Direct and indirect targets of the arabidopsis seed transcription factor ABSCISIC ACID INSENSITIVE3

Arabidopsis thalianaABSCISIC ACID INSENSITIVE3 (ABI3) is a transcription factor in the B3 domain family. ABI3, along with B3 domain transcription factors LEAFY COTYLEDON2 (LEC2) and FUSCA3 (FUS3), and LEC1, a subunit of the CCAAT box-binding complex, form the so-called LAFL network to control various aspects of seed development and maturation. ABI3 also contributes to the abscisic acid (ABA) response. We report on chromatin immunoprecipitation-tiling array experiments to map binding sites for ABI3 globally. We also assessed transcriptomes in response to ABI3 by comparing developingabi3-5and wild-type seeds and combined this information to ascertain direct and indirect responsive ABI3 target genes. ABI3 can induce and repress its transcription of target genes directly and some intriguing differences exist incismotifs between these groups of genes. Directly regulated targets reflect the role of ABI3 in seed maturation, desiccation tolerance, entry into a quiescent state and longevity. Interestingly, ABI3 directly represses a gene encoding a microRNA (MIR160B) that targetsAUXIN RESPONSE FACTOR(ARF)10andARF16that are involved in establishment of dormancy. In addition, ABI3, like FUS3, regulates genes encodingMIR156but while FUS3 only induces genes encoding this product, ABI3 induces these genes during the early stages of seed development, but represses these genes during late development. The interplay between ABI3, the otherLAFLgenes, and theVP1/ABI3-LIKE(VAL) genes, which are involved in the transition to seedling development are examined and reveal complex interactions controlling development.