Zea mays Transcriptome or Gene expression

KNOTTED1(KN1)-like homeobox (KNOX) transcription factors function in plant meristems, self-renewing structures consisting of stem cells and their immediate daughters. Despite their importance for plant development, the genomic network targeted by KNOX proteins is poorly understood. Using ChIP-seq, we defined the KN1 cistrome in maize inflorescences and found that KN1 binds to several thousand loci. To understand how these binding occupancies correlate with changes in transcriptional regulation, we performed RNA-seq on immature ears and tassels, and compared expression profiles between normal and loss-of-function kn1 plants, in addition to immature leaves from normal and gain-of-function Kn1 plants. We found that 643 of the KN1 targets were modulated in one or multiple tissues, with a strong enrichment for transcription factors (including other homeobox genes) and genes participating in several hormonal pathways, most significantly auxin, implicating KN1 at the crossroads of plant hormone signaling. The loss-of-function kn1 phenotype is reminiscent of auxin mutants and kn1 mis-expression in leaves correlates with increased auxin signaling. Our results demonstrate that KN1 plays a key role in orchestrating the upper levels of a hierarchical gene regulatory network that impacts plant meristem identity and function. Overall design: For loss-of-function mutant, kn1-e1 homozygote were compared to heterozygote or wild-type siblings (ears, tassels and shoot apical meristem). For gain-of-function mutant, Kn1-N homozygote were compared to wild-type siblings.Kn1-N heterozygote were compared to wild-type siblings. For each genotype and tissue, 2 biological replicates were sequenced, except for tassels (3 biological replicates). The whole data set thus includes a total of 20 samples/libraries.