Harnessing mobile genetic elements to explore gene regulation

Abstract

Sequences that regulate expression of a gene in cis but are located at large distances along the DNA from the gene, as found with most developmentally regulated genes in higher vertebrates, are difficult to identify if those sequences are not conserved across species. Mutating suspected gene-regulatory sequences to alter expression then becomes a hit-or-miss affair. The relaxed specificity of transposon insertions offers an opportunity to develop alternate strategies, to scan in an unbiased manner, pieces of chromosomal DNA cloned in BACs for transcription enhancing elements. This article illustrates how insertions of Tn10 with enhancer-traps into BAC DNA containing the gene, and its germ-line expression in zebrafish, have identified distal regulatory elements functionally. Transposition of Tn10 first introduces the enhancer-trap with a loxP site randomly into BAC DNA. Cre-recombination between the inserted loxP and the loxP endogenous to a BAC-end positions the enhancer-trap to the newly created truncated end of BAC DNA. The procedure generates a library of integration-ready enhancer-trap BACs with progressive truncations from an end in a single experiment. Individual enhancer-trap BACs from the library can be evaluated functionally in zebrafish or mice. Furthermore, the ability to readily alter sequences in a small transposon plasmid containing a regulatory domain of the gene allows re-introduction of altered parts of a BAC back into itself. It serves as a useful strategy to functionally dissect multiple discontinuous regulatory domains of a gene quickly. These methodologies have been successfully used in identifying novel regulatory domains of the Amyloid Precursor Protein (appb) gene in zebrafish, and provided important clues for regulation of the gene in humans.

Uniform Expression and Relatively Small Position Effects Characterize Sister Transformants in Maize and Soybean

“…Some differences in gene expression attributable to genomic location are likely caused by interaction with nearby genes, a phenomenon that has been clearly demonstrated in plants and other organisms (Eszterhas et al, 2002). For example, strong enhancers are known to increase the expression of nearby genes (Shakes et al, 2014), and upstream genes are known to repress downstream genes through a phenomenon known as transcriptional interference (Corbin and Maniatis, 1989). Both of these effects occur over relatively short distances of ≤20 kb (Akhtar et al, 2013).…”