Genome-wide identification of AphEIN3-targeted genes in A. philoxeroides

Ethylene play a key role in submergence stress. The invasive plant Alternanthera philoxeroides has strong resistance to submergence stress, but the related mechanisms are not clear. We found that the ethylene signaling component AphEIN3 may be involved. To investigate the genome-wide AphEIN3 binding sites, we performed a DNA affinity purification sequencing (DAP-seq) as described by (Bartlett et al., 2017). In two replicates, approximately 22,604 peaks (for 6,831 genes) and 29,912 peaks (for 8,547 genes) were identified as high-confidence AphEIN3 binding peaks. Combined with RNA-seq analysis, we found that submergence can induce AphEIN3 binds to a cluster of elongation genes to regulate theses gene expression. Overall design: A DNA affinity purification sequencing (DAP-seq) for transcription factor AphEIN3 in Alternanthera philoxeroides. To capture the HaloTag fusion proteins, we used magnetic beads containing Halo antibodies (Magne HaloTag Beads, Promega, G728A).