the anteroposterior axis of the embryo; negative interactions between neighboring gap genes are thought to be involved in establishing the expression domains. The gap gene activities in turn are required for the correct patterning of the pair-rule genes; little is known, however, about the underlying mechanisms. We have monitored the distribution of gap and pair-rule genes in wild-type embryos and in embryos in which the anteroposterior body pattern is greatly simplified due to combinations of maternal effect mutations (staufen exuperantia, vasa exuperantia, vasa exuperantia, bicoid oskar, bicoid oskar torsolike, vasa torso exuperantia). We show that the domains of protein distribution of the gap genes hunchback and Kruppel overlap in wild-type embryos. Based on the analysis of the maternal mutant combinations, we suggest an explanation of how this overlap is generated. Furthermore, our data show that different constellations of gap gene activities provide different input for the pair-rule genes, and thus strongly suggest that the overlap of hunchback and Kruppel in wild-type is functional in the formation of the patterns of pair-rule genes.

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Sommer, R., and D. Tautz. "Segmentation gene expression in the housefly Musca domestica." Development 113, no. 2 (October 1, 1991): 419–30. http://dx.doi.org/10.1242/dev.113.2.419.

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Drosophila and Musca both belong to the group of higher dipteran flies and show morphologically a very similar early development. However, these two species are evolutionary separated by at least 100 million years. This presents the opportunity for a comparative analysis of segmentation gene expression across a large evolutionary distance in a very similar embryonic background. We have analysed in detail the early expression of the maternal gene bicoid, the gap genes hunchback, Kruppel, knirps and tailless, the pair-rule gene hairy, the segment-polarity gene engrailed and the homoeotic gene Ultrabithorax. We show that the primary expression domains of these genes are conserved, while some secondary expression aspects have diverged. Most notable is the finding of hunchback expression in 11–13 stripes shortly before gastrulation, as well as a delayed expression of terminal domains of various genes. We conclude that the early developmental gene hierarchy, as it has been defined in Drosophila, is evolutionary conserved in Musca domestica.

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7

Schröder, Reinhard. "The genes orthodenticle and hunchback substitute for bicoid in the beetle Tribolium." Nature 422, no. 6932 (April 2003): 621–25. http://dx.doi.org/10.1038/nature01536.

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8

Moudgil, Anshika, Ranbir Chander Sobti, and Tejinder Kaur. "In-silico identification and comparison of transcription factor binding sites cluster in anterior-posterior patterning genes in Drosophila melanogaster and Tribolium castaneum." PLOS ONE 18, no. 8 (August 17, 2023): e0290035. http://dx.doi.org/10.1371/journal.pone.0290035.

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The cis-regulatory data that help in transcriptional regulation is arranged into modular pieces of a few hundred base pairs called CRMs (cis-regulatory modules) and numerous binding sites for multiple transcription factors are prominent characteristics of these cis-regulatory modules. The present study was designed to localize transcription factor binding site (TFBS) clusters on twelve Anterior-posterior (A-P) genes in Tribolium castaneum and compare them to their orthologous gene enhancers in Drosophila melanogaster. Out of the twelve A-P patterning genes, six were gap genes (Kruppel, Knirps, Tailless, Hunchback, Giant, and Caudal) and six were pair rule genes (Hairy, Runt, Even-skipped, Fushi-tarazu, Paired, and Odd-skipped). The genes along with 20 kb upstream and downstream regions were scanned for TFBS clusters using the Motif Cluster Alignment Search Tool (MCAST), a bioinformatics tool that looks for set of nucleotide sequences for statistically significant clusters of non-overlapping occurrence of a given set of motifs. The motifs used in the current study were Hunchback, Caudal, Giant, Kruppel, Knirps, and Even-skipped. The results of the MCAST analysis revealed the maximum number of TFBS for Hunchback, Knirps, Caudal, and Kruppel in both D. melanogaster and T. castaneum, while Bicoid TFBS clusters were found only in D. melanogaster. The size of all the predicted TFBS clusters was less than 1kb in both insect species. These sequences revealed more transversional sites (Tv) than transitional sites (Ti) and the average Ti/Tv ratio was 0.75.

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9

Stauber, M., H. Taubert, and U. Schmidt-Ott. "Function of bicoid and hunchback homologs in the basal cyclorrhaphan fly Megaselia (Phoridae)." Proceedings of the National Academy of Sciences 97, no. 20 (September 19, 2000): 10844–49. http://dx.doi.org/10.1073/pnas.190095397.

