Maize maintains growth in response to decreased nitrate supply through a highly dynamic and developmental stage-specific transcriptional response.

Elucidation of the gene networks underlying the response to N supply and demand will facilitate the improvement of the N uptake efficiency of plants. We undertook a transcriptomic analysis of maize to identify genes responding to both a non-growth-limiting decrease in NO3- provision and to development-based N demand changes at seven representative points across the life cycle. Gene co-expression networks were derived by cluster analysis of the transcript profiles. The majority of NO3--responsive transcription occurred at 11 (D11), 18 (D18) and 29 (D29) days after emergence, with differential expression predominating in the root at D11 and D29 and in the leaf at D18. A cluster of 98 probe sets was identified, the expression pattern of which is similar to that of the high-affinity NO3- transporter (NRT2) genes across the life cycle. The cluster is enriched with genes encoding enzymes and proteins of lipid metabolism and transport, respectively. These are candidate genes for the response of maize to N supply and demand. Only a few patterns of differential gene expression were observed over the entire life cycle; however, the composition of the classes of the genes differentially regulated at individual time points was unique, suggesting tightly controlled regulation of NO3--responsive gene expression.

Phylogenetic footprinting reveals multiple regulatory elements involved in control of the meiotic recombination gene, REC102.

REC102 is a meiosis-specific early exchange gene absolutely required for meiotic recombination in Saccharomyces cerevisiae. Sequence analysis of REC102 indicates that there are multiple potential regulatory elements in its promoter region, and a possible regulatory element in the coding region. This suggests that the regulation of REC102 may be complex and may include elements not yet reported in other meiotic genes. To identify potential cis-regulatory elements, phylogenetic footprinting analysis was used. REC102 homologues were cloned from other two Saccharomyces spp. and sequence comparison among the three species defined evolutionarily conserved elements. Deletion analysis demonstrated that the early meiotic gene regulatory element URS1 was necessary but not sufficient for proper regulation of REC102. Upstream elements, including the binding sites for Gcr1p, Yap1p, Rap1p and several novel conserved sequences, are also required for the normal regulation of REC102 as well as a Rap1p binding site located in the coding region. The data in this paper support the use of phylogenetic comparisions as a method for determining important sequences in complex promoters.