Identification of functionally significant elements in the second intron of the Drosophila melanogaster Trithorax-like gene

It is known that a lot of genes having a distinct expression pattern require the complex system of transcription regulation. The regulatory regions of such genes can include not only the 5′-flanking regions, but also other regions, particularly their intron sequences. The Drosophila melanogaster Trithorax-like (Trl) gene, encoding the GAGA protein, is one of the genes with complex expression pattern. GAGA is one of a few transcription factors that can regulate gene expression at multiple levels. The GAGA-mediated modulation of expression seems to be linked with modifications of the chromatin structure. Nowadays, the regulatory potential of the Trl 5′-flanking region that contains multiple GAGA binding sites has been analyzed, but the presence of the functionally significant elements in other Trl regions has not been examined. We found DNase I hypersensitive sites, evolutionary-conserved sequences and numerous GAGA binding sites in the second intron of the Trl gene. Interestingly, these sequences localize in two main regions of the intron in immediate proximity to preferred regions of transposon insertions. Additionally, we revealed that deletion of the intron fragment in the Trl1–72 mutants caused an alteration of the Trl expression pattern. These results allow us to conclude that the second intron of the Trl gene contains functionally significant elements.

► Regulatory potential of the second intron of the Trithorax-like gene was analyzed.
► DNase I hypersensitive sites, conserved regions and GAGA sites localize in intron.
► Deletions of the intron fragments disturb the Trithorax-like expression pattern.
► The second intron is essential for the Trithorax-like gene functioning.