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10

Bonneton, François, Philip J. Shaw, Claire Fazakerley, Min Shi, and Gabriel A. Dover. "Comparison of bicoid-dependent regulation of hunchback between Musca domestica and Drosophila melanogaster." Mechanisms of Development 66, no. 1-2 (August 1997): 143–56. http://dx.doi.org/10.1016/s0925-4773(97)00100-7.

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11

Reinitz, John, Eric Mjolsness, and David H. Sharp. "Model for cooperative control of positional information inDrosophila by bicoid and maternal hunchback." Journal of Experimental Zoology 271, no. 1 (January 1, 1995): 47–56. http://dx.doi.org/10.1002/jez.1402710106.

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12

Combs, Peter A., and Michael B. Eisen. "Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster." F1000Research 6 (January 12, 2017): 41. http://dx.doi.org/10.12688/f1000research.9720.1.

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Patterning in the Drosophila melanogaster embryo is affected by multiple maternal factors, but the effect of these factors on spatial gene expression has not been systematically analyzed. Here we characterize the effect of the maternal factors Zelda, Hunchback and Bicoid by cryosectioning wildtype and mutant blastoderm stage embryos and sequencing mRNA from each slice. The resulting atlas of spatial gene expression highlights the intersecting roles of these factors in regulating spatial patterns, and serves as a resource for researchers studying spatial patterning in the early embryo. We identify a large number of genes with both expected and unexpected patterning changes, and through integrated analysis of transcription factor binding data identify common themes in genes with complex dependence on these transcription factors.

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13

Simpson-Brose, Marcia, Jessica Treisman, and Claude Desplan. "Synergy between the hunchback and bicoid morphogens is required for anterior patterning in Drosophila." Cell 78, no. 5 (September 1994): 855–65. http://dx.doi.org/10.1016/s0092-8674(94)90622-x.

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14

Okabe-Oho, Yurie, Hiroki Murakami, Suguru Oho, and Masaki Sasai. "Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo." PLoS Computational Biology 5, no. 8 (August 28, 2009): e1000486. http://dx.doi.org/10.1371/journal.pcbi.1000486.

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15

Driever, Wolfgang, and Christiane Nüsslein-Volhard. "The bicoid protein is a positive regulator of hunchback transcription in the early Drosophila embryo." Nature 337, no. 6203 (January 1989): 138–43. http://dx.doi.org/10.1038/337138a0.

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16

McGregor, Alistair P., Philip J. Shaw, John M. Hancock, Daniel Bopp, Monika Hediger, Naomi S. Wratten, and Gabriel A. Dover. "Rapid restructuring of bicoid-dependent hunchback promoters within and between Dipteran species: implications for molecular coevolution." Evolution and Development 3, no. 6 (November 2001): 397–407. http://dx.doi.org/10.1046/j.1525-142x.2001.01043.x.

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17

Schulz, C., and D. Tautz. "Zygotic caudal regulation by hunchback and its role in abdominal segment formation of the Drosophila embryo." Development 121, no. 4 (April 1, 1995): 1023–28. http://dx.doi.org/10.1242/dev.121.4.1023.

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caudal (cad) is a maternally and zygotically expressed gene in Drosophila whereby the two phases of expression can functionally replace each other. The zygotic expression forms an abdominal and a posterior domain, whereby only the posterior domain has so far been studied with respect to its regulation and function. We show here that the abdominal cad domain is regulated by the hunchback (hb) gradient through repression at high concentrations and activation at low concentrations of HB protein. To study the function of the abdominal cad domain in the absence of redundant interactions, we have utilized an experimental system in which the embryo lacks the normal bicoid (bcd) and hb expression. An artificial hb gradient is then introduced into such embryos, which results in an induction of an ectopic zygotic cad domain in the more anterior region. Employing this system, we show that the cad domain functions by activating the expression of the abdominal gap genes knirps (kni) and giant (gt). We conclude that cad is the so far missing region-specific activator of abdominal segmentation genes.

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Stathopoulos, Angelike, and Michael Levine. "Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset." Development 129, no. 14 (July 15, 2002): 3411–19. http://dx.doi.org/10.1242/dev.129.14.3411.

