Role of chromatin factors in Arabidopsis root stem cell maintenance

Abstract

Stem cells replenish the cells present in an organism throughout its lifetime and sustain growth. They have unique characteristics: the capability to self-renew and the potential to differentiate into several cell types. Recently, it has become clear that chromatin factors support these unique features in mammalian stem cells (Chapter 1). The role of chromatin factors in plant stem cell control is just starting to be revealed. In this thesis, we describe investigations on the roles of chromatin factors in Arabidopsis root stem cell maintenance. We performed a genome-wide survey of chromatin factor to identify which classes of chromatin factors could be genetically linked to stem cell action. In addition, we investigated the relationship of these chromatin factors with existing stem cell regulatory pathways. We find that several classes of chromatin factors (histone acetyltransferase GCN5, the CAF-1 complex, histone deacetylases (HDACs), PRC2 Polycomb proteins) regulate root stem cell niche maintenance. We show that GCN5 affects root stem cell niche maintenance mainly through expression regulation of stem cell transcription factor PLETHORA (PLT) (Chapter 2). The GCN5 associated factor ADA2b is not involved in stem cell niche maintenance, but mediates proliferation of the transit amplifying cells directly. Furthermore, we show that the chromatin assembly factor 1 (CAF-1) complex and RETINOBLASTOMA RELATED (RBR) repress synergistically root stem cell proliferation through regulation of stem cell niche transcription factors and promote correct differentiation (Chapter 3). The CAF-1 complex acts in the SHORTROOT (SHR)/ SCARECROW (SCR) pathway. We provide evidence that the CAF-1 complex and RBR may ensure propagation of repressive epigenetic marks at overlapping target genes together with HDACs and in this way play an important role in epigenetic stem cell control. In addition, we show that PRC2 Polycomb proteins SWINGER (SWN) and CURLY LEAF (CLF) are redundantly required to maintain the stem cells and expression of the root stem cell transcription factor SCR (Chapter 4). Our data reveal a novel function for RBR: it is redundantly required with SWN and CLF to stimulate proliferation or prevent differentiation of the transit amplifying cells. Finally, the results described in this thesis are discussed in light of recent insights into the specialized chromatin state in stem cells (Chapter 5). In conclusion, the research performed in this thesis reveals that several classes of chromatin factors are required for root stem cell maintenance and play a role in both parallel pathways known to define the root stem cells. In mammals, pluripotent stem cell transcription factors probably regulate chromatin factors to obtain a special chromatin state in ES cells. Similarly, in Arabidopsis, stem cell transcription factors are sufficient to induce root or shoot stem cells and it is an interesting possibility that they regulate chromatin factors, whereas it is already evident that chromatin factors regulate stem cell transcription factors.