Ciselement length variability does not confer differential transcription factor occupancy at theD. melanogasterhistone locus

Abstract

AbstractHistone genes require precise regulation to maintain histone homeostasis and ensure nucleosome stoichiometry. Animal histone genes often have unique clustered genomic organization. However, there is variability of histone gene number and organization as well as differential regulation of the histone genes across species. TheDrosophila melanogasterhistone locus has unique organizational characteristics as it exists as a series of ∼100 highly regular, tandemly repeated arrays of the 5 replication-dependent histone genes at a single locus. YetD. melanogasterare viable with only 12 transgenic histone gene arrays. We hypothesized that the histone genes across the locus are differentially regulated. We discovered that the GA-repeat within theH3/H4promoter is the only variable sequence across the histone gene arrays. TheH3/H4promoter GA-repeat is targeted by CLAMP to promote histone gene expression. We also show two additional GA-binding transcription factors, GAGA Factor and Pipsqueak, target the GA-repeat. When we further examined CLAMP and GAF targeting, we determined that neither CLAMP nor GAF show bias for any GA-repeat lengths. Furthermore, we found that the distribution of GA-repeats targeted by both CLAMP and GAF do not change throughout early development. Together our results suggest that the transcription factors targeting theH3/H4GA-repeat do not impact differential regulation of the histone genes, but indicate that future studies should interrogate additionalciselements or factors that impact histone gene regulation.