Dissection of open chromatin domain formation by site-specific recombination in Drosophila

Abstract

Drosophila polytene interphase chromosomes provide an ideal test system to study the rules that define the structure of chromatin domains. We established a transgenic condensed chromatin domain cassette for the insertion of large pieces of DNA by site specific recombination. Insertion of this cassette into open chromatin generated a condensed domain, visible as an extra band on polytene chromosomes. Site specific recombination of DNA sequence variants into this ectopic band allowed us to compare their capacity for open chromatin formation by cytogenetic methods. We demonstrate that the 61C7-8 interband DNA maintains its open chromatin conformation and epigenetic state at an ectopic position. By deletion analysis we mapped the sequences essential for open chromatin formation to a 490 bp fragment in the proximal part of the 17 kb interband sequence. This fragment overlaps binding sites of the chromatin protein Chriz, the histone kinase Jil-1 and the boundary element protein CP190. It also overlaps a promoter region that locates in between the Rev1 and Med30 transcription units.