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Positional cues in pattern formation

Transcription factors (TFs) are usually localized to the nucleus and regulate gene expression. However, some TFs are found in cytoplasm and even traffic from cell to cell. MicroRNAs (miRNAs) that post-transcriptionally suppress gene expression can also act outside the site of production in some cases. Recent studies by our group and others have revealed that cell-cell trafficking of TFs and miRNAs plays important roles in root patterning.


Plant root tissues are organized into radially symmetric patterns. Among them is the endodermis that plays an important role in selective uptake of ions and nutrients to the vascular tissues. The endodermis invariably differentiates as a single cell layer adjacent to the central stele that includes vascular tissues.


Endodermis differentiation is controlled by the SHORT-ROOT (SHR) TF. SHR proteins are produced in the stele and move to the outer layer, where they promote endodermis differentiation.


In addition to the role for endodermis differentiation, SHR regulates vascular differentiation by activating miRNA production. The vascular tissues of Arabidopsis roots include two types of xylem cells, the protoxylem (PX) and the metaxylem (MX). Their differentiation status can be easily distinguished by microscopic observation of cell wall patterns. Correct patterning of PX and MX relies on restricted expression of the PHABULOSA (PHB) transcription factor to the central stele. This restriction of PHB expression domain is regulated post-transcriptionally by microRNA165 and 166 (collectively called miR165/6). Surprisingly, miR165/6 are not produced in the stele where the miRNA-mediated PHB suppression takes place, but it is produced specifically in the endodermis by the action of SHR.


In shr mutant roots, the levels of miR165/6 are severely reduced and the PHB expression domain is expanded to include the whole stele. As a result, MX differentiates in the place where PX normally forms. These observations indicate that the miR165/6 produced in the endodermis move to the stele and restrict PHB expression to the central stele. Therefore, root tissue patterning is regulated by bidirectional cell-cell signaling mediated by the mobile SHR TF and miR165/6.

Miyashima, S. et al., (2011) "Non-cell-autonomous microRNA165 acts in a dose-dependent manner to regulate multiple differentiation status in the Arabidopsis root." Development. 138, 2303-2313.  PubMed Publisher Press