An exonic splicing enhancer within a bidirectional coding sequence regulates alternative splicing of an antisense mRNA

The discovery of increasing numbers of genes with overlapping sequences highlights the problem of expression in the context of constraining regulatory elements from more than one gene. This study identifies regulatory sequences encompassed within two genes that overlap in an antisense orientation at their 3' ends. The genes encode the alpha-thyroid hormone receptor gene (TR alpha or NR1A1) and Rev-erb alpha (NR1D1). In mammals TR alpha pre-mRNAs are alternatively spliced to yield mRNAs encoding functionally antagonistic proteins: TR alpha 1, an authentic thyroid hormone receptor; and TR alpha 2, a non-hormone-binding variant that acts as a repressor. TR alpha 2-specific splicing requires two regulatory elements that overlap with Rev-erb alpha sequences. Functional mapping of these elements reveals minimal splicing enhancer elements that have evolved within the constraints of the overlapping Rev-erba sequence. These results provide insight into the evolution of regulatory elements within the context of bidirectional coding sequences. They also demonstrate the ability of the genetic code to accommodate multiple layers of information within a given sequence, an important property of the code recently suggested on theoretical grounds.