The function of a transcriptional circuit is compared in three closely related species of Drosophila. Using quantitative imaging of gene expression, targeted transgenic reporter ﬂy lines, and a computational framework, the sources of their differing expression outputs are identified

Bragdon, Meghan D.

Depace, Angela

Eckenrode, Kelly B

Lydiard-Martin, Tara

Pearl-Waserman, Sivanne

Wunderlich, Zeba Batool

Molecular Systems Biology

PubMed

Gene expression patterns can diverge between species due to changes in a gene's regulatory DNA or changes in the proteins, e.g., transcription factors (TFs), that regulate the gene. We developed a modeling framework to uncover the sources of expression differences in blastoderm embryos of three Drosophila species, focusing on the regulatory circuit controlling expression of the hunchback (hb) posterior stripe. Using this framework and cellular-resolution expression measurements of hb and its regulating TFs, we found that changes in the expression patterns of hb's TFs account for much of the expression divergence. We confirmed our predictions using transgenic D. melanogaster lines, which demonstrate that this set of orthologous cis-regulatory elements (CREs) direct similar, but not identical, expression patterns. We related expression pattern differences to sequence changes in the CRE using a calculation of the CRE's TF binding site content. By applying this calculation in both the transgenic and endogenous contexts, we found that changes in binding site content affect sensitivity to regulating TFs and that compensatory evolution may occur in circuit components other than the CRE

Wunderlich, Zeba

Bragdon, Meghan D

DePace, Angela H

eScholarship - University of California

English

Dissecting sources of quantitative gene expression pattern divergence between Drosophila species

Zeba Wunderlich

Meghan D Bragdon

Kelly B Eckenrode

Tara Lydiard‐Martin

Sivanne Pearl‐Waserman

Angela H DePace

Crossref

Dissecting sources of quantitative gene expression pattern divergence between<i>Drosophila</i>species

The function of a transcriptional circuit is compared in three closely related species of Drosophila. Using quantitative imaging of gene expression, targeted transgenic reporter ﬂy lines, and a computational framework, the sources of their differing expression outputs are identified.Version of Recor

Bragdon, Meghan

Harvard University - DASH

Dissecting Sources of Quantitative Gene Expression Pattern Divergence Between Drosophila Species

Abundant genetic variation in transcript level during early Drosophila development.

Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biol 7: e1000049

Evidence for stabilizing selection in a eukaryotic enhancer element.

Modeling Drosophila gene expression divergence Z Wunderlich et al &

Regulatoryandcodingregionsofthesegmentationgenehunchback are functionally conserved between Drosophila virilis and Drosophila melanogaster.

Shadow enhancers: frequently asked questions about distributed cis-regulatory information and enhancer redundancy.

Tracking rates of transcription and splicing in vivo.

http://dash.harvard.edu/bitstream/handle/1/10533609/3435502.pdf?sequence=1

Dissecting Sources of Quantitative Gene Expression Pattern Divergence Between Drosophila Species

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eScholarship - University of California

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Harvard University - DASH