A BEAF dependent chromatin domain boundary separates myoglianin and eyeless genes of Drosophila melanogaster

Abstract

Precise transcriptional control is dependent on specific interactions of a number of regulatory elements such as promoters, enhancers and silencers. Several studies indicate that the genome in higher eukaryotes is divided into chromatin domains with functional autonomy. Chromatin domain boundaries are a class of regulatory elements that restrict enhancers to interact with appropriate promoters and prevent misregulation of genes. While several boundary elements have been identified, a rational approach to search for such elements is lacking. With a view to identifying new chromatin domain boundary elements we analyzed genomic regions between closely spaced but differentially expressed genes of Drosophila melanogaster. We have identified a new boundary element between myoglianin and eyeless, ME boundary, that separates these two differentially expressed genes. ME boundary maps to a DNaseI hypersensitive site and acts as an enhancer blocker both in embryonic and adult stages in transgenic context. We also report that BEAF and GAF are the two major proteins responsible for the ME boundary function. Our studies demonstrate a rational approach to search for potential boundaries in genomic regions that are well annotated.

Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae

“…It is possible that these sites represent non-functional BEAF sites, because BEAF is believed to be absent from all the species other than Drosophilids (30). Moreover, none of these boundaries contains palindromic BEAF sites as frequently seen in BEAF-dependent boundaries in Drosophila (66). Taken together, this study shows that mosquito boundary elements identified here employ GAF and CP190 for their enhancer-blocking activity.…”

GATA simple sequence repeats function as enhancer blocker boundaries

“…Inverse PCR was performed following the published protocol 41 to determine the precise insertion site for useful lines. Embryos (0-12 h) were collected and stained for b-galactosidase (lacZ) activity according to the protocol 42 with minor changes 43 as outlined. Briefly, 0-to 12-h-old embryos were dechorionated in 50% bleach (sodium hypochlorite), washed and fixed in heptane saturated with 25% glutaraldehyde for 20 min.…”

The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species

“…5A). For example, the intergenic region between the genes myoglianin and eyeless contains a functional BEAF-32 binding site in D. melanogaster (Sultana et al 2011), but not in D. virilis. The distance between the two TSS's increased 10 times in D. virilis, and this change correlates with the loss of the BEAF-32 binding site in this species or the gain in D. melanogaster (Fig.…”