Abstract
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.
Highlights
In the early Drosophila melanogaster embryo, the spatially restricted activity of several maternally deposited factors establishes the main body axes of the animal by triggering cascades of patterned gene expression
We previously introduced a method for the genome-wide measurement of spatial patterns of expression in the Drosophila embryo based on cryosectioning individual embryos along the anteroposterior axes and sequencing the mRNA from each slice
Broad-reaching examinations of the effects of mutating these genes on their targets has not previously been possible, mutating bicoid results in the anterior adopting an anteriorlike fate[15,16], mutating zelda leads to shifts of expression patterns in time and space[12], and Hunchback binding has been implicated in multiple eve stripes, among many other expression patterns.[4,17]; all of these mutations are lethal
Summary
In the early Drosophila melanogaster embryo, the spatially restricted activity of several maternally deposited factors establishes the main body axes of the animal by triggering cascades of patterned gene expression. We previously introduced a method for the genome-wide measurement of spatial patterns of expression in the Drosophila embryo based on cryosectioning individual embryos along the anteroposterior axes and sequencing the mRNA from each slice. We extend this method to characterize embryos mutant for three maternal transcription factors (TFs): Bicoid, Zelda, and Hunchback. Hunchback is both maternally and zygotically expressed, and helps to specify the expression domains and levels of various gap and pair-rule genes in the thorax[4,13,14]. Given the crucial roles of each of these factors in spatial patterning, we expected that perturbing their levels would lead to widespread direct and indirect effects on patterned genes
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