Arabidopsis Gene Regulatory Information Server (AGRIS) is a database containing information on:
- All A. thaliana transcription factors (TFs), grouped into families based on conserved DNA-binding motifs
- All the Arabidopsis RNA pol II gene promoters with all the predicted and experimentally verified cis-regulatory elements (CREs)
- Interactions between TFs and CREs, forming regulatory motifs, the building blocks of gene regulatory networks
AGRIS aims to discover and visualize gene regulatory networks by compiling interactions between TFs and promoters or cis-regulatory elements. AGRIS features the Regulatory Network Interaction Viewer (ReIN), which offers researchers an online tool for the fast and easy visualization of networks of interactions in Arabidopsis, with the potential to be extended to other organisms.
ii. Stomata development in Arabidopsis leaves
Stomata, as the gate for gas exchange and water vapor, are essential for plant survival. In recent years, more and more studies focused on stomata development. Many genes were identified that are involved in controlling different stages during stomata development, such as TMM, YODA, MUTE, ER, FAMA, FLP and MYB88. Our interest focuses on the function of FLP/AtMYB88 in stomata development, research that is being carried in collaboration with Dr. Fred Sack. Based on the clustered guard cells phenotype in the flp mutant (four lips), FLP is suggested to participate in the transition of division to differentiation of guard cells. Uncovering the molecular function of FLP will lead to better understand how FLP control stomata development. Our biochemical and genetic data showed that FLP, as a MYB protein, is a transcription factor with a distinct DNA-binding specificity. By using microarray and ChIP-chip approaches, we have started to identify the direct targets of FLP during stomata development, uncovering unique mechanisms by which this atypical R2R3-MYB transcription factor regulates stomatal development.
It would be nice to get a figure from ChIP-chip here - nothing to revealing but something that shows what we are really doing.
iii. Regulatory Networks Participating in Trichome Development
Position-dependent cell fate determination and pattern formation are unique aspects of the development of plant structures. The establishment of single-celled leaf hairs (trichomes) from pluripotent epidermal (protodermal) cells in Arabidopsis thaliana provides a powerful system to determine the genetic/regulatory networks and positional signals involved in cell fate determination.
We have focused on the bHLH transcription factor GL3, as a window to explore the transcriptional regulatory networks that participate in trichome development. We have shown that trichome initiation is triggered within 4 hours of the induction of the GL3 protein function (Figure 1). Within this developmental window, GL3 binds to the promoters of at least three genes previously implicated in the development and patterning of trichomes (GL2, CPC, and ETC1) and activates their transcription. Chromatin immunoprecipitation (ChIP) experiments have shown the in vivo binding of GL3 to the promoters of these genes in the presence of the R2R3-MYB factor GL1, supporting a model in which a GL3-GL1 complex is part of the trichome initiation enhanceosome. In contrast, GL3 is recruited to its own promoter in a GL1-independent manner, resulting in decreased GL3 expression, suggesting the presence of a GL3 negative auto-regulatory loop (Figure 2). In addition to standard ChIP experiments, genome-wide location analyses (chip-chip) resulted in the identification of several novel GL3 and GL1 targets.
