Chromatin accessibility and translational landscapes of tea plants under chilling stress

Selective penetration of fullerenol through pea seed coats mitigates osmosis-repressed germination via chromatin remodeling and transcriptional reprograming

BACKGROUND

The alteration of chromatin accessibility plays an important role in plant responses to abiotic stress. Carbon-based nanomaterials (CBNMs) have attracted increasing interest in agriculture due to their potential impact on crop productivity, showcasing effects on plant biological processes at transcriptional levels; however, their impact on chromatin accessibility remains unknown.

RESULTS

This study found that fullerenol can penetrate the seed coat of pea to mitigate the reduction of seed germination caused by osmotic stress. RNA sequencing (RNA-seq) revealed that the application of fullerenol caused the high expression of genes related to oxidoreduction to return to a normal level. Assay for transposase accessible chromatin sequencing (ATAC-seq) confirmed that fullerenol application reduced the overall levels of chromatin accessibility of numerous genes, including those related to environmental signaling, transcriptional regulation, and metabolism.

CONCLUSION

This study suggests that fullerenol alleviates osmotic stress on various fronts, encompassing antioxidant, transcriptional, and epigenetic levels. This advances knowledge of the working mechanism of this nanomaterial within plant cells. © 2024 Society of Chemical Industry.

Importance of the ECM-receptor interaction for adaptive response to hypoxia based on integrated transcription and translation analysis

Low dissolved oxygen (LO) conditions represent a major environmental challenge to marine life, especially benthic animals. For these organisms, drastic declines in oxygen availability (hypoxic events) can trigger mass mortality events and thus, act as agents of selection influencing the evolution of adaptations. In sea cucumbers, one of the most successful groups of benthic invertebrates, the exposure to hypoxic conditions triggers adaptive adjustments in metabolic rates and behaviour. It is unclear, however, how these adaptive responses are regulated and the genetic mechanisms underpinning them. Here, we addressed this knowledge gap by assessing the genetic regulation (transcription and translation) of hypoxia exposure in the sea cucumber Apostichopus japonicus. Transcriptional and translational gene expression profiles under short- and long-term exposure to low oxygen conditions are tightly associated with extracellular matrix (ECM)-receptor interaction in which laminin and collagen likely have important functions. Finding revealed that genes with a high translational efficiency (TE) had a relatively short upstream open reading frame (uORF) and a high uORF normalized minimal free energy, suggesting that sea cucumbers may respond to hypoxic stress via altered TE. These results provide valuable insights into the regulatory mechanisms that confer adaptive capacity to holothurians to survive oxygen deficiency conditions and may also be used to inform the development of strategies for mitigating the harmful effects of hypoxia on other marine invertebrates facing similar challenges.

Chromatin accessibility mediated transcriptome changes contribute to flavor substance alterations and jasmonic acid hyperaccumulation during oolong tea withering process

During the oolong tea withering process, abiotic stresses induce significant changes in the content of various flavor substances and jasmonic acid (JA). However, the changes in chromatin accessibility during withering and their potential impact remain poorly understood. By integrating ATAC-seq, RNA-seq, metabolite, and hormone assays, we characterized the withering treatment-induced changes in chromatin accessibility, gene expression levels, important metabolite contents, and JA and JA-ILE contents. Additionally, we analyzed the effects of chromatin accessibility alterations on gene expression changes, content changes of important flavor substances, and JA hyperaccumulation. Our analysis identified a total of 3451 open- and 13 426 close-differentially accessible chromatin regions (DACRs) under withering treatment. Our findings indicate that close-DACRs-mediated down-regulated differentially expressed genes (DEGs) resulted in the reduced accumulation of multiple catechins during withering, whereas open-DACRs-mediated up-regulated DEGs contributed to the increased accumulation of important terpenoids, JA, JA-ILE and short-chain C5/C6 volatiles. We further highlighted important DACRs-mediated DEGs associated with the synthesis of catechins, terpenoids, JA and JA and short-chain C5/C6 volatiles and confirmed the broad effect of close-DACRs on catechin synthesis involving almost all enzymes in the pathway during withering. Importantly, we identified a novel MYB transcription factor (CsMYB83) regulating catechin synthesis and verified the binding of CsMYB83 in the promoter-DACRs regions of key catechin synthesis genes using DAP-seq. Overall, our results not only revealed a landscape of chromatin alters-mediated transcription, flavor substance and hormone changes under oolong tea withering, but also provided target genes for flavor improvement breeding in tea plant.

