Enhancer Blocking and Transvection at the DrosophilaapterousLocus

Abstract

Intra-and interchromosomal interactions have been implicated in a number of genetic phenomena in diverse organisms, suggesting that the higher-order structural organization of chromosomes in the nucleus can have a profound impact on gene regulation. In Drosophila, homologous chromosomes remain paired in somatic tissues, allowing for trans interactions between genes and regulatory elements on the two homologs. One consequence of homolog pairing is the phenomenon of transvection, in which regulatory elements on one homolog can affect the expression of a gene in trans. We report a new instance of transvection at the Drosophila apterous (ap) locus. Two different insertions of boundary elements in the ap regulatory region were identified. The boundaries are inserted between the ap wing enhancer and the ap promoter and have highly penetrant wing defects typical of mutants in ap. When crossed to an ap promoter deletion, both boundary inserts exhibit the interallelic complementation characteristic of transvection. To confirm that transvection occurs at ap, we generated a deletion of the ap wing enhancer by FRT-mediated recombination. When the wing-enhancer deletion is crossed to the ap promoter deletion, strong transvection is observed. Interestingly, the two boundary elements, which are inserted $10 kb apart, fail to block enhancer action when they are present in trans to one another. We demonstrate that this is unlikely to be due to insulator bypass. The transvection effects described here may provide insight into the role that boundary element pairing plays in enhancer blocking both in cis and in trans.

Comparing Enhancer Action in Cis and in Trans

“…Prior genetic analyses have shown that, for many genes, enhancer action in trans is reduced in the presence of a promoter in cis (Martinez-Laborda et al 1992;Casares et al 1997;Gohl et al 2008). Our data are consistent with the model that this reduction results from an enhancer sharing its activity between the two promoters.…”

“…Finally, in light of the extensive pairing in the Drosophila genome, how does an enhancer choose a target promoter when simultaneously presented with promoters in cis and in trans? For several genes, the presence of a promoter in cis reduces the strength of enhancer action in trans (Martinez-Laborda et al 1992;Casares et al 1997;Gohl et al 2008), suggesting that promoters in cis and in trans compete for an enhancer's activity. Because these observations have been largely based on mutant phenotypes in whole animals, the cellular basis for this competition is not yet clear.…”

The Capacity to Act in Trans Varies Among Drosophila Enhancers

“…Thus far, transvection has been observed at all genomic insertion sites tested, suggesting that the Drosophila genome is generally permissive to enhancer action in trans. Furthermore, transgenic experiments have demonstrated that promoters at allelic positions in cis and trans to an enhancer will compete for the enhancer's activity, consistent with earlier classical observations (Geyer et al 1990;Martinez-Laborda et al 1992;Casares et al 1997;Morris et al 1999;Gohl et al 2008). However, enhancer activation of promoters in cis and trans are not equivalent, with enhancers showing a strong preference for a promoter in cis, and frequently showing cell-to-cell variability in the activation of a promoter in trans (Bateman et al 2012a;Mellert and Truman 2012).…”

“…Thus, it is conceivable that enhancers that were scored negatively for transvection in the previous study were, in fact, restricted from acting in trans at detectable levels due to competition from the promoter in cis, whereas other enhancers in the study may have been less sensitive to the promoter in cis. Consistent with this hypothesis, the enhancers of the yellow gene do not appear to act in trans in the presence of a strong promoter in cis (Geyer et al 1990;Morris et al 1999), whereas enhancers from other genes will show low levels of transvection when juxtaposed to a strong cis-promoter and higher levels of transvection in the absence of a cis-promoter (Martinez-Laborda et al 1992;Casares et al 1997;Gohl et al 2008;Bateman et al 2012a;Mellert and Truman 2012). We also found that two enhancers from our study differed in sensitivity to a promoter in cis, as Cre/loxP removal of the LTL promoter increased transvection by the klu enhancer but not by the pax enhancer.…”

“…The close proximity of homologous chromosomes in Drosophila can permit an enhancer to act in trans on a promoter on the paired homolog, a form of pairing-dependent gene regulation called transvection (Lewis 1954). Evidence for enhancer action in trans has been uncovered at a handful of genes in the Drosophila genome, often providing an explanation for unexpected intragenic complementation of loss-of-function alleles (Lewis 1954;Gelbart 1982;Geyer et al 1990;Leiserson et al 1994;Hendrickson and Sakonju 1995;Casares et al 1997;Morris et al 1998;Southworth and Kennison 2002;Marin et al 2004;Coulthard et al 2005;Gohl et al 2008;Juni and Yamamoto 2009) paired mutant and wild-type alleles (Gibson et al 2000;Lum and Merritt 2011;Bing et al 2014). More recently, transgenic approaches based on site-specific recombination have been developed for Drosophila to query specific enhancer fragments and genomic positions for support of transvection (Chen et al 2002;Kravchenko et al 2005;Bateman et al 2012a;Mellert and Truman 2012; also see Kassis et al 1991).…”