Allele-specific expression elucidates cis-regulatory logic

Concurrently, efforts have been done to more precisely delineate temporal transcriptional differences in the maternal-zygotic transition in Drosophila [8] and across tissues [9] and developmental stages in C. elegans [10]. Because these organisms have two copies of the genome, CRMs can differ between alleles of each copy. [...]quantification of ASE can augment these studies by allowing us to ask which sequences on the same allele (in cis) are important in orchestrating gene expression during development. ASE, allele-specific expression; CRM, cis-regulatory module; SNP, single nucleotide polymorphism. https://doi.org/10.1371/journal.pgen.1007690.g001 A single SNP drives species-specific spatial hunchback expression Using a modeling approach [14], the authors narrowed down the transcription factor binding motifs in the hunchback CRMs with the largest effects on hunchback expression. Implications for the evolution of development Because ASE is the read-out of differential cis- and trans-regulation, the molecular mechanisms that drive ASE can only be elucidated if comprehensive information regarding the presence of cis-regulatory regions, transcription factor binding motifs, and epigenetic modifications is known across tissues, cell types, timing in development, and disease states.