Plant stem cell homeostasys: Phylogeny and expression pattern of different components.

In Arabidopsis, the shoot apical meristem (SAM) homeostasis is finely regulated by the WUSCHEL-CLAVATA antagonism. WUSCHEL (WUS) encodes for a homeodomain protein essential for the SAM maintenance and its expression marks the organizing center (OC). On the other hand, the interaction between the three CLAVATA (CLV) proteins, which all together code for a heterodimeric transmembrane leucin-rich repeat (LRR) receptor like kinase (CLV1-2) and its specific ligand (CLV3), correctly restricts the WUS expression to the OC. In contrast to Arabidopsis, in maize two different WUS orthologs and a single CLV1 ortholog, Thick tassel Dwarf1 (TD1), have been so far characterized. Like in Arabidopsis, the TD1 and ZmWUS2 expression domains overlap but, unlike Arabidopsis, their expression is detected in cells recruited for leaf primordia. Conversely, ZmWUS1 is expressed within the SAM dome, not in a OC-type manner but rather in a dynamic fashion that always correlates to phytomer establishment. The expression of the single CLV1 ortholog TD1 does not overlap with ZmWUS1 expression domain, leaving an open question over the putative regulator of ZmWUS1 function. To answer this question, the closest TD1 paralogs were identified and their expression pattern elucidated. Unfortunately, none of the three maize candidate genes identified has shown the potential to regulate ZmWUS1 activity, indicating that none of the closest CLV1 relatives in maize are able to regulate ZmWUS1 activity. WUSCHEL is the founding member of a large gene family, the WUSCHEL-related homeobox (WOX) genes, which appear to be involved in several aspects of plant development, from defining the organizers of the shoot and root apical meristems, to conferring distinct cell fates as early as the 2-cell stage during Arabidopsis embryogenesis. The WOX gene family is present throughout the plant kingdom, from the most basal algae and land plants to the most evolved angiosperms. As the members of this gene family take part in key plant developmental aspects, it is intriguing to study the evolution of the WOX gene family. In this respect, the lycophyte scenario is described in this work, in which both Selaginella kraussiana and S.moellendorffii has been the object of study. As for moss Physcomitrella patens, also the Selaginella WOX genes belong to the WOX13-like clade. S.moellendorffii genome has nine putative WOX homeodomains, six of them grouping together in a S.moellendorffii specific WOX13 sister group, whereas only three WOX-like gene were identified by degenerate primer PCR in S.kraussiana, all belonging to the WOX13-like clade. Despite the expression analysis of the three S.kraussiana WOX13-like genes and their S.moellendorffii closer orthologs demonstrate their subfunctionalization and their high conservation through the Selaginellaceae evolution, the phylogenetic reconstruction is in favor of the presence of only a single ancestor WOX13-like gene before the separation of the lycophyte and euphyllophyte lineage, which was probably present from the dawn of the plant kingdom

TCP Transcription Factor, BRANCH ANGLE DEFECTIVE 1 (BAD1), Is Required for Normal Tassel Branch Angle Formation in Maize

In grass inflorescences, a structure called the “pulvinus” is found between the inflorescence main stem and lateral branches. The size of the pulvinus affects the angle of the lateral branches that emerge from the main axis and therefore has a large impact on inflorescence architecture. Through EMS mutagenesis we have identified three complementation groups of recessive mutants in maize having defects in pulvinus formation. All mutants showed extremely acute tassel branch angles accompanied by a significant reduction in the size of the pulvinus compared with normal plants. Two of the complementation groups correspond to mutations in the previously identified genes, RAMOSA2 (RA2) and LIGULELESS1 (LG1). Mutants corresponding to a third group were cloned using mapped-based approaches and found to encode a new member of the plant-specific TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL NUCLEAR ANTIGEN FACTOR) family of DNA-binding proteins, BRANCH ANGLE DEFECTIVE 1 (BAD1). BAD1 is expressed in the developing pulvinus as well as in other developing tissues, including the tassels and juvenile leaves. Both molecular and genetics studies show that RA2 is upstream of BAD1, whereas LG1 may function in a separate pathway. Our findings demonstrate that BAD1 is a TCP class II gene that functions to promote cell proliferation in a lateral organ, the pulvinus, and influences inflorescence architecture by impacting the angle of lateral branch emergence

Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis

Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase. hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers

Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis

International audienceEnhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase І hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers