Histone code dynamics during nitrogen response in tomato
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ABSTRACT:
PROVIDER: PRJNA807664 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18052900_1.fastq.gz | Fastqsanger.gz | |||
| SRR18052900_2.fastq.gz | Fastqsanger.gz | |||
| SRR18052901_1.fastq.gz | Fastqsanger.gz | |||
| SRR18052901_2.fastq.gz | Fastqsanger.gz | |||
| SRR18052902_1.fastq.gz | Fastqsanger.gz |
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Project description:In plants, environmental stimuli trigger rapid transcriptional reprogramming of relevant gene suites. Regulation occurs down to the local chromatin landscape of the genes, and while epigenetic modifications proceed in a manner dependent on specific organ and tissue contexts, detailed investigations at this level remain limited. To better understand the organ specificity of dynamic chromatin modifications in response to external signals, we treated nitrogen-limited tomato seedlings with a supply of nitrate and measured the genome-wide changes of four histone marks, the permissive histone marks H3K27ac, H3K4me3, and H3K36me3 and repressive mark H3K27me3, in shoots and roots separately. We observed dynamic histone acetylation and methylation events which are largely organ-specific in scope at functionally relevant gene loci. Integration of transcriptomic and epigenomic datasets generated from the same tissue samples revealed largely syngenetic relations between changes in transcript levels and histone modifications, with the exception of H3K27me3 where an increased level at genes up-regulated in response to nitrate supply is observed in only the shoots. This non-canonical pattern of H3K27me3 deposition could possibly function to prevent over-expression of certain activated genes. To study the determinant roles of histone code in predicting gene regulation at the genome-wide level we applied a machine learning approach. While gene regulation could be best predicted using all four histone marks together, we observed different rules regarding the importance of individual histone marks between shoots, where H3K36me3 is the most successful mark in predicting gene activation and repression events, and the roots, where H3K4me3 is the strongest individual predictor. In summary, our integrated study substantiates a view that during plant environmental responses, the histone code dynamics that govern relationships between chromatin modification and gene regulation are highly dependent on tissue specific contexts.
2023-11-08 | GSE196887 | GEO
Project description:Histone posttranslational modifications play an important role in regulating plant responses to environmental cues, however, few studies have focused on the role of histone lysine methylation in regulating plant responses to nutrient availability, especially in agriculturally important species. Here, we describe the functions of two paralogous histone lysine methyltransferases, SET Domain Group 33 (SDG33) and SDG34, in mediating nitrogen responses in tomato through genetic and transcriptome analyses. Our transcriptome analysis comparing tomato lines demonstrated that SDG33 and SDG34 have overlapping yet distinctly regulated targets in tomato. Importantly, both SDG33 and SDG34 mediate gene regulation in response to changes in nitrogen level, with organ specificity. In roots, SDG33 and SDG34 are required for the regulation of a gene network that includes nitrate transporter NRT1.1, as well as auxin responsive SAUR genes. Consistently, mutations in sdg33 or sdg34 abolish the root growth response to N. In shoots, SDG33 and SDG34 affect the expression of photosynthesis genes and chlorophyll a/b ratio in response to nitrogen. Overall, we show that SDG33 and SDG34 regulate nitrogen responsive gene expression and hence physiological responses to nitrogen nutrients in an organ specific manner in the roots and shoots.
2022-08-01 | GSE195546 | GEO
Project description:Nucleosome conformation dictates the histone code
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Project description:Histone methyltransferases SlSDG33 and SlSDG34 mediate organ-specific nitrogen responses in tomato
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Project description:Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized “codes” that are read by specialized domains (reader domains) in chromatin associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP - histone PTM] specificity, and in doing so to decipher the histone code. However, this has largely been done using a reductive approach of isolated reader domains and histone peptides, with the assumption that PTM readout is unaffected by any higher order considerations. Here we show that histone PTM specificity is in fact dependent on nucleosomal context, necessitating we re-define the ‘histone code’ concept and further interrogate it at the nucleosomal level.
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Project description:Recent studies indicate that thousands of genes are expressed from bidirectional promoters (BDPs). Gene regulation at BDPs is poorly understood, in particular how the cell is able to regulate them differently. Here we investigate the effect of histone Modifications in BDP regulation. In this study, we model the gene activity using different gene expression assays, such as RNA-Seq, GRO-cap, and CAGE around the BDP transcription start sites (TSSs) using different histone modifications in various cell types. We develop a new statistical approach that links histone modifications to gene expression at BDPs. It improves over previous methods, because it is able to capture spatial dependencies of histone modifications along a promoter and leads to more interpretable results. We predict a general histone code that is independent of transcript orientation, cell type, and promoter configuration. The histone code at BDPs reveals that promoters are regulated unidirectionally, such that the majority of histone marks associated with gene expression occur downstream of the gene's TSS. By contrasting associations of histone marks with steady-state levels of capped RNAs in CAGE and nascent capped RNAs in GRO-cap, we show which histone marks have a preference for initiating polymerases and actively elongating polymerases. Using single-cell data we show that the bidirectional histone signal of activating marks is often due averaging of a heterogeneous cell population. Our results have implications for other experiments where the relationship between histone modification and gene initiation or gene elongation is investigated on a genome-wide scale.
