Idefix insulator activity can be modulated by nearby regulatory elements

Abstract

Insulators play important roles in controlling gene activity and maintaining regulatory independence between neighbouring genes. In this article, we show that the enhancer-blocking activity of the insulator present within the LTR retrotransposon Idefix can be abolished if two copies of the region containing the insulator—specifically, the long terminal repeat (LTR)—are fused to the retrotransposon's 5′ untranslated region (5′ UTR). The presence of this combination of two [LTR-5′ UTR] modules is a prerequisite for the loss of enhancer-blocking activity. We further show that the 5′ UTR causes flanking genomic sequences to be displaced to the nuclear periphery, which is not observed when two insulators are present by themselves. This study thus provides a functional link between insulators and independent genomic modules, which may cooperate to allow the specific regulation of defined genomic loci via nuclear repositioning. It further illustrates the complexity of genomic regulation within a chromatic environment with multiple functional elements.

Interaction between a pair of gypsy insulators or between heterologous gypsy and Wari insulators modulates Flp site-specific recombination in Drosophila melanogaster

“…Cancelation of the enhancerblocking activity upon tandem pairing was also reported for several other insulators (Conte et al 2002;Brasset et al 2007;Chetverina et al 2008;Maksimenko et al 2008;Kyrchanova et al 2007Kyrchanova et al , 2008aKuhn-Parnell et al 2008); i.e., this property is not unique to the gypsy insulator. The insulator named Wari was identified on the 3′ side of the white gene (Chetverina et al 2008).…”

GATA simple sequence repeats function as enhancer blocker boundaries

“…Much of this non-coding DNA consists of a variety of repetitive DNA including transposable elements (TEs) and simple sequence repeats (SSRs). Certain repetitive sequences have been implicated in chromatin-mediated transcriptional regulation, chromosome organization, imprinting, chromatin domain boundary function and complex nuclear features such as heterochromatin, telomeres and nucleolar organization [1][2][3][4][5][6][7][8] . SSRs, on the other hand, have not been directly implicated in such regulatory roles although this class of DNA has also accumulated in complex genomes, particularly in vertebrates 9,10 .…”

The Idefix enhancer-blocking insulator also harbors barrier activity

“…According to the homogeneous phenotype of the 14 IZWI transgenic lines, it is unlikely that the 3′ Idefix and Wary mutually neutralize their action. It is more probable that either Wary reinforces the enhancerblocking activity of Idefix as already reported for two copies of Idefix insulators placed in tandem arrays (Brasset et al, 2007), or that one or the other is sufficient to block efficiently the neighboring chromatin. Since a better insulation has been found in several transgenic lines when both Idefix were present, we favor the first hypothesis in which two Idefix insulators are implicated in the protection against both positive and negative chromosomal position, a property that is increased by the presence of Wary.…”

“…Several models have been proposed for how enhancer-blocking insulators disrupt the communication between enhancers and promoters. These models have been discussed in (Brasset et al, 2007;Bushey et al, 2008).…”