ARS | Publication request: Unraveling the KNOTTED1 regulatory network in maize meristems

Submitted to: Genes and Development
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 12, 2012
Publication Date: August 20, 2012
Citation: Bolduc, N., Yilmaz, A., Mejia-Guerra, M.K., Morohashi, K., O'Connor, D., Grotewold, E., Hake, S.C. 2012. Unraveling the KNOTTED1 regulatory network in maize meristems. Genes and Development. 26:1685-1690.

Interpretive Summary: KNOTTED1 (KN1)-like homeobox (KNOX) transcription factors function in plant meristems, self-renewing structures consisting of stem cells and their immediate daughters. We defined the KN1 cistrome in maize inflorescences and found that KN1 binds to several thousand loci, including 643 genes that are modulated in one or multiple tissues. These KN1 direct targets are strongly enriched for transcription factors (including other homeobox genes) and genes participating in hormonal pathways, most significantly auxin, demonstrating that KN1 plays a key role in orchestrating the upper levels of a hierarchical gene regulatory network that impacts plant meristem identity and function.

Technical Abstract: We carried out whole genome analysis to determine the genes that are differentially expressed in gain- and loss-of-function mutants and to identify the maize genomic regions that KN1 binds. We performed RNA-seq experiments aimed at identifying the genes differentially expressed between normal and kn1 loss-of-function tassel primordia, ear primordia, and shoot apices. We also queried gene expression differences between normal, heterozygous (Kn1-N/+) and homozygous (Kn1-N/Kn1-N) gain of function mutant leaf primordia prior to phenotypic differences. We found about 3000 genes that were differentially expressed in at least one tissue. 600 genes were differentially expressed and bound by KN1.