Integrated analysis of transcriptome, translatome and proteome reveals insights into yellow catfish (Pelteobagrus fulvidraco) brain in response to hypoxia

Brain plays a central role in adapting to environmental changes and is highly sensitive to the oxygen level. Although previous studies investigated the molecular response of brain exposure to acute hypoxia in fish, the lack of studies at the translational level hinders further understanding of the regulatory mechanism response to hypoxia from multi-omics levels. Yellow catfish (Pelteobagrus fulvidraco) is an important freshwater aquaculture species; however, hypoxia severely restricts the sustainable development of its breeding industry. In the present study, the transcriptome, translatome, and proteome were integrated to study the global landscapes of yellow catfish brain response to hypoxia. The evidently increased amount of cerebral cortical cells with oedema and pyknotic nuclei has been observed in hypoxia group of yellow catfish. A total of 2750 genes were significantly changed at the translational level. Comparative transcriptional and translational analysis suggested the HIF-1 signaling pathway, autophagy and glycolysis/gluconeogenesis were up-regulated after hypoxia exposure. KEGG enrichment of translational efficiency (TE) differential genes suggested that the lysosome and autophagy were highly enriched. Our result showed that yellow catfish tends to inhibit the TE of genes by increasing the translation of uORFs to adapt to hypoxia. Correlation analysis showed that transcriptome and translatome exhibit higher correlation. In summary, this study demonstrated that hypoxia dysregulated the cerebral function of yellow catfish at the transcriptome, translatome, and proteome, which provides a better understanding of hypoxia adaptation in teleost.

Translational Landscape of Medicago truncatula Seedlings under Salt Stress

The expression of plant genes under salt stress at the transcriptional level has been extensively studied. However, less attention has been paid to gene translation regulation under salt stress. In this study, Ribo-seq and RNA-seq analyses were conducted in Medicago truncatula seedlings grown under normal and salt stress conditions. The results showed that salt stress significantly altered the gene expression at the transcriptional and translational levels, with 2755 genes showing significant changes only at the translational level. Salt stress significantly inhibited the gene translation efficiency. Small ORFs (including uORFs in the 5'UTR, dORFs in 3'UTRs, and sORFs in lncRNAs) were identified throughout the genome of M. truncatula. The efficiency of gene translation was simultaneously regulated by the uORFs, dORFs, and miRNAs. In summary, our results provide valuable information about translatomic resources and new insights into plant responses to salt stress.

Low temperature-induced regulatory network rewiring via WRKY regulators during banana peel browning

Banana (Musa spp.) fruits, as typical tropical fruits, are cold sensitive, and lower temperatures can disrupt cellular compartmentalization and lead to severe browning. How tropical fruits respond to low temperature compared to the cold response mechanisms of model plants remains unknown. Here, we systematically characterized the changes in chromatin accessibility, histone modifications, distal cis-regulatory elements, transcription factor binding, and gene expression levels in banana peels in response to low temperature. Dynamic patterns of cold-induced transcripts were generally accompanied by concordant chromatin accessibility and histone modification changes. These upregulated genes were enriched for WRKY binding sites in their promoters and/or active enhancers. Compared to banana peel at room temperature, large amounts of banana WRKYs were specifically induced by cold and mediated enhancer-promoter interactions regulating critical browning pathways, including phospholipid degradation, oxidation, and cold tolerance. This hypothesis was supported by DNA affinity purification sequencing, luciferase reporter assays, and transient expression assay. Together, our findings highlight widespread transcriptional reprogramming via WRKYs during banana peel browning at low temperature and provide an extensive resource for studying gene regulation in tropical plants in response to cold stress, as well as potential targets for improving cold tolerance and shelf life of tropical fruits.

