Polymorphisms in Chromatin Accessibility State During D.melanogaster Embryogenesis

Changes in gene expression level underlie many important phenotypes and one of the early steps in regulating expression is the binding of transcription factors to cis-regulatory modules (CRMs). Previous work has shown that there is extensive quantitative variation in the binding of the transcription factors that control anterior-posterior patterning in the early embryo between two closely related species: D. melanogaster and D. yakuba. Gain and loss of binding sites for these factors play a significant role in their binding divergence.  It was also observed that binding divergence is effected by a coordinated local process that is likely to be connected to the accessibilty of the CRM to the transcription factors and regulated by the packing of the DNA with nucleosomes into chromatin.  In order to examine changes in chromatin states and the effect of sequence changes on these states, we have now examined the within population sequence variation in D. melanogaster and measured the accessibility of the CRMs to transcription factors in the early embryo.  By cutting accessible DNA with DNAse-I and measuring the genome wide DNAse-hypersensitivity we show that DNA accessibility variation correlates with heritable variation in transcription factor binding. These data have been measured separately and pooled with a high correlation between methods, and also compared to previous measurements of transcription factors. We are piloting the use of pooled samples from many strains as an efficient means of identifying regions harboring polymorphisms that affect chromatin accessibilty state, and therefore transcription factor binding to CRMs.