Trithorax Group Factor Research Articles

ULTRAPETALA 1 regulates the growth and development of rice plants to promote resilience to salinity stress

Rice, one of the most important agronomically crops, when challenged by high salinity affects its growth at the seedling stage and reproductive phase. Thus, investigating the intricate molecular mechanisms that regulate its developmental process throughout its life cycle is essential for better stress resilience. We have investigated the role of rice trithorax group factor ULTRAPETALA1 (OsULT1) that orchestrates rice development and stress response. A genome-wide chromatin immunoprecipitation analysis revealed OsULT1 enrichment at transcription regulators, oxidative stress signaling, ROS scavengers, and K+ uptake transporters, during salinity stress. Interestingly, loci associated with root development, plant height, inflorescence development, panicles, spikelet numbers, and seed development showed OsULT1 occupancy under control and salt stress. Expression of these genes was regulated by chromatin modifications such as H3K4me3 and H3K27me3. Further, DNA binding analysis showed OsULT1 binding at AP2/ERF core motif A/GCCGAC during salinity stress. OsULT1 overexpression causes developmental changes with enhanced plant height, increase in basal internode length, robust root architecture, and increase in tiller and panicle numbers. Moreover, OsULT1OE showed salinity tolerance with enhanced seed germination, reduced ROS content, low Na+/K+ ratio in shoot and root tissue, and improved post-stress recovery. Collectively, our results indicate that ULT1 regulates different plant developmental pathways for better protection and adaptation against environmental stress.

The trithorax group factor ULTRAPETALA1 controls flower and leaf development in woodland strawberry

The trithorax group (TrxG) factors play a critical role in the regulation of gene transcription by modulating histone methylation. However, the biological functions of the TrxG components are poorly characterized in different plant species. In this work, we identified three allelic ethyl methane-sulfonate-induced mutants P7, R67 and M3 in the woodland strawberry Fragaria vesca. These mutants show an increased number of floral organs, a lower pollination rate, raised achenes on the surface of the receptacle and increased leaf complexity. The causative gene is FvH4_6g44900, which contains severe mutations leading to premature stop codons or alternative splicing in each mutant. This gene encodes a protein with high similarity to ULTRAPETALA1, a component of the TrxG complex, and is therefore named as FveULT1. Yeast-two-hybrid and split-luciferase assays revealed that FveULT1 can physically interact with the TrxG factor FveATX1 and the PcG repressive complex 2 (PRC2) accessory protein FveEMF1. Transcriptome analysis revealed that several MADS-box genes, FveLFY and FveUFO were significantly up-regulated in fveult1 flower buds. The leaf development genes FveKNOXs, FveLFYa and SIMPLE LEAF1 were strongly induced in fveult1 leaves, and their promoter regions showed increased H3K4me3 levels and decreased H3K27me3 levels in fveult1 compared to WT. Taken together, our results demonstrate that FveULT1 is important for flower, fruit and leaf development and highlight the potential regulatory functions of histone methylation in strawberry.

Drosophila Hox genes induce melanized pseudo-tumors when misexpressed in hemocytes

Hox genes are early determinants of cell identity along the anterior–posterior body axis across bilaterians. Several late non-homeotic functions of Hox genes have emerged in a variety of processes involved in organogenesis in several organisms, including mammals. Several studies have reported the misexpression of Hox genes in a variety of malignancies including acute myeloid leukemia. The Hox genes Dfd, Ubx, abd-A and Abd-B were overexpressed via the UAS-Gal4 system using Cg-Gal4, Lsp2-Gal4, He-Gal4 and HmlD3-Gal4 as specific drivers. Genetic interaction was tested by bringing overexpression lines in heterozygous mutant backgrounds of Polycomb and trithorax group factors. Larvae were visually scored for melanized bodies. Circulating hemocytes were quantified and tested for differentiation. Pupal lethality was assessed. Expression of Dfd, Ubx and abd-A, but not Abd-B in the hematopoietic compartment of Drosophila led to the appearance of circulating melanized bodies, an increase in cell number, cell-autonomous proliferation, and differentiation of hemocytes. Pupal lethality and melanized pseudo-tumors were suppressed in Psc1 and esc2 backgrounds while polycomb group member mutations Pc1 and Su(z)123 and trithorax group member mutation TrlR85 enhanced the phenotype. Dfd, Ubx and abd-A are leukemogenic. Mutations in Polycomb and trithorax group members modulate the leukemogenic phenotype. Our RNAseq of Cg-Gal4 > UAS-abd-A hemocytes may contain genes important to Hox gene induced leukemias.

