Allele-specific expression elucidates cis-regulatory logic
Fig 1
Schematic of Combs and Fraser's model for ASE of hunchback.
In the F1 hybrid embryo (from a D. melanogaster × D. simulans cross), there is a maternal gradient of Bicoid protein, with greater concentration toward the anterior. Bicoid acts as a trans-activator of the zygotic gene hunchback, which has CRMs upstream of the transcription start-site (arrow). The canonical CRM has a cluster of binding sites for Bicoid, indicated by green triangles. The melanogaster and simulans alleles of hunchback differ in that the simulans form has an additional (sixth) Bicoid binding site in its canonical CRM, and it has two weak binding sites for the transcription factor Huckebein, which could act as a repressor. Given these differences in their CRMs, the two species’ hunchback alleles “see” the trans-acting milieu differently. In F1 hybrid embryos, there is greater expression of the melanogaster allele at the anterior end (blue [melanogaster] versus red [simulans] transcripts; detected by identifying SNPs in the RNA sequencing reads). Further posterior in the embryo, Bicoid concentration is lower, and the two alleles of hunchback are transcribed at equal levels. ASE, allele-specific expression; CRM, cis-regulatory module; SNP, single nucleotide polymorphism.