Haplotype-Resolution Transcriptome Analysis Reveals Important Responsive Gene Modules and Allele-Specific Expression Contributions under Continuous Salt and Drought in Camellia sinensis

The tea plant, Camellia sinensis (L.) O. Kuntze, is one of the most important beverage crops with significant economic and cultural value. Global climate change and population growth have led to increased salt and drought stress, negatively affecting tea yield and quality. The response mechanism of tea plants to these stresses remains poorly understood due to the lack of reference genome-based transcriptional descriptions. This study presents a high-quality genome-based transcriptome dynamic analysis of C. sinensis' response to salt and drought stress. A total of 2244 upregulated and 2164 downregulated genes were identified under salt and drought stress compared to the control sample. Most of the differentially expression genes (DEGs) were found to involve divergent regulation processes at different time points under stress. Some shared up- and downregulated DEGs related to secondary metabolic and photosynthetic processes, respectively. Weighted gene co-expression network analysis (WGCNA) revealed six co-expression modules significantly positively correlated with C. sinensis' response to salt or drought stress. The MEpurple module indicated crosstalk between the two stresses related to ubiquitination and the phenylpropanoid metabolic regulation process. We identified 1969 salt-responsive and 1887 drought-responsive allele-specific expression (ASE) genes in C. sinensis. Further comparison between these ASE genes and tea plant heterosis-related genes suggests that heterosis likely contributes to the adversity and stress resistance of C. sinensis. This work offers new insight into the underlying mechanisms of C. sinensis' response to salt and drought stress and supports the improved breeding of tea plants with enhanced salt and drought tolerance.

The BrAFP1 promoter drives gene-specific expression in leaves and stems of winter rapeseed (Brassica rapa L.) under cold induction

BrAFP1(antifreeze protein in winter turnip rape) effectively limits recrystallization and growth of ice crystals. The BrAFP1 expression level determines whether the freezing-induced damage to winter turnip rape plants is avoided. This study analyzed the activity of the BrAFP1 promoters of several varieties at various cold tolerance levels. We cloned the BrAFP1 promoters from five winter rapeseed cultivars. The multiple sequence alignment revealed the presence of one inDel and eight single-nucleotide mutations (SNMs) in the promoters. One of these SNMs (base mutation from C to T) at the -836 site away from the transcription start site (TSS) enhanced the transcriptional activity of the promoter at low temperature. The promoter activity was specific in cotyledons and hypocotyls during the seedling stage and was referential in stems, leaves, and flowers but not the calyx. This consequently drove the downstream gene to be specifically expressed in leaves and stems, but not in roots at low temperature. The truncated fragment GUS staining assays revealed that the core region of the BrAFP1 promoter was included in the 98 bp fragment from the -933 to -836 site away from the TSS, which was necessary for transcriptional activity. The LTR element of the promoter significantly enhanced expression at low temperatures and suppressed expression at moderate temperatures. Moreover, the BrAFP1 5'-UTR intron bound the scarecrow-like transcription factor and enhanced expression at low temperature.

The spatiotemporal profile of Dendrobium huoshanense and functional identification of bHLH genes under exogenous MeJA using comparative transcriptomics and genomics

Introduction

Alkaloids are one of the main medicinal components of Dendrobium species. Dendrobium alkaloids are mainly composed of terpene alkaloids. Jasmonic acid (JA) induce the biosynthesis of such alkaloids, mainly by enhancing the expression of JA-responsive genes to increase plant resistance and increase the content of alkaloids. Many JA-responsive genes are the target genes of bHLH transcription factors (TFs), especially the MYC2 transcription factor.

Methods

In this study, the differentially expressed genes involved in the JA signaling pathway were screened out from Dendrobium huoshanense using comparative transcriptomics approaches, revealing the critical roles of basic helix-loop-helix (bHLH) family, particularly the MYC2 subfamily.