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Project description:Nutrient-driven histone code determines exhausted CD8+ T cell fates
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Project description:Histone post-translational modifications (PTMs) are frequently co-occurring on the same chromatin domains or even the same molecule. It is now established that these ‘histone codes’ are the result of cross-talk between enzymes that catalyse multiple PTMs with univocal readout as compared to these PTMs in isolation. Here, we performed a comprehensive identification and quantification of histone codes of the malaria parasite, Plasmodium falciparum. We used advanced quantitative middle-down proteomics to identify combinations of PTMs in both the proliferative, asexual stages and transmissible, sexual gametocyte stages of P. falciparum. We provide an updated, high-resolution compendium of 72 PTMs on H3 and H3.3, of which 30 newly identified. Several co-existing PTMs with unique stage distinction was identified, indicating that many of these combinatorial PTMs are associated to specific stages of the parasite life cycle. We focused on the code H3R17me2K18acK23ac for its unique presence in mature gametocytes; chromatin proteomics identified a gametocyte-specific SAGA-like effector complex including the transcription factor AP2-G2 which we associated to this specific histone code, as involved in regulating gene expression in mature gametocytes. Ultimately, this study unveils previously undiscovered histone PTMs and their functional relationship with co-existing partners. These results highlight that investigating chromatin regulation in the parasite using single histone PTM assays might overlook higher order gene regulation for distinct proliferation and differentiation processes.
2022-05-19 | PXD030181 | Pride
Project description:Nitrogen (N), the primary limiting factor for plant growth and yield in agriculture, has a patchy distribution in soils due to fertilizer application or decomposing organic matter. Studies in solution culture over-simplify the complex soil environment where microbial competition and spatial and temporal heterogeneity challenge roots’ ability to acquire adequate amounts of nutrients required for plant growth. In this study, various ammonium treatments (as 15N) were applied to a discrete volume of soil containing tomato (Solanum lycopersicum) roots to simulate encounters with a localized enriched patch of soil. Transcriptome analysis was used to identify genes differentially expressed in roots 53 hrs after treatment. Results: The ammonium treatments resulted in significantly higher concentrations of both ammonium and nitrate in the patch soil. The plant roots and shoots exhibited increased levels of 15N over time, indicating a sustained response to the enriched environment. Root transcriptome analysis identified 585 genes differentially regulated 53 hrs after the treatments. Nitrogen metabolism and cell growth genes were induced by the high ammonium (65 ug NH4+-N g-1 soil), while stress response genes were repressed. The complex regulation of specific transporters following the ammonium pulse reflects a simultaneous and synergistic response to rapidly changing concentrations of both forms of inorganic N in the soil patch. Transcriptional analysis of the phosphate transporters demonstrates cross-talk between N and phosphate uptake pathways and suggests that roots increase phosphate uptake via the arbuscular mycorrhizal symbiosis in response to N. Conclusion: This work enhances our understanding of root function by providing a snapshot of the response of the tomato root transcriptome to a pulse of ammonium in a complex soil environment. This response includes an important role for the mycorrhizal symbiosis in the utilization of an N patch.
2010-03-24 | GSE21020 | GEO
Project description:Cell growth rate is regulated in response to resource availability including the abundance, and molecular form, of essential nutrients. In the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen impacts both cell growth rate and mRNA expression. Disentangling causal relationships between nitrogen availability, cell growth rate and differential gene expression poses a considerable challenge. Using experimental control of cell growth rate using chemostats, we studied the effect of variation in environmental nitrogen on differential gene expression. We find that the primary determinant of nitrogen-regulated gene expression is nitrogen abundance whereas variation in nitrogen source affects the expression of only a small number of transcripts with highly specialized functions. To study the dynamics of nitrogen-responsive gene expression we perturbed steady-state nitrogen-limited chemostat cultures by addition of either proline or glutamine. Addition of either proline or glutamine to cells growing in nitrogen-limited chemostats results in repression of the nitrogen catabolite repression (NCR) regulon consistent with nitrogen abundance, and not nitrogen source, being the primary determinant of nitrogen-regulated gene expression. We find that a transition from nitrogen-limited to nitrogen-replete conditions is accompanied by rapid induction of transcripts required for protein translation. We identified a reciprocal relationship between specific regulons required for protein translation (RP and RiBi) and the NCR regulon. Using mathematical modeling we find evidence that cells adopt a metabolically inefficient growth mode during this transition. By means of high resolution time series analysis we find evidence that rapid, and potentially accelerated, mRNA degradation plays an important role in remodeling gene expression programs in response to change in environmental nitrogen. We propose that the evolutionarily conserved TORC1 signaling pathway orchestrates the balance between protein translation and assimilation of nitrogen sources at the transcriptional level to optimize rates of cell proliferation.
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