ArticlePLoS genetics2013
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed, 103 citations in OpenAlex.
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- Evidence for compensatory evolution within pleiotropic regulatory elements.Genome research · 2024Article
- Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro.Nature communications · 2024Article
- Multifaceted effects on even-skipped transcriptional dynamics upon Krüppel dosage changes.Development (Cambridge, England) · 2024Article
- Understanding species-specific and conserved RNA-protein interactionsbioRxiv : the preprint server for biology · 2024Article
- Prediction and analysis of cis-regulatory elements in Dorsal and Ventral patterning genes of Tribolium castaneum and its comparison with Drosophila melanogaster.Molecular and cellular biochemistry · 2024Article
- Evolutionary Consequences of Functional and Regulatory Divergence of HD-Zip I Transcription Factors as a Source of Diversity in Protein Interaction Networks in Plants.Journal of molecular evolution · 2023Review
- Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube.Development (Cambridge, England) · 2023Article
- Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes.NAR genomics and bioinformatics · 2022Article
- Evolution of transcription factor binding through sequence variations and turnover of binding sites.Genome research · 2022Article
- Transcriptional Regulation and Implications for ControllingJournal of developmental biology · 2022Review
- Relative specificity as an important consideration in the big data era.Frontiers in genetics · 2022Article
- Article
- The developmental hourglass model is applicable to the spinal cord based on single-cell transcriptomes and non-conserved cis-regulatory elements.Development, growth & differentiation · 2021Article
- Evolutionarily conserved hierarchical gene regulatory networks for plant salt stress response.Nature plants · 2021Article
- Heart Enhancers: Development and Disease Control at a Distance.Frontiers in genetics · 2021Review
- Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data.Molecular biology and evolution · 2020Article
- Independent evolution of transcript abundance and gene regulatory dynamics.Genome research · 2020Article
- Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster.Nucleic acids research · 2019Article
- Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of FiveG3 (Bethesda, Md.) · 2019Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
To better characterize how variation in regulatory sequences drives divergence in gene expression, we undertook a systematic study of transcription factor binding and gene expression in blastoderm embryos of four species, which sample much of the diversity in the 40 million-year old genus Drosophila: D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. We compared gene expression, measured by mRNA-seq, to the genome-wide binding, measured by ChIP-seq, of four transcription factors involved in early anterior-posterior patterning. We found that mRNA levels are much better conserved than individual transcription factor binding events, and that changes in a gene's expression were poorly explained by changes in adjacent transcription factor binding. However, highly bound sites, sites in regions bound by multiple factors and sites near genes are conserved more frequently than other binding, suggesting that a considerable amount of transcription factor binding is weakly or non-functional and not subject to purifying selection.
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Registered trials
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.