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Genome-wide measurement of spatial expression in mutants of Drosophila Melanogaster

ABSTRACT: We sequenced mRNA from transverse slices of embryos from a variety of D. melanogaster mutants (bicoid over-expression, bicoid knockdown, hunchback knocdown, and zelda mutant) at the blastoderm stage to determine genome-wide patterns of gene expression. mRNA from transverse sections of single D. melanogaster embryos mutant for patterning TFs was sequenced.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Peter Combs

PROVIDER: E-GEOD-71137 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide measurement of spatial expression in mutants of Drosophila Melanogaster

Project description:We sequenced mRNA from transverse slices of embryos from a variety of D. melanogaster mutants (bicoid over-expression, bicoid knockdown, hunchback knocdown, and zelda mutant) at the blastoderm stage to determine genome-wide patterns of gene expression.

2015-07-22 | GSE71137 | GEO

Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression

Project description:We sequenced mRNA from transverse slices of 3 wild-type and 3 high bcd copy-number embryos at the blastoderm stage to determine genome-wide patterns of gene expression. mRNA from transverse sections of single D. melanogaster embryos was sequenced

2013-01-16 | E-GEOD-43506 | biostudies-arrayexpress

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1)

Project description:We sequenced mRNA from blastoderm embryos of Drosophila melanogaster, Drosophila yakuba, Drosophila pseudoobscura and Drosophila virilis. Two samples contain pooled mRNA from several species, and the remaining 24 samples contain mRNA from a single species. Methods: Retinal mRNA profiles of Blastoderm embryos Comparison of the evolution of gene expression and regulatory TF binding in early Drosophila embryos.

2013-09-12 | E-GEOD-50766 | biostudies-arrayexpress

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Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1)

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Bicoid binding along anteroposterior axis of Drosophila Melanogaster embryos

Project description:Bicoid binding along anteroposterior axis of Drosophila Melanogaster embryos

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Concentration dependent binding states of the Bicoid Homeodomain Protein

Project description:We have measured by ChIP-seq the distribution of Bicoid protein in Wild Type embryos, and in embryos in which the sole source of Bicoid is expressed at single concentrations representative of individual positions along the morphogen gradient. In addition, we have measured chromatin accessibility and nucleosome positioning by ATAC seq in Wild Type, bicoid mutant, uniform bicoid, and zelda mutant embryos.

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Distinct Global Shifts in Genomic Binding Profiles of Limb Malformation Associated HOXD13 Mutations

Project description:We applied ChIP-seq to explore the effect of missense mutations in TFs on their genome wide binding profile. Using a retroviral expression system in chicken mesenchymal stem cells, we elucidated the mechanism underlying a novel missense mutation in HOXD13 (Q317K) associated with a complex hand and foot malformation phenotype. The glutamine at position 317 (position 50 of the homeodomain) is conserved in most homeodomains, a notable exception being bicoid-type homeodomains that have K at this position. Our results show that the mutation results in a shift in the binding profile of the mutant towards a bicoid/PITX1 motif. Gene expression analysis and functional assays using in vivo overexpression studies confirm that the mutation results in a partial conversion of HOXD13 into a TF with bicoid/PITX1 properties. A similar shift was not observed with the mutation Q317R, which is associated with brachysyndactyly, suggesting that the bicoid/PITX1-shift observed for Q317K might be related to the severe clinical phenotype.

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Early developmental transcriptome of Musca domestica.

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