Characterization of open chromatin in response to cold reveals transcription factor association with preferred binding distances in cassava

Abstract

Cassava is a tropical root crop that is sensitive to low temperature. While the transcriptome for cold-responsive genes has been extensively studied, information on their regulation is largely unavailable. Here, we conducted assays of plant morphology, the transcriptome, and open chromatin in cassava under moderate cold stress (10 ℃). We observed reversible morphological changes in cassava plants under continuous cold stress, in which plants showed wilting of the apical leaf blade and petiole at 5 h and recovery at 48 h. Consistently, distinct expressional dynamics for genes in response to cold were detected at 5 h and 48 h in both tissues. We examined the genome-wide DNase I-hypersensitive sites (DHSs) and their dynamics using cold-treated leaf blades and petioles. We revealed that cold-induced DHSs (coiDHSs) substantially differed among tissues and treatments. However, the putative coiDHS-derived transcription factors (TFs) largely co-occurred across tissues and treatments, and 61 TFs commonly shared by all samples were isolated. A putative functional network with 30 interconnected TFs was created. The frequent empirical interactions among these TFs indicate their roles in the cold response. Notably, we found that the two pairs of known cold-responsive TFs AGL20-RGA and ERF5-ERF105 showed highly frequent co-occurrence in coiDHSs. Moreover, the binding-site distances differed among TF pairs or samples, indicating that there are preferred distances between cooperative TFs and that such distances may depend on biological conditions. The identification of conserved TFs and their cooperativity provides valuable information for elucidating the transcriptional networks underlying cold gene expression in cassava.