Registration of the expression patterns of Drosophila
  segmentation genes by two independent methods

Myasnikova, Ekaterina; Samsonova, A. A.; Kozlov, Konstantin; Samsonova, Maria; Reinitz, John

doi:10.1093/bioinformatics/17.1.3

Cited by 109 publications

(125 citation statements)

References 17 publications

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“…Each selected embryo was assigned to one of five age classes as described in SI Fig. 7 (substages 4-8 on the Fly-Ex web Site, http://flyex.ams.sunysb.edu/flyex) (38).…”

Section: Methodsmentioning

confidence: 99%

Canalization of segmentation and its evolution in Drosophila

Lott

Kreitman

Pálsson

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

161

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Segmentation in Drosophila embryogenesis occurs through a hierarchical cascade of regulatory gene expression driven by the establishment of a diffusion-mediated morphogen gradient. Here, we investigate the response of this pattern formation process to genetic variation and evolution in egg size. Specifically, we ask whether spatial localization of gap genes Kruppel (Kr) and giant (gt) and the pair-rule gene even-skipped (eve) during cellularization is robust to genetic variation in embryo length in three Drosophila melanogaster isolines and two closely related species. We identified two wild-derived strains of D. melanogaster whose eggs differ by Ϸ25% in length when reared under identical conditions. These two lines, a D. melanogaster laboratory stock (w1118), and offspring from crosses between the lines all exhibit precise scaling in the placement of gap and pair-rule gene expression along the anterior-posterior axis in relation to embryo length. Genetic analysis indicates that this scaling is maternally controlled. Maternal regulation of scaling must be required for consistent localization of segmentation gene expression because embryo size, a genetically variable and adaptive trait, is maternally inherited. We also investigated spatial scaling between these D. melanogaster lines and single lines of Drosophila sechellia and Drosophila simulans, the latter two differing by Ϸ25% in egg length. In contrast to the robust scaling we observed within species, localization of gene expression relative to embryo length differs significantly between the three species. Thus, the developmental mechanism that assures robust scaling within a species does not prevent rapid evolution between species.buffering ͉ development ͉ embryo size ͉ genetic variation ͉ scaling

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“…Each selected embryo was assigned to one of five age classes as described in SI Fig. 7 (substages 4-8 on the Fly-Ex web Site, http://flyex.ams.sunysb.edu/flyex) (38).…”

Section: Methodsmentioning

confidence: 99%

Canalization of segmentation and its evolution in Drosophila

Lott

Kreitman

Pálsson

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

161

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“…First, as explained at the outset, we would like to measure the information carried by a snapshot of the expression levels, so we need to make measurements on embryos at a well-defined time, and we use the length of the cellularization membrane as a precisely calibrated proxy for time (29)(30)(31)(32). We choose this time to be the window from 38 to 48 min after the start of nuclear cycle 14, because we have seen that gap gene expression levels are at a plateau in this window.…”

Section: Information Carried By Single Gap Genesmentioning

confidence: 99%

Positional information, in bits

Dubuis

Tkačik

Wieschaus

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

174

195

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Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for "positional information." We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as would be expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ∼ 1% along the anterior/posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.gene regulatory networks | embryonic development | optimization B uilding a complex, differentiated body requires that individual cells in the embryo make decisions, and ultimately adopt fates, that are appropriate to their position. There are wildly diverging models for how cells acquire this "positional information" (1), but there is general consensus that they encode positional information in the expression levels of various key genes. A classic example is provided by anterior/posterior patterning in the fruit fly, Drosophila melanogaster, where a small set of gap genes and then a larger set of pair rule and segment polarity genes are involved in the specification of the body plan (2). These genes have expression levels that vary systematically along the body axis, forming a blueprint for the segmented body of the developed larva that we can "read" within hours after the start of development (3).Although there is consensus that particular genes carry positional information, less is known quantitatively about how much information is being represented by the expression levels in individual cells. Do the broad, smooth expression profiles of the gap genes, for example, provide enough information to specify the exact pattern of development, cell by cell, along the anterior/ posterior axis? How much information does the whole embryo use in making this pattern? Answering these questions is important, in part, because we know that crucial molecules involved in the regulation of gene expression are present at low concentrations and even low absolute copy numbers, so that expression is noisy (4-10), and this noise must limit the transmission of information (11)(12)(13)(14). Is it possible, as suggested theoretically (15)(16)(17)(18), that the information transmitted through these regulatory networks is close to the physical limits set by the irreducible randomness of counting individual molecular events? To answer this and other questions, we need to measure position...

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“…Stripes 3, 4, 5, and 6 resolve next, more or less simultaneously 18 . Once resolved (by late cycle 14), the stripes are positioned at ,31, 40, 48, 55, 62, 69, and 78% EL 19 . The pattern of Even-skipped expression was monitored at the T-step of 20 8C/27 8C (Fig.…”

mentioning

confidence: 99%