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Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster

View ORCID ProfilePeter A. Combs, View ORCID ProfileMichael B. Eisen
doi: https://doi.org/10.1101/046128
Peter A. Combs
1Graduate Program in Biophysics, University of California, Berkeley, California, United States of America
2Current Address: Department of Biology, Stanford University, Stanford, California, United States of America
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Michael B. Eisen
3Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
4Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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Abstract

Genome sequencing has become commonplace, but the understanding of how those genomes ultimately specify cell fate during development is still elusive. Extrapolating insights from deep investigation of a handful of developmentally important Drosophila genes to understanding the regulation of all genes is a major challenge. The developing embryo provides a unique opportunity to study the role of gene expression in pattern specification; the precise and consistent spatial positioning of key transcription factors essentially provides separate transcriptional-readout experiments at a critical point in development.

We cryosectioned and sequenced mRNA from single Drosophila melanogaster embryos at the blastoderm stage to screen for spatially-varying regulation of transcription. Expanding on our previous screening of wild type embryos, here we present data from dosage mutants for key maternally provided regulators, including depletion of zelda and hunchback and both over-expression and depletion of bicoid. These data recapitulate all of the expected patterning changes driven by these regulators; for instance, we show spatially-confined up-regulation of expression in the bicoid over-expression condition, and down-regulation of those genes in the bicoid knock-down case, consistent with bicoid’s known function as an anterior-localized activator.

Our data highlight the role of combinatorial regulation of patterning gene expression. When comparing changes in multiple conditions, genes responsive to one mutation tend to respond to other mutations in a similar fashion. Furthermore, genes that respond differently to these mutations tend to have more complex patterns of TF binding.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 29, 2016.
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Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster
Peter A. Combs, Michael B. Eisen
bioRxiv 046128; doi: https://doi.org/10.1101/046128
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Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster
Peter A. Combs, Michael B. Eisen
bioRxiv 046128; doi: https://doi.org/10.1101/046128

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