Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects.

SWI2/SNF2 chromatin remodeling ATPases play important roles in plant and metazoan development. Whereas metazoans generally encode one or two SWI2/SNF2 ATPase genes, Arabidopsis encodes four such chromatin regulators: the well-studied BRAHMA and SPLAYED ATPases, as well as two closely related non-canonical SWI2/SNF2 ATPases, CHR12 and CHR23. No developmental role has as yet been described for CHR12 and CHR23. Here, we show that although strong single chr12 or chr23 mutants are morphologically indistinguishable from the wild type, chr12 chr23 double mutants cause embryonic lethality. The double mutant embryos fail to initiate root and shoot meristems, and display few and aberrant cell divisions. Weak double mutant embryos give rise to viable seedlings with dramatic defects in the maintenance of both the shoot and the root stem cell populations. Paradoxically, the stem cell defects are correlated with increased expression of the stem cell markers WUSCHEL and WOX5. During subsequent development, the meristem defects are partially overcome to allow for the formation of very small, bushy adult plants. Based on the observed morphological defects, we named the two chromatin remodelers MINUSCULE 1 and 2. Possible links between minu1 minu2 defects and defects in hormone signaling and replication-coupled chromatin assembly are discussed.

Histone modifications and dynamic regulation of genome accessibility in plants.

In all eukaryotes chromatin physically restricts the accessibility of the genome to regulatory proteins such as transcription factors. Plant model systems have been instrumental in demonstrating that this restriction is dynamic and changes during development and in response to exogenous cues. Among the multiple epigenetic mechanisms that alter chromatin to regulate gene expression, histone modifications play a major role. Recent studies in Arabidopsis have provided the first genome-wide histone modification maps, revealed important biological roles for histone modifications, and advanced our understanding of stimulus-dependent changes in histone modifications.

Unique, shared, and redundant roles for the Arabidopsis SWI/SNF chromatin remodeling ATPases BRAHMA and SPLAYED.

Chromatin remodeling is emerging as a central mechanism for patterning and differentiation in multicellular eukaryotes. SWI/SNF chromatin remodeling ATPases are conserved in the animal and plant kingdom and regulate transcriptional programs in response to endogenous and exogenous cues. In contrast with their metazoan orthologs, null mutants in two Arabidopsis thaliana SWI/SNF ATPases, BRAHMA (BRM) and SPLAYED (SYD), are viable, facilitating investigation of their role in the organism. Previous analyses revealed that syd and brm null mutants exhibit both similar and distinct developmental defects, yet the functional relationship between the two closely related ATPases is not understood. Another central question is whether these proteins act as general or specific transcriptional regulators. Using global expression studies, double mutant analysis, and protein interaction assays, we find overlapping functions for the two SWI/SNF ATPases. This partial diversification may have allowed expansion of the SWI/SNF ATPase regulatory repertoire, while preserving essential ancestral functions. Moreover, only a small fraction of all genes depends on SYD or BRM for expression, indicating that these SWI/SNF ATPases exhibit remarkable regulatory specificity. Our studies provide a conceptual framework for understanding the role of SWI/SNF chromatin remodeling in regulation of Arabidopsis development.

A role for chromatin remodeling in regulation of CUC gene expression in the Arabidopsis cotyledon boundary.

The CUP-SHAPED COTYLEDON (CUC) genes CUC1, CUC2 and CUC3 act redundantly to control cotyledon separation in Arabidopsis. In order to identify novel regulators of this process, we have performed a phenotypical enhancer screen using a null allele of cuc2, cuc2-1. We identified three nonsense alleles of AtBRM, an Arabidopsis SWI/SNF chromatin remodeling ATPase, that result in strong cotyledon fusion in cuc2-1. atbrm also enhances cotyledon fusion in loss-of-function cuc1 and cuc3 mutants, suggesting a general requirement for this ATPase in cotyledon separation. By contrast, a null allele of SPLAYED (SYD), the closest homolog of AtBRM in Arabidopsis, enhances only the loss-of-function cuc1 mutant. By investigating the activities of the CUC promoters in the cotyledon boundary during embryogenesis in sensitized backgrounds, we demonstrate that AtBRM upregulates the transcription of all three CUC genes, whereas SYD upregulates the expression of CUC2. Our results uncover a specific role for both chromatin remodeling ATPases in the formation and/or maintenance of boundary cells during embryogenesis.

The role of SEUSS in auxin response and floral organ patterning.

Genetic and physiological analyses implicate auxin flux in patterning, initiation and growth of floral organs. Within the Arabidopsis flower, the ETTIN/ARF3 transcription factor responds to auxin to effect perianth organ number and reproductive organ differentiation. This work describes a modifier of ettin that causes filamentous, mispositioned outer whorl organs and reduced numbers of malformed stamens in the double mutant. The modifier was discovered to be a new allele of the seuss (seu) mutant. SEU encodes a novel protein that is predicted to transcriptionally co-repress the AGAMOUS floral organ identity gene. The effects of seu on ett are shown to be independent of the SEU-AG pathway. Furthermore, morphological, physiological and genetic evidence implicate SEU in auxin-regulated growth and development. seu has a pleiotropic phenotype that includes reductions in several classic auxin responses such as apical dominance, lateral root initiation, sensitivity to exogenous auxin and activation of the DR5 auxin response reporter. seu displays a synergistic interaction with the auxin response mutant pinoid, producing flowers with few outer whorl organs. Collectively, these data suggest that SEU is a novel factor affecting auxin response. A model is proposed in which SEU functions jointly with ETT in auxin response to promote floral organ patterning and growth.

Identification of a developmental transition in plasmodesmatal function during embryogenesis in Arabidopsis thaliana.

Plasmodesmata provide routes for communication and nutrient transfer between plant cells by interconnecting the cytoplasm of adjacent cells. A simple fluorescent tracer loading assay was developed to monitor patterns of cell-to-cell transport via plasmodesmata specifically during embryogenesis. A developmental transition in plasmodesmatal size exclusion limit was found to occur at the torpedo stage of embryogenesis in Arabidopsis; at this time, plasmodesmata are down-regulated, allowing transport of small (approx. 0.5 kDa) but not large (approx. 10 kDa) tracers. This assay system was used to screen for embryo-defective mutants, designated increased size exclusion limit of plasmodesmata (ise), that maintain dilated plasmodesmata at the torpedo stage. The morphology of ise1 and ise2 mutants discussed here resembled that of the wild-type during embryo development, although the rate of their embryogenesis was slower. The ISE1 gene was mapped to position 13 cM on chromosome I using PCR-based biallelic markers. ise2 was found to be allelic to the previously characterized mutant emb25 which maps to position 100 cM on chromosome I. The results presented have implications for intercellular signaling pathways that regulate embryonic development, and furthermore represent the first attempt to screen directly for mutants of Arabidopsis with altered size exclusion limit of plasmodesmata.