Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

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.Author Summary: Inter-species differences in gene expression during development are a major source of phenotypic diversity, yet the molecular origins of such differences are poorly understood. In this study we use a combination of biochemical and genomic methods to explore how an important component of the machinery of gene regulation varies between species. We mapped the genomic sites bound by four specific proteins regulating gene expression along the head to tail axis of young embryos of four diverse species of fruit flies. We were surprised at the extent of variation we observed, especially as we found far less variation in gene expression between these same species' embryos. We conclude, based on various analyses of our binding divergence data, that most of the time these regulators bind to DNA they have no effect on gene expression, and therefore natural selection does not act to preserve these interactions between species.