NEW YORK (GenomeWeb News) – In a paper appearing in today's issue of Science, an international research team reported that they have started deciphering the gene expression changes that occur when the transcription factor APETALA1 — also known as AP1 — is turned on in Arabidopsis, gaining new insights into flower development in the plant.
Through a combination of gene expression and chromatin binding and sequencing experiments, the researchers uncovered a set of AP1-regulated genes that appear to contribute to flowering. Their findings indicate that the transcription factor acts, in part, by controlling transcription factors. Moreover, AP1 appears to repress the transcription of some genes early in flower development but ramp up the expression of others during later stages.
"Our results suggest distinct functions of AP1 during the initiation of flower development … [A]t more advanced stages of flower development AP1 initiates downstream pathways required for floral organ specification," senior author José Luis Riechmann, an agricultural genomics and biology researcher affiliated with the California Institute of Technology and two Barcelona-based research centers, and colleagues wrote.
"Thus, AP1 acts as a true hub in the regulatory network that mediates the switch from floral induction to flower formation," they added.
Past studies have shown that AP1, a so-called MADS-domain transcription factor, controls Arabidopsis flowering by working in collaboration with CAULIFLOWER, or CAL, a paralogous transcription factor with partially redundant activity, the researchers explained.
Previous research has turned up a handful of early flower development genes whose expression is curbed by AP1. Even so, the transcription factors role in flowering and the complete network of genes it controls is largely unknown.
To further explore this process, Riechmann and his team used two microarrays — one from Operon Biotechnologies and one from Agilent — to assess gene expression in an Arabidopsis strain lacking the AP1 and CAL genes but expressing a version of AP1 that's fused to a glucocorticoid receptor hormone-binding domain. Using this construct provided the researchers with a tool for switching AP1 on and off by treating the plant with a compound called dexamethasone.
Twelve hours after AP1 activation, the researchers found 1,366 genes with altered expression.
To help distinguish between direct and indirect effects on expression, they also identified AP1-interacting genes using chromatin immunoprecipitation combined with sequencing. That experiment yielded more than 1,900 regions bound by AP1, falling near the 5' or 3' ends of 2,298 genes.
When they compared their microarray and ChIP-Seq data, the researchers found that roughly 44 percent of genes found near AP1 binding regions also have altered expression when the transcription factor is turned on. Of these, 249 showed at least 1.8-fold changes in expression when AP1 is active.
The team also found evidence that AP1 controls the expression of a slew of other transcription factors, including transcription factors regulating the AP1 gene itself.
By looking at the subsets of genes with altered expression at various time points (two, four, eight, and 12 hours) after AP1 activation, the team outlined AP1's changing role in the early and late stages of Arabidopsis flower development.
During the so-called "floral initiation" stage of flowering, the transcription factor represses more than 80 percent of its targets, the researchers noted, whereas it ramps up the expression of other genes — including some governing organ growth — in subsequent flower development stages.
"Although AP1 acts predominantly as a transcriptional repressor during the earliest stages of flower development, at more advanced stages it also activates regulatory genes required for floral organ formation, indicating a dynamic mode of action," the researchers explained. "Our results further imply that AP1 orchestrates floral initiation by integrating growth, patterning, and hormonal pathways."