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.

KNOTTED1 (KN1)-like homeobox (KNOX) transcription factors are involved in the establishment and maintenance of plant meristems; however, few direct targets of KNOX proteins have been recognized. Using a combination of double mutant analysis and biochemistry, we found that in maize (Zea mays), KN1 negatively modulates the accumulation of gibberellin (GA) through the control of ga2ox1, which codes for an enzyme that inactivates GA. The ga2ox1 mRNA level is elevated in immature leaves of dominant KNOX mutants and downregulated in reproductive meristems of the null allele kn1-e1. KN1 binds in vivo to an intron of ga2ox1 through a cis-regulatory element containing two TGAC motifs. VP16-KN1 activates transcription in planta from a chimeric promoter containing this binding site. The domains of expression of kn1 and ga2ox1 mRNAs overlap at the base of the shoot apical meristem and the base of newly initiated leaves, suggesting that KN1-mediated activation of ga2ox1 maintains a boundary between meristem cell identity and rapidly elongating cells of the shoot. The KN1 binding site is conserved in ga2ox1 genes of different grasses, suggesting that the local regulation of bioactive GA levels through KNOX proteins is a common theme in grasses.

Protein coding genes constitute approximately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., ''whole exome'') have the potential to contribute our understanding of human diseases. We used a method for whole-exome sequencing coupling Agilent whole-exome capture to the Illumina DNA-sequencing platform, and investigated two unrelated fetuses from nonconsanguineous families with Fowler Syndrome (FS), a stereotyped phenotype lethal disease. We report novel germline mutations in feline leukemia virus subgroup C cellular-receptor-family member 2, FLVCR2, which has recently been shown to cause FS. Using this technology, we identified three types of genetic abnormalities: point-mutations, insertionsdeletions, and intronic splice-site changes (first pathogenic report using this technology), in the fetuses who both were compound heterozygotes for the disease. Although revealing a high level of allelic heterogeneity and mutational spectrum in FS, this study further illustrates the successful application of whole-exome sequencing to uncover genetic defects in rare Mendelian disorders. Of importance, we show that we can identify genes underlying rare, monogenic and recessive diseases using a limited number of patients (n 5 2), in the absence of shared genetic heritage and in the presence of allelic heterogeneity. Hum Mutat 31:918-923,

Maize leaves have distinct tissues that serve specific purposes. The blade tilts back to photosynthesize and the sheath wraps around the stem to provide structural support and protect young leaves. At the junction between blade and sheath are the ligule and auricles, both of which are absent in the recessive liguleless1 (lg1) mutant. Using an antibody against LG1, we reveal LG1 accumulation at the site of ligule formation and in the axil of developing tassel branches. The dominant mutant Wavy auricle in blade1 (Wab1-R) produces ectopic auricle tissue in the blade and increases the domain of LG1 accumulation. We determined that wab1 encodes a TCP transcription factor by positional cloning and revertant analysis. Tassel branches are few and upright in the wab1 revertant tassel and have an increased branch angle in the dominant mutant. wab1 mRNA is expressed at the base of branches in the inflorescence and is necessary for LG1 expression. wab1 is not expressed in leaves, except in the dominant mutant. The domain of wab1 expression in the Wab1-R leaf closely mirrors the accumulation of LG1. Although wab1 is not needed to induce lg1 expression in the leaf, LG1 is needed to counteract the severe phenotype of the dominant Wab1-R mutant. The regulatory interaction of LG1 and WAB1 reveals a link between leaf shape and tassel architecture, and suggests the ligule is a boundary similar to that at the base of lateral organs.