Systems Biology Update: Cell Type-Specific Transcriptional Regulatory Networks

Plant cells use regulatory networks composed of numerous components, such as DNA, RNA, proteins, and small molecules, to regulate multiple biological processes, allowing plants to adapt to changing environments or to respond to developmental cues. The availability of high-throughput experimental methods enables researchers to determine the expression levels for thousands of genes and protein– protein or protein– DNA interactions. Systems biology approaches can allow scientists to integrate these large amounts of information and to understand the properties of these biological systems in specific cells or tissues. Dynamic mathematical modeling approaches used to characterize plant transcriptional networks can reveal emergent properties of these networks. This review highlights some currently available methodologies used to obtain systems-scale data such as Laser Capture Microdissection (LCM), Fluorescent Activated Cell Sorting (FACS), ChIP-on-chip, proteomics, and modeling approaches that are most useful to explore plant transcriptional networks at the cellular level. We also provide two examples of transcriptional networks in single cell types and detail how such methods and data sets have been used to map and reveal emergent properties of gene regulatory networks that regulate cell identity specification.