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Differential activation of the Toll receptor leads to the formation of a broad Dorsal nuclear gradient that specifies at least three patterning thresholds of gene activity along the dorsoventral axis of precellular embryos. We investigate the activities of the Pelle kinase and Twist basic helix-loop-helix (bHLH) transcription factor in transducing Toll signaling. Pelle functions downstream of Toll to release Dorsal from the Cactus inhibitor. Twist is an immediate-early gene that is activated upon entry of Dorsal into nuclei. Transgenes misexpressing Pelle and Twist were introduced into different mutant backgrounds and the patterning activities were visualized using various target genes that respond to different thresholds of Toll-Dorsal signaling. These studies suggest that an anteroposterior gradient of Pelle kinase activity is sufficient to generate all known Toll-Dorsal patterning thresholds and that Twist can function as a gradient morphogen to establish at least two distinct dorsoventral patterning thresholds. We discuss how the Dorsal gradient system can be modified during metazoan evolution and conclude that Dorsal-Twist interactions are distinct from the interplay between Bicoid and Hunchback, which pattern the anteroposterior axis.

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Fu, Dechen, Chen Zhao, and Jun Ma. "Enhancer Sequences Influence the Role of the Amino-Terminal Domain of Bicoid in Transcription." Molecular and Cellular Biology 23, no. 13 (July 1, 2003): 4439–48. http://dx.doi.org/10.1128/mcb.23.13.4439-4448.2003.

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ABSTRACT Bicoid (Bcd) is a Drosophila melanogaster morphogenetic gradient that controls embryonic patterning by activating target gene expression in a concentration-dependent manner. In this study we describe experiments to determine how different enhancers respond to Bcd distinctively, focusing on two natural Bcd-responsive enhancer elements, hunchback (hb) and knirps (kni). Our results show that, on the hb enhancer element, the amino-terminal domain of Bcd (residues 1 to 91) plays primarily an inhibitory role, whereas on the kni enhancer element this same Bcd domain plays a positive role at low protein concentrations. We further demonstrate that while the amino-terminal domain is largely dispensable for cooperative binding to the hb enhancer element, it is preferentially required for cooperative binding to the kni enhancer element. Alteration of the arrangement of Bcd binding sites in the kni enhancer element reduces the role of the amino-terminal domain in cooperative DNA binding but increases the effectiveness of the self-inhibitory function. In addition, elimination of symmetric pairs of Bcd binding sites in the kni enhancer element reduces both DNA binding and activation by Bcd. We propose that the amino-terminal domain of Bcd is an enhancer-specific switch that contributes to the protein's ability to activate different target genes in distinct manners.

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Pelegri, F., and R. Lehmann. "A role of polycomb group genes in the regulation of gap gene expression in Drosophila." Genetics 136, no. 4 (April 1, 1994): 1341–53. http://dx.doi.org/10.1093/genetics/136.4.1341.

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Abstract Anteroposterior polarity of the Drosophila embryo is initiated by the localized activities of the maternal genes, bicoid and nanos, which establish a gradient of the hunchback (hb) morphogen. nanos determines the distribution of the maternal Hb protein by regulating its translation. To identify further components of this pathway we isolated suppressors of nanos. In the absence of nanos high levels of Hb protein repress the abdomen-specific genes knirps and giant. In suppressor-of-nanos mutants, knirps and giant are expressed in spite of high Hb levels. The suppressors are alleles of Enhancer of zeste (E(z)) a member of the Polycomb group (Pc-G) of genes. We show that E(z), and likely other Pc-G genes, are required for maintaining the expression domains of knirps and giant initiated by the maternal Hb protein gradient. We have identified a small region of the knirps promoter that mediates the regulation by E(z) and hb. Because Pc-G genes are thought to control gene expression by regulating chromatin, we propose that imprinting at the chromatin level underlies the determination of anteroposterior polarity in the early embryo.

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Kraut, R., and M. Levine. "Spatial regulation of the gap gene giant during Drosophila development." Development 111, no. 2 (February 1, 1991): 601–9. http://dx.doi.org/10.1242/dev.111.2.601.

