Reorganization of three-dimensional chromatin architecture in<i>Medicago truncatula</i>under phosphorus deficiency

Wang, Tianzuo; Wang, Jing; Chen, Li; Yao, Jiaying; Yuan, Zan; Zhang, Dong; Zhang, Wenhao

doi:10.1093/jxb/erac517

Cited by 3 publications

(3 citation statements)

References 59 publications

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“…Significantly higher gene expression levels were found in the A compartments under both low-and normal-Pi conditions than in the B compartments (Figure 2b). Certain earlier investigations have also revealed parallel outcomes in maize and other plant species, indicating notably elevated gene expression levels in A compartments compared to B compartments (Dong et al, 2017(Dong et al, , 2018Wang et al, 2018Wang et al, , 2023. Similarly, levels of mCHH, mCHG, and mCG were significantly higher in compartments A than in B, with the most drastic decrease and the largest range in difference between the compartments in mCHH (Figure 2a,b); mCG and mCHG levels differed significantly between compartments A and B, but the range was small (Figure 2b).…”

Section: Gene Expression and Methylation Patterns In The A/b Compartm...mentioning

confidence: 80%

“…In this study, the partition of compartments A and B remained unchanged between low‐ and normal‐Pi conditions, with no inverted regions between the compartments observed under these two nutritional conditions (Figure 2a; Figure S1). In a recent study conducted in Medicago truncatula , it was demonstrated that the partitioning of A/B compartments remained consistent under both low and normal phosphorus conditions, with the exception of a few minor intervals that exhibited a shift between these two conditions (Wang et al., 2023).…”

Section: Resultsmentioning

confidence: 97%

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Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize

Luo,

Zhang,

et al. 2023

The Plant Journal

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SUMMARYChromatin in eukaryotes folds into a complex three‐dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low‐Pi treatment led to greater chromatin volume. Furthermore, low‐Pi stress increased the insulation score and the number of TAD‐like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD‐like boundaries, whereas RdDM peak levels at conserved TAD‐like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome‐wide RdDM sites near TAD‐like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low‐Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low‐Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP‐seq results revealed that ZmDDM1A could bind to Pi‐ and root development‐related genes. Strong associations were found between interacting genes in significantly different chromatin‐interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low‐Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.

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Section: Gene Expression and Methylation Patterns In The A/b Compartm...mentioning

confidence: 80%

Section: Resultsmentioning

confidence: 97%

Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize

Luo,

Zhang,

et al. 2023

The Plant Journal

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“…Furthermore, the functional role of the ABCG40 transporter is implicated in importing ABA to stomatal cells and drought stress [ 112 ]. In Medicago, the overexpression of the Chr6g0452171 gene that encodes ABC transporter B family protein enriched the histone mark under phosphorus deficiency (PD) and their possible role in PD-induced root system architecture (RSA) remodeling has been reported [ 113 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

Ayyappan,

Sripathi,

Xie

et al. 2024

BMC Genomics

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Background Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress. Results In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls. Conclusion Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.

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Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation

Yan,

Wang,

Feng

et al. 2023

Biotechnol Biofuels

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Background Genomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized. Results Accordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the ‘fatty acid metabolism’, ‘response to stress’, ‘carbon fixation’ and ‘photosynthesis’ functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression. Conclusions Overall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.

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Reorganization of three-dimensional chromatin architecture inMedicago truncatulaunder phosphorus deficiency

Cited by 3 publications

References 59 publications

Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize

Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize

Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation

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