Results and discussion

Microsynteny-based comparative genomics demonstrated that whole genome duplication (WGD) and segmental duplication events drove bHLH genes expansion and functional divergence. Tandem duplication accelerated the generation of bHLH paralogs. Multiple sequence alignments showed that all bHLH proteins included bHLH-zip and ACT-like conserved domains. The MYC2 subfamily had a typical bHLH-MYC_N domain. The phylogenetic tree revealed the classification and putative roles of bHLHs. The analysis of cis-acting elements revealed that promoter of the majority of bHLH genes contain multiple regulatory elements relevant to light response, hormone responses, and abiotic stresses, and the bHLH genes could be activated by binding these elements. The expression profiling and qRT-PCR results indicated that bHLH subgroups IIIe and IIId may have an antagonistic role in JA-mediated expression of stress-related genes. DhbHLH20 and DhbHLH21 were considered to be the positive regulators in the early response of JA signaling, while DhbHLH24 and DhbHLH25 might be the negative regulators. Our findings may provide a practical reference for the functional study of DhbHLH genes and the regulation of secondary metabolites.

Integrative transcriptomic and proteomic analyses reveal a positive role of BES1 in salt tolerance in Arabidopsis

INTRODUCTION

Salt stress is a major environmental factor limiting plant growth and development. Previous studies have indicated that the steroidal hormones-brassinosteroids (BRs) are important regulators of plant responses to salt stress. However, the underlying molecular mechanisms have not been fully understood.

METHODS

(1) Phenotypic analysis of bes1-D, BES1-RNAi and their wild-type (Col-0) under salt treatments with different concentrations of NaCl. (2) Transcriptomic and proteomic profiling of BES1-regulated genes and proteins under salt treatment; (3) qRT-PCR validation of selected BES1-regulated genes under salt stress; (4) Transient transcriptional assay of BES1 regulation on its putative target genes in Arabidopsis protoplasts; (5) Electrophoresis Mobility Shift Assay (EMSA) of BES1 binding with its potential target genes.

RESULTS AND DISCUSSION

Phenotypic analysis indicated that bes1-D, a gain-of-function mutant of the BR-regulated transcription factor BES1 in Arabidopsis showed better salt tolerance than the wild-type plant, while a BES1 RNA interference (BES1-RNAi) line was more sensitive to salt stress. Global gene expression profiling and time series clustering analyses identified a total of 1,170 genes whose expression was boosted in bes1-D under salt stress. Further GO enrichment and gene functional network analyses identified several key modules that are regulated by BES1 and most sensitive to salt stress perturbations, including stress response, response to ABA and ROS, flavonoid biosynthesis and transmembrane transport. A comparative proteomic analysis performed under the same stress conditions supported the results from the transcriptome analysis. In addition, transient gene transcription assays in Arabidopsis protoplasts and in vitro DNA binding assays verified that BES1 regulates the expression of some ion transporter genes directly and indirectly. Taken together, our results support a positive role of BES1 in plant salt tolerance.

Cytosolic and mitochondrial ribosomal proteins mediate the locust phase transition via divergence of translational profiles

The phase transition from solitary to gregarious locusts is crucial in outbreaks of locust plague, which threaten agricultural yield and food security. Research on the regulatory mechanisms of phase transition in locusts has focused primarily on the transcriptional or posttranslational level. However, the translational regulation of phase transition is unexplored. Here, we show a phase-dependent pattern at the translation level, which exhibits different polysome profiles between gregarious and solitary locusts. The gregarious locusts exhibit significant increases in 60S and polyribosomes, while solitary locusts possess higher peaks of the monoribosome and a specific "halfmer." The polysome profiles, a molecular phenotype, respond to changes in population density. In gregarious locusts, ten genes involved in the cytosolic ribosome pathway exhibited increased translational efficiency (TE). In solitary locusts, five genes from the mitochondrial ribosome pathway displayed increased TE. The high expression of large ribosomal protein 7 at the translational level promotes accumulation of the free 60S ribosomal subunit in gregarious locusts, while solitary locusts employ mitochondrial small ribosomal protein 18c to induce the assembly of mitochondrial ribosomes, causing divergence of the translational profiles and behavioral transition. This study reveals the translational regulatory mechanism of locust phase transition, in which the locusts employ divergent ribosome pathways to cope with changes in population density.

