Polymorphic core promoter GA-repeats alter gene expression of the early embryonic developmental genes

• Polymorphic core promoter GA-repeats alter gene expression in developmental genes.
• Threshold for the length of GA-repeats and their incremental effect on gene expression.
• Ideal medium and maximal expression of MECOM and GABRA3 in human, respectively.
• Evolutionary conservation of the GABRA3 and MECOM core promoter GA-repeats.
• Selective advantage for length and complexity of MECOM core promoter GA-repeats in human.

Protein complexes that bind to ‘GAGA’ DNA elements are necessary to replace nucleosomes to create a local chromatin environment that facilitates a variety of site-specific regulatory responses. Three to four elements are required for the disruption of a preassembled nucleosome. We have previously identified human protein-coding gene core promoters that are composed of exceptionally long GA-repeats. The functional implication of those GA-repeats is beginning to emerge in the core promoter of the human SOX5 gene, which is involved in multiple developmental processes. In the current study, we analyze the functional implication of GA-repeats in the core promoter of two additional genes, MECOM and GABRA3, whose expression is largely limited to embryogenesis. We report a significant difference in gene expression as a result of different alleles across those core promoters in the HEK-293 cell line. Across-species homology check for the GABRA3 GA-repeats revealed that those repeats are evolutionary conserved in mouse and primates (p < 1 × 10− 8). The MECOM core promoter GA-repeats are also conserved in numerous species, of which human has the longest repeat and complexity. We propose a novel role for GA-repeat core promoters to regulate gene expression in the genes involved in development and evolution.