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We describe the regulated expression of the segmentation gene giant (gt) during early embryogenesis. The gt protein is expressed in two broad gradients in precellular embryos, one in anterior regions and the other in posterior regions. Double immunolocalization studies show that the gt patterns overlap with protein gradients specified by the gap genes hunchback (hb) and knirps (kni). Analysis of all known gap mutants, as well as mutations that disrupt each of the maternal organizing centers, indicate that maternal factors are responsible for initiating gt expression, while gap genes participate in the subsequent refinement of the pattern. The maternal morphogen bicoid (bcd) initiates the anterior gt pattern, while nanos (nos) plays a role in the posterior pattern. Gene dosage studies indicate that different thresholds of the bcd gradient might trigger hb and gt expression, resulting in overlapping but noncoincident patterns of expression. We also present evidence that different concentrations of hb protein are instructive in defining the limits of kni and gt expression within the presumptive abdomen. These results suggest that gt is a bona fide gap gene, which acts with hb, Kruppel and kni to initiate striped patterns of gene expression in the early embryo.

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Arnosti, D. N., S. Barolo, M. Levine, and S. Small. "The eve stripe 2 enhancer employs multiple modes of transcriptional synergy." Development 122, no. 1 (January 1, 1996): 205–14. http://dx.doi.org/10.1242/dev.122.1.205.

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Previous studies have provided a detailed model for the regulation of even-skipped (eve) stripe 2 expression in the Drosophila embryo. The bicoid (bcd) regulatory gradient triggers the expression of hunchback (hb); these work synergistically to activate the stripe in the anterior half of the embryo, bcd also coordinates the expression of two repressors, giant (gt) and Kruppel (Kr), which define the anterior and posterior borders of the stripe, respectively. Here, we report the findings of extensive cis- and trans- complementation analyses using a series of defective stripe 2 enhancers in transgenic embryos. This study reaches two primary conclusions. First, the strip 2 enhancer is inherently ‘sensitized’ for repression by gt. We propose that gt specifies the sharp anterior stripe border by blocking two tiers of transcriptional synergy, cooperative binding to DNA and cooperative contact of bound activators with the transcription complex. Second, we find that the synergistic activity of hb and bcd is ‘promiscuous’. For example, a maternally expressed Gal4-Sp1 fusion protein can functionally replace hb in the stripe 2 enhancer. This finding challenges previous proposals for dedicated hb and bcd interactions in the segmentation process.

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23

Murakami, Hiroki, Yurie Okabe, and Masaki Sasai. "3P339 Stochastic three-dimensional simulation of Bicoid and Hunchback in the early Drosophila embryo(Development and differentiation,Poster Presentations)." Seibutsu Butsuri 47, supplement (2007): S287. http://dx.doi.org/10.2142/biophys.47.s287_4.

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24

Ling, Jia, Kristaley Yui Umezawa, Theresa Scott, and Stephen Small. "Bicoid-Dependent Activation of the Target Gene hunchback Requires a Two-Motif Sequence Code in a Specific Basal Promoter." Molecular Cell 75, no. 6 (September 2019): 1178–87. http://dx.doi.org/10.1016/j.molcel.2019.06.038.

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25

Margolis, J. S., M. L. Borowsky, E. Steingrimsson, C. W. Shim, J. A. Lengyel, and J. W. Posakony. "Posterior stripe expression of hunchback is driven from two promoters by a common enhancer element." Development 121, no. 9 (September 1, 1995): 3067–77. http://dx.doi.org/10.1242/dev.121.9.3067.

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The gap gene hunchback (hb) is required for the formation and segmentation of two regions of the Drosophila embryo, a broad anterior domain and a narrow posterior domain. Accumulation of hb transcript in the posterior of the embryo occurs in two phases, an initial cap covering the terminal 15% of the embryo followed by a stripe at the anterior edge of this region. By in situ hybridization with transcript-specific probes, we show that the cap is composed only of mRNA from the distal transcription initiation site (P1), while the later posterior stripe is composed of mRNA from both the distal and proximal (P2) transcription initiation sites. Using a series of genomic rescue constructs and promoter-lacZ fusion genes, we define a 1.4 kb fragment of the hb upstream region that is both necessary and sufficient for posterior expression. Sequences within this fragment mediate regulation by the terminal gap genes tailless (tll) and a huckebein, which direct the formation of the posterior hb stripe. We show that the tll protein binds in vitro to specific sites within the 1.4 kb posterior enhancer region, providing the first direct evidence for activation of gene expression by tll. We propose a model in which the anterior border of the posterior hb stripe is determined by tll concentration in a manner analogous to the activation of anterior hb expression by bicoid.