Regulatory dynamics distinguishing desiccation tolerance strategies within resurrection grasses

Desiccation tolerance has evolved recurrently in grasses using two unique strategies of either protecting or dismantling the photosynthetic apparatus to minimize photooxidative damage under life without water (anhydrobiosis). Here, we surveyed chromatin architecture and gene expression during desiccation in two closely related grasses with distinguishing desiccation tolerance strategies to identify regulatory dynamics underlying these unique adaptations. In both grasses, we observed a strong association between nearby chromatin accessibility and gene expression in desiccated tissues compared to well-watered, reflecting an unusual chromatin stability under anhydrobiosis. Integration of chromatin accessibility (ATACseq) and expression data (RNAseq) revealed a core desiccation response across these two grasses. This includes many genes with binding sites for the core seed development transcription factor ABI5, supporting the long-standing hypothesis that vegetative desiccation tolerance evolved from rewiring seed pathways. Oropetium thomaeum has a unique set of desiccation induced genes and regulatory elements associated with photoprotection, pigment biosynthesis, and response to high light, reflecting its adaptation of protecting the photosynthetic apparatus under desiccation (homoiochlorophyly). By contrast, Eragrostis nindensis has unique accessible and expressed genes related to chlorophyll catabolism, scavenging of amino acids, and hypoxia, highlighting its poikilochlorophyllous adaptations of dismantling the photosynthetic apparatus and degrading chlorophyll under desiccation. Together, our results highlight the complex regulatory and expression dynamics underlying desiccation tolerance in grasses.

Allele-specific expression and chromatin accessibility contribute to heterosis in tea plants (Camellia sinensis)

Heterosis is extensively used to improve crop productivity, yet its allelic and chromatin regulation remains unclear. Based on our resolved genomes of the maternal TGY and paternal HD, we analyzed the contribution of allele-specific expression (ASE) and chromatin accessibility of JGY and HGY, the artificial hybrids of oolong tea with the largest cultivated area in China. The ASE genes (ASEGs) of tea hybrids with maternal-biased were mainly related to the energy and terpenoid metabolism pathways, whereas the ASEGs with paternal-biased tend to be enriched in glutathione metabolism, and these parental bias of hybrids may coordinate and lead to the acquisition of heterosis in more biological pathways. ATAC-seq results showed that hybrids have significantly higher accessible chromatin regions (ACRs) compared with their parents, which may confer broader and stronger transcriptional activity of genes in hybrids. The number of ACRs with significantly increased accessibility in hybrids was much greater than decreased, and the associated alleles were also affected by differential ACRs across different parents, suggesting enhanced positive chromatin regulation and potential genetic effects in hybrids. Core ASEGs of terpene and purine alkaloid metabolism pathways with significant positive heterosis have greater chromatin accessibility in hybrids, and were potentially regulated by several members of the MYB, DOF and TRB families. The binding motif of CsMYB85 in the promoter ACR of the rate-limiting enzyme CsDXS was verified by DAP-seq. These results suggest that higher numbers and more accessible ACRs in hybrids contribute to the regulation of ASEGs, thereby affecting the formation of heterotic metabolites.

Asymmetric subgenomic chromatin architecture impacts on gene expression in resynthesized and natural allopolyploid Brassica napus

Although asymmetric subgenomic epigenetic modification and gene expression have been revealed in the successful establishment of allopolyploids, the changes in chromatin accessibility and their relationship with epigenetic modifications and gene expression are poorly understood. Here, we synthetically analyzed chromatin accessibility, four epigenetic modifications and gene expression in natural allopolyploid Brassica napus, resynthesized allopolyploid B. napus, and diploid progenitors (B. rapa and B. oleracea). “Chromatin accessibility shock” occurred in both allopolyploidization and natural evolutionary processes, and genic accessible chromatin regions (ACRs) increased after allopolyploidization. ACRs associated with H3K27me3 modifications were more accessible than those with H3K27ac or H3K4me3. Although overall chromatin accessibility may be defined by H3K27me3, the enrichment of H3K4me3 and H3K27ac and depletion of DNA methylation around transcriptional start sites up-regulated gene expression. Moreover, we found that subgenome C_n exhibited higher chromatin accessibility than A_n, which depended on the higher chromatin accessibility of C_n-unique genes but not homologous genes.

Changes in chromatin accessibility occuring during the process of allopolyploidization of Brassica napus are analysed using ATAC and ChIPseq, with differences in asymmetric chromatin accessibility between subgenomes of B. napus investigated.