The Trithorax Group Factor ULTRAPETALA1 Regulates Developmental as Well as Biotic and Abiotic Stress Response Genes in Arabidopsis.

In eukaryotes, Polycomb group (PcG) and trithorax group (trxG) factors oppositely regulate gene transcription during development through histone modifications, with PcG factors repressing and trxG factors activating the expression of their target genes. Although plant trxG factors regulate many developmental and physiological processes, their downstream targets are poorly characterized. Here we use transcriptomics to identify genome-wide targets of the Arabidopsis thaliana trxG factor ULTRAPETALA1 (ULT1) during vegetative and reproductive development and compare them with those of the PcG factor CURLY LEAF (CLF). We find that genes involved in development and transcription regulation are over-represented among ULT1 target genes. In addition, stress response genes and defense response genes such as those in glucosinolate metabolic pathways are enriched, revealing a previously unknown role for ULT1 in controlling biotic and abiotic response pathways. Finally, we show that many ULT1 target genes can be oppositely regulated by CLF, suggesting that ULT1 and CLF may have antagonistic effects on plant growth and development in response to various endogenous and environmental cues.

ULTRAPETALA1 maintains Arabidopsis root stem cell niche independently of ARABIDOPSIS TRITHORAX1.

During plant development, morphogenetic processes rely on the activity of meristems. Meristem homeostasis depends on a complex regulatory network constituted by different factors and hormone signaling that regulate gene expression to coordinate the correct balance between cell proliferation and differentiation. ULTRAPETALA1, a transcriptional regulatory protein described as an Arabidopsis Trithorax group factor, has been characterized as a regulator of the shoot and floral meristems activity. Here, we highlight the role of ULTRAPETALA1 in root stem cell niche maintenance. We found that ULTRAPETALA1 is required to regulate both the quiescent center cell division rate and auxin signaling at the root tip. Furthermore, ULTRAPETALA1 regulates columella stem cell differentiation. These roles are independent of the ARABIDOPSIS TRITHORAX1, suggesting a different mechanism by which ULTRAPETALA1 can act in the root apical meristem of Arabidopsis. This work introduces a new component of the regulatory network needed for the root stem cell niche maintenance.

Rice Trithorax factor ULTRAPETALA 1 (OsULT1) specifically binds to “GAGAG” sequence motif present in Polycomb response elements

Co-ordinated interplay between Polycomb group (PcG) and Trithorax group (TrxG) of proteins regulate chromatin state and maintain the transcription “off” and “on” state of a gene in higher eukaryotes. Targeting PcG complex to a specific locus is mediated by DNA sequences known as Polycomb response elements. Interestingly, these PREs are also recognized by TrxG proteins to antagonise PcG mediated gene repression. In this study, we have characterised DNA binding property of rice trithorax group factor ULTRAPETALA1 (OsULT1) which has a SAND domain and B–box motif. Chromatin immunoprecipitation assay indicates cold induced enrichment of OsULT1 occupancy and a decrease in H3K27me3 mark in the promoter region of OsDREB1b gene, during transcription activation. OsULT1 binds to the cis motif “GAGAG”, and the sequence specificity is contributed mainly by the SAND domain. GAGAG is one of the cis motifs present in PREs that are recognized by Drosophila GAGA factor and Pipsqueak. Thus, binding of OsULT1 to GAGAG motif, along with a decrease in H3K27me3 suggests that OsULT1 antagonises the repressive effect of PcG complex for transcriptional activation of OsDREB1b. Moreover, OsULT1 interacts with rice SET domain-containing methyltransferase TRX1, suggesting OsULT1 is an integral part of plant Trithorax group complex. Furthermore, the increase in ULT1 levels during environmental cues suggests its involvement in the transcriptional regulation of stress responsive genes. Collectively, these results suggest that the antagonistic functions of PcG and TrxG proteins and the mechanism of recruitment of these complexes to target loci are evolutionarily conserved for gene expression regulation across kingdoms.