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Hoch, M., E. Seifert, and H. Jäckle. "Gene expression mediated by cis-acting sequences of the Krüppel gene in response to the Drosophila morphogens bicoid and hunchback." EMBO Journal 10, no. 8 (August 1991): 2267–78. http://dx.doi.org/10.1002/j.1460-2075.1991.tb07763.x.

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Douglas, Kristin R. "A Kinesthetic Model Demonstrating Molecular Interactions Involved in Anterior-Posterior Pattern Formation in Drosophila." CBE—Life Sciences Education 7, no. 1 (March 2008): 74–81. http://dx.doi.org/10.1187/cbe.07-11-0096.

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Prerequisites for the Developmental Biology course at Augustana College are introductory courses in zoology and cell biology. After introductory courses students appreciate the fact that proteins have three-dimensional structures; however, they often fail to recognize how protein interactions with other cellular components can lead to specific cellular responses. One of the first topics covered in Augustana's Developmental Biology course is anterior-posterior axis determination in Drosophila. In the past, the subject was taught with a series of graphs demonstrating mRNA and protein concentrations along the anterior-posterior axis. However, this pedagogy was too conceptual for the majority of students enrolled in the course. To aid their understanding, a kinesthetic model of the molecular interactions involving bicoid, nanos, hunchback, and caudal transcripts and proteins utilizing colored pipe cleaners and beads was created. Students model molecular interactions between proteins (beads) and transcripts (pipe cleaners) by placing the appropriate bead on the appropriate pipe cleaner. After working with the model, the concept of molecular interactions became more concrete to students, and they were able to conceptualize anterior-posterior axis determination in Drosophila more clearly. Throughout the rest of the course, students were able to understand molecular interactions without the aid of additional models.

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French, Vernon. "Gradients and insect segmentation." Development 104, Supplement (October 1, 1988): 3–16. http://dx.doi.org/10.1242/dev.104.supplement.3.

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`Morphogen' gradients have long been invoked as a means of specifying spatial patterns of developmental fate, and it has now been demonstrated that they are indeed involved in the early steps of insect segmentation. In many insects, including Drosophila, ligature and transplantation experiments have shown that the segment pattern develops through interactions between the ends of the egg. These results, plus those from irradiation and centrifugation of chironomid eggs, suggest that specific maternally synthesized RNAs are localized at the ends of the oocyte, and act as sources of opposing anterior and posterior gradients in the early egg. In Drosophila, different groups of maternal `segmentation' genes are required for depositing within the oocyte terminal, anterior and posterior spatial cues. Injection of wild-type cytoplasm into mutant eggs which lack the anterior (bicoid or posterior (oskar) cue suggests that these are normally distributed as gradients from strictly localized sources. It has now been shown directly that bicoid RNA passes into the oocyte from the nurse cells, remains localized in the anterior tip, and is later translated into protein which forms an exponential concentration gradient down the early egg. Genes required for posterior spatial information have not yet been cloned, so a posterior gradient (most likely to consist of nanos product) has yet to be directly demonstrated. Analysis of zygotic `segmentation' genes has shown that the different segment primordia are not directly specified by small changes in the anterior or (postulated) posterior gradient. It seems likely that the maternal cues specify a few bands of expression of zygotic gap genes such as hunchback, Krüppel and knirps, and that the pattern is then elaborated through interactions between these. The anterior gradient seems to form by diffusion of bicoid protein, but the posterior signal seems to be capable of reorganization in some injection experiments. This could imply a diffusion/reaction mechanism, or could result simply from the way in which the terminal, anterior and posterior cues act via gap gene activity. Hence the segment pattern formed after injection (and after irradiation of chironomid eggs) will not always correspond to the gradient profile. Other types of insect egg develop with no nurse cells or external anterior source of RNA and, in these, there is some evidence of a posterior gradient but not of a similar signal from the anterior end. It is now clear from the analysis of segmentation in Drosophila that the determinants and gradients inferred from earlier studies do provide a positional framework within which the segment pattern is gradually elaborated. Investigation of segmentation in other eggs will be greatly assisted if the molecular techniques can be transferred from Drosophila.

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Ludwig, M. Z., N. H. Patel, and M. Kreitman. "Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change." Development 125, no. 5 (March 1, 1998): 949–58. http://dx.doi.org/10.1242/dev.125.5.949.

