Genome-Wide Characterization ofcis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework ofOpaque2in Maize

Abstract

Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we studied the transcriptome of o2 mutants using RNA sequencing (RNA-Seq) and determined O2 DNA binding targets using chromatin immunoprecipitation coupled to highthroughput sequencing (ChIP-Seq). The RNA-Seq analysis revealed 1605 differentially expressed genes (DEGs) and 383 differentially expressed long, noncoding RNAs. The DEGs cover a wide range of functions related to nutrient reservoir activity, nitrogen metabolism, stress resistance, etc. ChIP-Seq analysis detected 1686 O2 DNA binding sites distributed over 1143 genes. Overlay of the RNA-Seq and ChIP-Seq results revealed 35 O2-modulated target genes. We identified four O2 binding motifs; among them, TGACGTGG appears to be the most conserved and strongest. We confirmed that, except for the 16-and 18-kD zeins, O2 directly regulates expression of all other zeins. O2 directly regulates two transcription factors, genes linked to carbon and amino acid metabolism and abiotic stress resistance. We built a hierarchical regulatory model for O2 that provides an understanding of its pleiotropic biological effects.

Feedback Regulation of ABA Signaling and Biosynthesis by a bZIP Transcription Factor Targets Drought-Resistance-Related Genes

“…OsbZIP23 mainly binds to the regions 500 bp upstream of the TSSs in all three samples (Fig. 3A), which is consistent with the transcription factor role of OsbZIP23 and with the previous ChIP-Seq results of other transcription factors in Arabidopsis and maize (Zea mays L.; Zhang et al, 2011;Ram et al, 2014;Li et al, 2015aLi et al, , 2015b. Moreover, we found that the conserved ABREs are significantly enriched in the OsbZIP23-bound regions (Fig.…”

“…Moreover, we observed a rapid dehydration phenotype of the OsPP2C49 over-expression lines when compared to the wild type and the negative transgenic controls (Fig. 7D), which is similar to the phenotype observed in the overexpression plants of another ABI1-like OsPP2C gene (Li et al, 2015a). These results together indicate that OsPP2C49 acts as an important negative regulator in ABA signaling and drought response in rice.…”

“…Both OsPP2C30 and OsABIL2 could deactivate SAPK2 and then negatively regulate the expression of downstream genes mainly through bZIP transcription factors (Kim et al, 2012;Li et al, 2015aLi et al, , 2015b. In this work, we found that SAPK2 could interact with OsPP2C49.…”

“…Recently, another clade A PP2C gene OsABIL2 was demonstrated as a negative regulator in ABA signaling (Li et al, 2015a(Li et al, , 2015b. In the presence of ABA, the OsPYL1-ABAOsABIL2 complex causes a subcellular redistribution of OsABL2 and releases the inhibition on SAPK8 and SAPK10 in the nucleus (Li et al, 2015a(Li et al, , 2015b.…”

Maize endosperm-specific transcription factors O2 and PBF network the regulation of protein and starch synthesis

“…For example, lysine degradation, which is related to the nutritional quality and is under regulation by O2 (30), was significantly enriched in the down-regulated genes of the o2 and PbfRNAi;o2 mutants. The Gene Ontology (GO) terms associated with ribosome, translation, protein folding, and so forth were also enriched in the differentially expressed genes in the three mutants, especially in PbfRNAi;o2 (Dataset S2), consistent with the recent study of the O2 regulatory network (31). Among them, the nutrient reservoir activity (GO: 0045735), mainly containing zein genes, was significantly enriched in the down-regulated genes of all of the three mutants.…”