Changes in Non-Volatile and Volatile Metabolites Associated with Heterosis in Tea Plants (Camellia sinensis)

Heterosis or hybrid vigor is extensively used in plant breeding. However, the contribution of metabolites to heterosis is still elusive. Here, we systematically identified the non-volatile and volatile metabolites of two hybrids and their parents in Camellia sinensis. The metabolomics analysis showed prevalent non-additive accumulation in hybrids, among which the non-additive nucleotides, alkaloids, organic acids, and tannins contribute to the positive heterosis of hybrids, including typical inosine, guanosine, adenosine, caffeine, succinic acid, adipic acid, xylonic acid, and gallic acid. The catechins and free amino acids in hybrids showed negative heterosis compared to its maternal cultivar TGY. Furthermore, the significant accumulation of non-additive terpenes combined with the mild heterosis of other types of volatiles contributes to the aroma of tea plant hybrids. The genetics of volatiles from different parents affect the aroma of hybrids processed into oolong tea. The comprehensive heterosis of these non-additive metabolites may play an important role in the formation of desirable breeding traits for hybrids. Our results provide insights into the utilization of heterosis breeding and the regulation of heterosis metabolites in tea plants.

Identification of Co-Expressed Genes Related to Theacrine Synthesis in Tea Flowers at Different Developmental Stages

Jiaocheng kucha is the first reported tea germplasm resource which contains theacrine founded in Fujian Province. Currently, the anabolic mechanism of theacrine within tea leaves is clear, but there are few studies focused on its flowers. In order to further explore the mechanism of theacrine synthesis and related genes in flowers, current study applied Jiaocheng kucha flowers (JC) as test materials and Fuding Dabaicha flowers (FD) as control materials to make transcriptome sequencing, and determination of purine alkaloid content in three different developmental periods (flower bud stage, whitening stage and full opening stage). The results showed that the flower in all stages of JC contained theacrine. The theacrine in the flower bud stage was significantly higher than in the other stages. The differentially expressed genes (DEGs) at three different developmental stages were screened from the transcriptome data, and were in a total of 5642, 8640 and 8465. These DEGs related to the synthesis of theacrine were primarily annotated to the pathways of purine alkaloids. Among them, the number of DEGs in xanthine synthesis pathway was the largest and upregulated in JC, while it was the smallest in caffeine synthesis pathway and downregulated in JC. Further weighted gene co-expression network (WGCNA) indicated that ADSL (CsTGY03G0002327), ADSL (CsTGY09G0001824) and UAZ (CsTGY06G0002694) may be a hub gene for the regulation of theacrine metabolism in JC. Our results will contribute to the identification of candidate genes related to the synthesis of theacrine in tea flowers, and explore the molecular mechanism of theacrine synthesis in JC at different developmental stages.

R2R3-MYB transcription factor family in tea plant (Camellia sinensis): Genome-wide characterization, phylogeny, chromosome location, structure and expression patterns

MYB transcription factors play essential roles in many biological processes and environmental stimuli. However, the functions of the MYB transcription factor family in tea plants have not been elucidated. Here, a total of 122 CsR2R3-MYB genes were identified from the chromosome level genome of tea plant (Camellia sinensis). The CsR2R3-MYB genes were phylogenetically classified into 25 groups. Results from the structure analysis of the gene, conserved motifs, and chromosomal distribution supported the relative conservation of the R2R3-MYB genes family in the tea plant. Synteny analysis indicated that 122, 34, and 112 CsR2R3-MYB genes were orthologous to Arabidopsis thaliana, Oryza sativa and C. sinensis var. 'huangdan' (HD), respectively. Tissue-specific expression showed that all CsR2R3-MYB genes had different expression patterns in the tea plant tissues, indicating that these genes may perform diverse functions. The expression patterns of representative R2R3-MYB genes and the regulatory network of the main anthocyanin components were analyzed, which suggested that CsMYB17 may played a key role in the regulation of cya-3-O-gal, del-3-O-gal, cya-3-O-glu and pel-3-O-glu. Results from the qRT-PCR validation of selected genes suggested that CsR2R3-MYB genes were induced in response to drought, cold, GA, and ABA treatments. Overall, this study provides comprehensive and systematic information for research on the function of R2R3-MYB genes in tea plants.