The ULTRAPETALA1 trxG factor contributes to patterning the Arabidopsis adaxial-abaxial leaf polarity axis

The SAND domain protein ULTRAPETALA1 (ULT1) functions as a trithorax group factor that regulates a variety of developmental processes in Arabidopsis. We have recently shown that ULT1 regulates developmental patterning in the gynoecia and leaves. ULT1 acts together with the KANADI1 (KAN1) transcription factor to pattern the apical-basal axis during gynoecium formation, whereas the 2 genes act antagonistically to pattern the adaxial-abaxial axis during both gynoecium and leaf formation. In particular, our data showed that ULT1 is necessary for the kan1 adaxialized organ phenotype. Here, we observe the internal structure of ult1, kan1 and ult1 kan1 rosette leaves to better understand the suppression of the kan1 adaxialized leaf polarity defect by ult1 mutations. Our results indicate that ULT1 and KAN1 act antagonistically to pattern the adaxial-abaxial axis in leaves by establishing the asymmetry of the internal cell layers.

EMBRYONIC FLOWER1 and ULTRAPETALA1 Act Antagonistically on Arabidopsis Development and Stress Response.

Epigenetic regulation of gene expression is of fundamental importance for eukaryotic development. EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene that participates in Polycomb group-mediated transcriptional repression of target genes such as the flower MADS box genes AGAMOUS, APETALA3, and PISTILLATA. Here, we investigated the molecular mechanism underlying the curly leaf and early flowering phenotypes caused by reducing EMF1 activity in the leaf primordia of LFYasEMF1 transgenic plants and propose a combined effect of multiple flower MADS box gene activities on these phenotypes. ULTRAPETALA1 (ULT1) functions as a trithorax group factor that counteracts Polycomb group action in Arabidopsis (Arabidopsis thaliana). Removing ULT1 activity rescues both the abnormal developmental phenotypes and most of the misregulated gene expression of LFYasEMF1 plants. Reducing EMF1 activity increases salt tolerance, an effect that is diminished by introducing the ult1-3 mutation into the LFYasEMF1 background. EMF1 is required for trimethylating lysine-27 on histone 3 (H3K27me3), and ULT1 associates with ARABIDOPSIS TRITHORAX1 (ATX1) for trimethylating lysine-3 on histone 4 (H3K4me3) at flower MADS box gene loci. Reducing EMF1 activity decreases H3K27me3 marks and increases H3K4me3 marks on target gene loci. Removing ULT1 activity has the opposite effect on the two histone marks. Removing both gene activities restores the active and repressive marks to near wild-type levels. Thus, ULT1 acts as an antirepressor that counteracts EMF1 action through modulation of histone marks on target genes. Our analysis indicates that, instead of acting as off and on switches, EMF1 and ULT1 mediate histone mark deposition and modulate transcriptional activities of the target genes.

The SAND domain protein ULTRAPETALA1 acts as a trithorax group factor to regulate cell fate in plants

During development, trithorax group (trxG) chromatin remodeling complexes counteract repression by Polycomb group (PcG) complexes to sustain active expression of key regulatory genes. Although PcG complexes are well characterized in plants, little is known about trxG activities. Here we demonstrate that the Arabidopsis SAND (Sp100, AIRE-1, NucP41/75, DEAF-1) domain protein ULTRAPETALA1 (ULT1) functions as a trxG factor that counteracts the PcG-repressive activity of CURLY LEAF. In floral stem cells, ULT1 protein associates directly with the master homeotic locus AGAMOUS, inducing its expression by regulating its histone methylation status. Our analysis introduces a novel mechanism that mediates epigenetic switches controlling post-embryonic stem cell fates in plants.

Chromatin multiprotein complexes involved in the maintenance of transcription patterns

In Drosophila, the maintenance of active and inactive patterns of gene expression during development involves the activity of two genetically complex systems. Molecular analysis of the components, apparently acting in large multiprotein complexes, has allowed a substantial advancement in our understanding of the role of chromatin higher order structures in gene regulation and nuclear organization. The Polycomb-group factors induce heterochromatin-like structures on genes that need to be stably and heritably inactivated. The role of the trithorax-group factors is to counteract these repressed chromatin domains and thus to render the genes accessible to activating factors.