Positive feedback and feedforward loops between PERIANTHIA, WUSCHEL-RELATED HOMEOBOX5 and GRF-INTERACTING FACTOR 1 modulate gene expression and function in the Arabidopsis root

Abstract

The Arabidopsis root meristem consists of populations of stem cells that surround the mitotically less active cells known as the Quiescent Center (QC). The QC maintains the stem cells in a noncell-autonomous manner through the function of the transcription factor (TF) WUSCHEL-RELATED HOMEOBOX5 (WOX5), which is required for columella stem cell (CSC) maintenance. However, whether WOX5 has a regulatory role in any other adjacent stem cells is less understood. To this end, we identified a set of TFs downstream of WOX5 in both QC and Cortex Endodermis Initial (CEI) cells. We then utilized Gene Regulatory Network (GRN) inference to identify GRF-INTERACTING FACTOR 1 (GIF1) as a key gene involved in positive feedback and feedforward loops with WOX5 as well as another stem cell regulator, PERIANTHIA (PAN). Finally, we constructed an ordinary differential equation model based on this inferred GRN to simulate GIF1, PAN, and WOX5 expression over time, which suggests the precise temporal expression of WOX5 and GIF1 is important to sustain QC function.2

Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks

“…We next wanted to identify if the most biologically important genes in the network were cell-specific, cell-ubiquitous, or both, as most results in animals assume that core TFs must be expressed in a cell-specific manner 1 . To predict biological significance, we developed a Network Motif Score (NMS) to quantifies the number of times each gene appears in certain network motifs, such a feedback and feedforward loops 12 . These motifs were chosen as they were significantly enriched in our biological network versus a random network of the same size, and have been shown to often contain genes that have important biological functions 13–15 (Extended Data Fig 2).…”