Fangnan Sun, Yaxin Deng, Weihua Zhao, Yixue Xiong, Lingxia Zhao et al.
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.
Fangnan Sun, Yaxin Deng, Weihua Zhao, Yixue Xiong, Lingxia Zhao, Lida Zhang. High-throughput quantitative assessment of ABA-responsive elements at single-nucleotide resolution. 2025-01-30. https://doi.org/10.1002/qub2.87
A synthetic STARR-seq library tested randomized 10-bp ABRE sequences covering the ACGT core and the flanking positions in transiently infiltrated Nicotiana benthamiana leaves. Three biological replicates were measured under matched untreated-control and 25 μM ABA-treated conditions, and the processed table contains the 2,554 variants with complete source activity values.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 5 files (ZIP)source_notes.txtsra_runinfo.csvsupplementary_table_s3_promoter_strength.tsvsupplementary_table_s4_aba_responsive.tsvsupporting_information_s1.pdf