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Experimental investigations of eukaryotic enhancers suggest that multiple binding sites and trans-acting regulatory factors are often required for wild-type enhancer function. Genetic analysis of the stripe 2 enhancer of even-skipped (eve), an important developmental gene in Drosophila, provides support for this view. Given the importance of even-skipped expression in early Drosophila development, it might be predicted that many structural features of the stripe 2 enhancer will be evolutionarily conserved, including the DNA sequences of protein binding sites and the spacing between them. To test this hypothesis, we compared sequences of the stripe 2 enhancer between four species of Drosophila: D. melanogaster, D. yakuba, D. erecta and D. pseudoobscura. Our analysis revealed a large number of nucleotide substitutions in regulatory protein binding sites for bicoid, hunchback, Kruppel and giant, as well as a systematic change in the size of the enhancer. Some of the binding sites in D. melanogaster are either absent or modified in other species. One functionally important bicoid-binding site in D. melanogaster appears to be recently evolved. We, therefore, investigated possible functional consequences of sequence differences among these stripe 2 enhancers by P-element-mediated transformation. This analysis revealed that the eve stripe 2 enhancer from each of the four species drove reporter gene expression at the identical time and location in D. melanogaster embryos. Double staining of native eve protein and transgene mRNA in early embryos showed that the reporter gene mimicked native eve expression and, in every case, produced sharply defined stripes at the blastoderm stage that were coincident with eve stripe 2 protein. We argue that stripe 2 eve expression in Drosophila evolution can be viewed as being under constant stabilizing selection with respect to the location of the anterior and posterior borders of the stripe. We further hypothesize that the stripe 2 enhancer is functionally robust, so that its evolution may be governed by the fixation of both slightly deleterious and adaptive mutations in regulatory protein binding sites as well as in the spacing between binding sites. This view allows for a slow but continual turnover of functionally important changes in the stripe 2 enhancer.

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Okabe, Yurie, Hiroki Murakami, and Masaki Sasai. "3P338 Effects of stochastic diffusion and cooperative binding of Bicoid on expression of hunchback in Drosophila embryo(Development and differentiation,Poster Presentations)." Seibutsu Butsuri 47, supplement (2007): S287. http://dx.doi.org/10.2142/biophys.47.s287_3.

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Okabe, Yurie, Hiroki Murakami, and Masaki Sasai. "1P-127 Precise spatial patterns of Bicoid and Hunchback in the early Drosophila embryo(The 46th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 48, supplement (2008): S41. http://dx.doi.org/10.2142/biophys.48.s41_1.

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Porcher, A., A. Abu-Arish, S. Huart, B. Roelens, C. Fradin, and N. Dostatni. "The time to measure positional information: maternal Hunchback is required for the synchrony of the Bicoid transcriptional response at the onset of zygotic transcription." Development 137, no. 16 (July 27, 2010): 2795–804. http://dx.doi.org/10.1242/dev.051300.

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Andrioli, Luiz Paulo Moura, Vikram Vasisht, Ekaterina Theodosopoulou, Adam Oberstein, and Stephen Small. "Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms." Development 129, no. 21 (November 1, 2002): 4931–40. http://dx.doi.org/10.1242/dev.129.21.4931.

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The striped expression pattern of the pair-rule gene even skipped(eve) is established by five stripe-specific enhancers, each of which responds in a unique way to gradients of positional information in the earlyDrosophila embryo. The enhancer for eve stripe 2(eve 2) is directly activated by the morphogens Bicoid (Bcd) and Hunchback (Hb). As these proteins are distributed throughout the anterior half of the embryo, formation of a single stripe requires that enhancer activation is prevented in all nuclei anterior to the stripe 2 position. The gap genegiant (gt) is involved in a repression mechanism that sets the anterior stripe border, but genetic removal of gt (or deletion of Gt-binding sites) causes stripe expansion only in the anterior subregion that lies adjacent to the stripe border. We identify a well-conserved sequence repeat, (GTTT)4, which is required for repression in a more anterior subregion. This site is bound specifically by Sloppy-paired 1 (Slp1),which is expressed in a gap gene-like anterior domain. Ectopic Slp1 activity is sufficient for repression of stripe 2 of the endogenous eve gene,but is not required, suggesting that it is redundant with other anterior factors. Further genetic analysis suggests that the(GTTT)4-mediated mechanism is independent of the Gt-mediated mechanism that sets the anterior stripe border, and suggests that a third mechanism, downregulation of Bcd activity by Torso, prevents activation near the anterior tip. Thus, three distinct mechanisms are required for anterior repression of a single eve enhancer, each in a specific position. Ectopic Slp1 also represses eve stripes 1 and 3 to varying degrees,and the eve 1 and eve 3+7 enhancers each contain GTTT repeats similar to the site in the eve 2 enhancer. These results suggest a common mechanism for preventing anterior activation of three different eve enhancers.

