Keywords: a. core promoters and general transcription factors; e. enhancers
Despite the crowded nuclear environment, transcription factors locate and bind cis elements across the genome while performing context-specific functions. To explore this phenomenon, we broadly aim to understand how transcription factors integrate cis sequence and genomic context to function uniquely at different loci, which is critical for development and disease. One example of a context-specific transcription factor is Chromatin-Linked Adapter for MSL Proteins (CLAMP), which targets GA-rich cis elements while performing several distinct functions throughout the genome. CLAMP primes the male X-chromosome for dosage compensation, regulates the accessibility of promoters genome-wide, and promotes formation of the conserved histone locus body (HLB), which regulates expression of the replication-dependent histone genes. Although CLAMP targets similar cis elements in all three contexts, it recruits very different locus-specific transcription factors. Here we investigate how the function of CLAMP at the histone locus is impacted by the origin of its cis binding elements. CLAMP binds a long GA-repeat element in the bidirectional promoter of histone genes 3 and 4 (H3H4p). We engineered flies to carry a transgenic histone locus in which we replaced the natural GA-repeating cis element in the H3H4p with CLAMP-recruiting GA-rich elements from the X chromosome. We assessed how X-linked cis elements impact HLB formation by staining third instar larval polytene chromosomes with antibodies specific to a core HLB protein as well as proteins found in the other CLAMP binding contexts on the X chromosome. When we replaced the H3H4p with an X-linked CLAMP recruiting region, HLB factors were not recruited but X chromosome factors were recruited to the transgene. However, when we replaced only the natural GA-repeats with GA-rich regions originating from the X chromosome, the transgene retained both the ability to recruit the HLB factor or the X-chromosome factors to the transgene. Our observations indicate that both sequence and context dictate CLAMP function. In the future, we will assess how the different GA-rich cis elements impact histone gene trasction using qRT-PCR to further evaluate locus function.