ArticleMolecular systems biology2012
Dissecting sources of quantitative gene expression pattern divergence between Drosophila species.
Article in Molecular systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 29 citations in OpenAlex.
- Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo.Genetics · 2021Article
- An Atlas of Transcription Factors Expressed in Male Pupal Terminalia ofG3 (Bethesda, Md.) · 2019Article
- Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of FiveG3 (Bethesda, Md.) · 2019Article
- Novel approach to quantitative spatial gene expression uncovers genetic stochasticity in the developing Drosophila eye.Evolution & development · 2019Article
- Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.Cell reports · 2017Article
- Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle.Cell systems · 2017Article
- Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks.Current biology : CB · 2016Article
- Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers.Cell reports · 2015Article
- A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate.Development (Cambridge, England) · 2015Article
- Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Article
- High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita.Scientific data · 2015Article
- Evidence for deep regulatory similarities in early developmental programs across highly diverged insects.Genome biology and evolution · 2014Article
- Comparing mRNA levels using in situ hybridization of a target gene and co-stain.Methods (San Diego, Calif.) · 2014Article
- Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes.PLoS genetics · 2014Article
- Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species.BMC genomics · 2013Article
- Article
- TALE-mediated modulation of transcriptional enhancers in vivo.Nature methods · 2013Article
- Article
- Boolean modeling of gene regulatory networks: Driesch redux.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.