A team of biologists and computer scientists at New York University (NYU) has mapped out a network of interactions for how plant genes coordinate their response to nitrogen, a crucial nutrient and the main component of fertilizer.
The team focused on gene regulatory networks, which consist of transcription factors and the target genes that they regulate. These gene regulatory networks enable organisms to adapt to fluctuating surroundings. However, multi-cellular organisms present a challenge for mapping all connections as the nature of interactions within these complex networks are difficult to experimentally validate using common methods.
Using Arabidopsis, the team combined innovative experimental and computational methods to characterize the gene network underlying nitrogen responses. They scaled-up a cell-based technique that allowed them to experimentally determine more than 85,000 connections between 33 early nitrogen-responsive transcription factors and the target genes they regulate in approximately two months' time. Collectively, the 33 transcription factors regulate 88 percent of the nitrogen response genes in plants. Through the approach they call Network Walking, the scientists could use this vast amount of data to chart a path for a transcription factor from its direct gene targets in root cells to indirect gene targets in plants.