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Fernandes, Gonçalo, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez Romero, Cécile Fradin, Mathieu Coppey, Aleksandra M. Walczak, and Nathalie Dostatni. "Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription." eLife 11 (April 1, 2022). http://dx.doi.org/10.7554/elife.74509.

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For over 40 years, the Bicoid-hunchback (Bcd-hb) system in the fruit fly embryo has been used as a model to study how positional information in morphogen concentration gradients is robustly translated into step-like responses. A body of quantitative comparisons between theory and experiment have since questioned the initial paradigm that the sharp hb transcription pattern emerges solely from diffusive biochemical interactions between the Bicoid transcription factor and the gene promoter region. Several alternative mechanisms have been proposed, such as additional sources of positional information, positive feedback from Hb proteins or out-of-equilibrium transcription activation. By using the MS2-MCP RNA-tagging system and analysing in real time, the transcription dynamics of synthetic reporters for Bicoid and/or its two partners Zelda and Hunchback, we show that all the early hb expression pattern features and temporal dynamics are compatible with an equilibrium model with a short decay length Bicoid activity gradient as a sole source of positional information. Meanwhile, Bicoid’s partners speed-up the process by different means: Zelda lowers the Bicoid concentration threshold required for transcriptional activation while Hunchback reduces burstiness and increases the polymerase firing rate.

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Eck, Elizabeth, Jonathan Liu, Maryam Kazemzadeh-Atoufi, Sydney Ghoreishi, Shelby A. Blythe, and Hernan G. Garcia. "Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility." eLife 9 (October 19, 2020). http://dx.doi.org/10.7554/elife.56429.

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Thermodynamic models of gene regulation can predict transcriptional regulation in bacteria, but in eukaryotes, chromatin accessibility and energy expenditure may call for a different framework. Here, we systematically tested the predictive power of models of DNA accessibility based on the Monod-Wyman-Changeux (MWC) model of allostery, which posits that chromatin fluctuates between accessible and inaccessible states. We dissected the regulatory dynamics of hunchback by the activator Bicoid and the pioneer-like transcription factor Zelda in living Drosophila embryos and showed that no thermodynamic or non-equilibrium MWC model can recapitulate hunchback transcription. Therefore, we explored a model where DNA accessibility is not the result of thermal fluctuations but is catalyzed by Bicoid and Zelda, possibly through histone acetylation, and found that this model can predict hunchback dynamics. Thus, our theory-experiment dialogue uncovered potential molecular mechanisms of transcriptional regulatory dynamics, a key step toward reaching a predictive understanding of developmental decision-making.

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Bothma, Jacques P., Hernan G. Garcia, Samuel Ng, Michael W. Perry, Thomas Gregor, and Michael Levine. "Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo." eLife 4 (August 12, 2015). http://dx.doi.org/10.7554/elife.07956.

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Metazoan genes are embedded in a rich milieu of regulatory information that often includes multiple enhancers possessing overlapping activities. In this study, we employ quantitative live imaging methods to assess the function of pairs of primary and shadow enhancers in the regulation of key patterning genes-knirps, hunchback, and snail-in developing Drosophila embryos. The knirps enhancers exhibit additive, sometimes even super-additive activities, consistent with classical gene fusion studies. In contrast, the hunchback enhancers function sub-additively in anterior regions containing saturating levels of the Bicoid activator, but function additively in regions where there are diminishing levels of the Bicoid gradient. Strikingly sub-additive behavior is also observed for snail, whereby removal of the proximal enhancer causes a significant increase in gene expression. Quantitative modeling of enhancer–promoter interactions suggests that weakly active enhancers function additively while strong enhancers behave sub-additively due to competition with the target promoter.

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Desponds, Jonathan, Massimo Vergassola, and Aleksandra M. Walczak. "A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute." eLife 9 (July 29, 2020). http://dx.doi.org/10.7554/elife.49758.

