The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots

Abstract

Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis thaliana root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context. To understand the output of the PLT gradient, we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient can regulate cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, enforcing their role as master regulators of organ development.

The BABY BOOM Transcription Factor Activates the LEC1-ABI3-FUS3-LEC2 Network to Induce Somatic Embryogenesis

“…BiNGO analysis (Maere et al, 2005) of the top 1,000 potential target genes in these chromatin immunoprecipitation (ChIP) experiments was performed to identify overrepresented Gene Ontology categories (Supplemental Data Set S1; a selection of which is shown in Supplemental Table S1). Genes involved in auxin biosynthesis, transport, and signaling, as well root development, meristem initiation, and maintenance, were overrepresented in the ChIP-seq data sets, as expected from BBM's function in the root and in line with studies of other AIL proteins (Horstman et al, 2014;Santuari et al, 2016). Genes involved in adaxial/ abaxial polarity specification and shoot development also were overrepresented among BBM-bound genes (Supplemental Data Set S1; Supplemental Table S1).…”

“…ANT/AIL DNA-binding motifs were determined previously in vitro by SELEX and electrophoretic mobility shift assay (Nole-Wilson and Krizek, 2000;Yano et al, 2009;O'Malley et al, 2016;Santuari et al, 2016). MEME analysis (Bailey and Elkan, 1994) of in vivo BBM-bound regions identified an overrepresented sequence motif that resembles the ANT/AIL DNAbinding motif (Supplemental Fig.…”

“…MEME analysis (Bailey and Elkan, 1994) of in vivo BBM-bound regions identified an overrepresented sequence motif that resembles the ANT/AIL DNAbinding motif (Supplemental Fig. S1B; Santuari et al, 2016). The BBM-bound region in LEC1, LEC2, and FUS3 contains this BBM-binding motif, while the ABI3-bound region contains a slightly degenerate version thereof (Supplemental Fig.…”

Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis

“…ChIP-seq and transcriptome data sets for a number of ETT partners are already available in the public domain (Bencivenga et al, 2016;Santuari et al, 2016) and comparative studies are therefore possible to identify common targets and unravel modes of regulation. Here, we compared the list of 77 target genes bound and regulated by ETT in an IAA-dependent manner with the target gene data set of the ETT-interacting REPLUMLESS (RPL) protein (Bencivenga et al, 2016) ( Figure 5A).…”

Plant cortical microtubule dynamics and cell division plane orientation

“…High levels of PLT in the stem-cell zone and distinct nature of cell division, cell growth and division plane orientation in this zone, suggests a significant role of these transcription factors in controlling cellular processes like cell growth and cell division. Consistently, the activated target genes of the PLT transcription factors are enriched for genes involved in cell division and growth (Santuari et al, 2016). It has been shown that the expression of the PLT transcription factors strongly correlates with a transcriptional response maximum to the plant hormone auxin in the root tip (Aida et al, 2004;Xu et al, 2006).…”