High-throughput quantitative assessment of ABA-responsive elements at single-nucleotide resolution

Abstract

Abscisic acid (ABA)-responsive elements (ABREs) are the major cis-regulatory elements in ABA-induced gene expression. However, the impact of sequence variations on ABRE function is not yet well-understood. Here, we used synthetic STARR-seq to quantitatively assess the effects of single-nucleotide substitutions on ABRE activity. Our results revealed that the nucleotide substitutions in both the ACGT-core and ACGT-flank regions affected transcriptional strength. Alterations in the ACGT-core sequence had a more significant impact on ABRE activity than changes in the flanking region. Interestingly, we observed that the ACGT-flank variants with high activity exhibited a strong sequence preference in the downstream region, whereas the highly active core variants were diverse in sequence patterns. Our studies provide a quantitative map of ABRE activity at single-nucleotide resolution, which will facilitate the design of ABA-responsive promoters with desired activities in plants.

Keywords

STARR-seq / abscisic acid responsive element / cis-regulatory element / enhancer / synthetic promoter

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The Author(s). Quantitative Biology published by John Wiley & Sons Australia, Ltd on behalf of Higher Education Press.