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Cell fate decisions in the fly embryo are rapid: hunchback genes decide in minutes whether nuclei follow the anterior/posterior developmental blueprint by reading out positional information in the Bicoid morphogen. This developmental system is a prototype of regulatory decision processes that combine speed and accuracy. Traditional arguments based on fixed-time sampling of Bicoid concentration indicate that an accurate readout is impossible within the experimental times. This raises the general issue of how speed-accuracy tradeoffs are achieved. Here, we compare fixed-time to on-the-fly decisions, based on comparing the likelihoods of anterior/posterior locations. We found that these more efficient schemes complete reliable cell fate decisions within the short embryological timescales. We discuss the influence of promoter architectures on decision times and error rates, present concrete examples that rapidly readout the morphogen, and predictions for new experiments. Lastly, we suggest a simple mechanism for RNA production and degradation that approximates the log-likelihood function.

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Lee, Kristen M., Amanda M. Linskens, and Chris Q. Doe. "Hunchback activates Bicoid in Pair1 neurons to regulate synapse number and locomotor circuit function." Current Biology, May 2022. http://dx.doi.org/10.1016/j.cub.2022.04.025.

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Kong, Ka Kit, Chunxiong Luo, and Feng Liu. "A phase diagram structure determines the optimal sensitivity-precision trade-off in signaling systems." Communications Physics 7, no. 1 (March 4, 2024). http://dx.doi.org/10.1038/s42005-024-01567-z.

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AbstractSignal transduction is crucial for many biological functions. However, it is still unclear how signaling systems function accurately under noisy situations. More specifically, such systems operate in a regime of low response noise, while maintaining high sensitivity to signals. To gain further insight on this regime, here we derive a fundamental trade-off between response sensitivity and precision in biological signaling processes under the static noise condition. We find that the optimal trade-off in signaling networks can be better characterized by a phase diagram structure rather than topological structures. We confirm that the patterning network of early Drosophila embryos agrees with our derived relationship, and apply the optimal phase diagram structure to quantitatively predict the patterning position shifts of the downstream genes, including hunchback, Krüppel, giant, knirps and even-skipped, upon the dosage perturbation of the morphogen Bicoid.

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Wang, Jingyao, Shihe Zhang, Hongfang Lu, and Heng Xu. "Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction." Nature Communications 13, no. 1 (May 17, 2022). http://dx.doi.org/10.1038/s41467-022-30315-6.

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AbstractMany eukaryotic genes contain alternative promoters with distinct expression patterns. How these promoters are differentially regulated remains elusive. Here, we apply single-molecule imaging to quantify the transcriptional regulation of two alternative promoters (P1 and P2) of the Bicoid (Bcd) target gene hunchback in syncytial blastoderm Drosophila embryos. Contrary to the previous notion that Bcd only activates P2, we find that Bcd activates both promoters via the same two enhancers. P1 activation is less frequent and requires binding of more Bcd molecules than P2 activation. Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. Bcd binding at either enhancer primarily activates P2, while P1 activation relies more on Bcd binding at both enhancers. These results provide a quantitative framework for understanding the kinetic mechanisms of complex eukaryotic gene regulation.

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Park, Jeehae, Javier Estrada, Gemma Johnson, Ben J. Vincent, Chiara Ricci-Tam, Meghan DJ Bragdon, Yekaterina Shulgina, et al. "Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity." eLife 8 (June 21, 2019). http://dx.doi.org/10.7554/elife.41266.

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Developmental enhancers integrate graded concentrations of transcription factors (TFs) to create sharp gene expression boundaries. Here we examine the hunchback P2 (HbP2) enhancer which drives a sharp expression pattern in the Drosophila blastoderm embryo in response to the transcriptional activator Bicoid (Bcd). We systematically interrogate cis and trans factors that influence the shape and position of expression driven by HbP2, and find that the prevailing model, based on pairwise cooperative binding of Bcd to HbP2 is not adequate. We demonstrate that other proteins, such as pioneer factors, Mediator and histone modifiers influence the shape and position of the HbP2 expression pattern. Comparing our results to theory reveals how higher-order cooperativity and energy expenditure impact boundary location and sharpness. Our results emphasize that the bacterial view of transcription regulation, where pairwise interactions between regulatory proteins dominate, must be reexamined in animals, where multiple molecular mechanisms collaborate to shape the gene regulatory function.

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Journal articles on the topic 'Bicoid-Hunchback'

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