The existence of microhomologies between promoter sequences and the T-DNA LB flanking sequence was also consistent with T-DNA integration to host DNA mediated by homologous recombination based on the microhomology-mediated end-joining pathway.
Although the association between promoter sequence identity and HI among essential genes was insignificant, suggesting a strong confounding effect, we included this property in our model because it improves predictive performance.
Thus, the non-concordance between proximal promoter sequence and gene expression is unexpected.
In the second step, UMPS cDNA was cloned and sandwiched between a promoter sequence and a terminator sequence.
In this plasmid, the distance between the promoter sequence and the P14K gene was shortened and the strong RBS was inserted upstream of each gene.
A second explanation for non-concordance between proximal promoter sequence and gene expression is that the expression of the genes in the first geneset actually does not differ between strains.
Previous combinatorial mutagenesis work with the bacterial Pm promoter has shown that there can be a strong context dependency between the promoter sequence and the coding region of the reporter gene which often affects the expression level in an unpredictable manner [ 5, 18].
Homology between the X. laevis ALF promoter sequence and those from human, chimpanzee, macaque, mouse, rat, cow, pig, horse, dog, chicken and X. tropicalis was relatively low, making it difficult to use such comparisons to identify putative regulatory elements.
