Similar Datasets
Project description:To elucidate the epigenetic regulation of salt-responsive genes helps to understand the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms function in regulating the salt-responsive genes in rice and other crops at a global level. In this study, we mainly focused on dynamic changes in transcriptome and histone marks between rice leaf and root tissues during salt treatment by using RNA-seq and ChIP-seq approaches. We demonstrated that the majority of salt-related differentially expressed genes (DEGs) display tissue-dependent changes. Similarly, tissue-dependent chromatin changes have been detected between leaf and root tissues during salt treatment. Most importantly, our study indicates that chromatin states with a combination of marks, rather than an individual mark, most likely play crucial roles in regulating differential expression of salt-responsive genes between leaf and root tissues. Especially, a special CS containing bivalent marks, H3K4me3 and H3K27me3 with a functional exclusion with each other, displays distinct functions in regulating expression of DEGs between leaf and root tissues, H3K27me3-related repressive mark mainly regulates expression of DEGs in root, but H3K4me3-releated active mark dominantly functions in regulation of down-regulated genes and possibly antagonize the repressive role of H3K27me3 in up-regulated genes in leaf. Thus, our findings indicate salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice, which provides new insights in the understanding of chromatin-based epigenetic mechanisms that confer salt tolerance in plants.
2019-06-19 | GSE109616 | GEO
Project description:To elucidate the epigenetic regulation of salt-responsive genes helps to understand the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms function in regulating the salt-responsive genes in rice and other crops at a global level. In this study, we mainly focused on dynamic changes in transcriptome and histone marks between rice leaf and root tissues during salt treatment by using RNA-seq and ChIP-seq approaches. We demonstrated that the majority of salt-related differentially expressed genes (DEGs) display tissue-dependent changes. Similarly, tissue-dependent chromatin changes have been detected between leaf and root tissues during salt treatment. Most importantly, our study indicates that chromatin states with a combination of marks, rather than an individual mark, most likely play crucial roles in regulating differential expression of salt-responsive genes between leaf and root tissues. Especially, a special CS containing bivalent marks, H3K4me3 and H3K27me3 with a functional exclusion with each other, displays distinct functions in regulating expression of DEGs between leaf and root tissues, H3K27me3-related repressive mark mainly regulates expression of DEGs in root, but H3K4me3-releated active mark dominantly functions in regulation of down-regulated genes and possibly antagonize the repressive role of H3K27me3 in up-regulated genes in leaf. Thus, our findings indicate salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice, which provides new insights in the understanding of chromatin-based epigenetic mechanisms that confer salt tolerance in plants.
2019-06-19 | GSE109617 | GEO
Project description:Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice
| PRJNA431536 | ENA
Project description:Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [RNA-Seq]
| PRJNA431539 | ENA
Project description:Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [ChIP-Seq]
| PRJNA431540 | ENA
Project description:Cultivated soybean (Glycine max (L.)), the world's most important legume crop, has high-to-moderate salt sensitivity. Being the frontier for sensing and controlling solute transport, membrane proteins could be involved in cell signaling, osmoregulation, and stress-sensing mechanisms, but their roles in abiotic stresses are still largely unknown. By analyzing salt-induced membrane proteomic changes in the roots and leaves of salt-sensitive soybean cultivar (C08) seedlings germinated under NaCl, we detected 972 membrane proteins, with those present in both leaves and roots annotated as receptor kinases, calcium-sensing proteins, abscisic acid receptors, cation and anion channel proteins, proton pumps, amide and peptide transporters, and vesicle transport-related proteins etc. Endocytosis, linoleic acid metabolism, and fatty acid biosynthesis pathway-related proteins were enriched in roots whereas phagosome, spliceosome and soluble NSF attachment protein receptor (SNARE) interaction-related proteins were enriched in leaves. Using label-free quantitation, 129 differentially expressed membrane proteins were found in both tissues upon NaCl treatment. Additionally, the 140 NaCl-induced proteins identified in roots and 57 in leaves are vesicle-, mitochondrial-, and chloroplast-associated membrane proteins and those with functions related to ion transport, protein transport, ATP hydrolysis, protein folding, and receptor kinases, etc. Our proteomic results were verified against corresponding gene expression patterns from published C08 RNA-seq data, demonstrating the importance of solute transport and sensing in salt stress responses.
| S-EPMC9655375 | biostudies-literature
Project description:Separation of proteins based on the physicochemical properties with different molecular weight and isoelectric points would be more accurate. In the current research, the 45-day-old seedlings were treated with 0 (control) and 12 dS m(-1) of sodium chloride in the hydroponic system. After 15 days of salt exposure, the total protein of the fresh leaves and roots was extracted and analyzed using two-dimensional electrophoresis system (2-DE). The analysis led to the detection of 32 induced proteins (19 proteins in leaf and 13 proteins in the root) as well as 12 upregulated proteins (four proteins in leaf and eight proteins in the root) in the salt-treated plants. Of the 44 detected proteins, 12 were sequenced, and three of them matched with superoxide dismutase, ascorbate peroxidase and ribulose-1, 5-bisphosphate oxygenase whereas the rest remained unknown. The three known proteins associate with plants response to environmental stresses and could represent the general stress proteins in the present study too. In addition, the proteomic feedback of different accessions of A. paniculata to salt stress can potentially be used to breed salt-tolerant varieties of the herb.
| S-EPMC4244106 | biostudies-literature
Project description:Senescence, a highly programmed process, largely determines yield and quality of crops. However, knowledge about the onset and progression of leaf senescence in crop plants is still limited. Here, we report that salt-induced protein (salT), a new gene, may be involved in leaf senescence. Overexpressing salT could prolong the duration of leaves with higher concentrations of chlorophyll compared with the wild type. Moreover, overexpression of salT could delay the senescence of rice leaves though the inhibition of senescence associated genes (SAGs). Overall, the characterization of salT suggested that it is a new gene affecting the leaf senescence induced by natural and dark conditions.
| S-EPMC6428123 | biostudies-literature
Project description:Salt stress is a major constraint on plant growth and yield. Nitrogen (N) fertilizers are known to alleviate salt stress. However, the underlying molecular mechanisms remain unclear. Here, we show that nitrate-dependent salt tolerance is mediated by OsMADS27 in rice. The expression of OsMADS27 is specifically induced by nitrate. The salt-inducible expression of OsMADS27 is also nitrate dependent. OsMADS27 knockout mutants are more sensitive to salt stress than the wild type, whereas OsMADS27 overexpression lines are more tolerant. Transcriptomic analyses revealed that OsMADS27 upregulates the expression of a number of known stress-responsive genes as well as those involved in ion homeostasis and antioxidation. We demonstrate that OsMADS27 directly binds to the promoters of OsHKT1.1 and OsSPL7 to regulate their expression. Notably, OsMADS27-mediated salt tolerance is nitrate dependent and positively correlated with nitrate concentration. Our results reveal the role of nitrate-responsive OsMADS27 and its downstream target genes in salt tolerance, providing a molecular mechanism for the enhancement of salt tolerance by nitrogen fertilizers in rice. OsMADS27 overexpression increased grain yield under salt stress in the presence of sufficient nitrate, suggesting that OsMADS27 is a promising candidate for the improvement of salt tolerance in rice.
| S-EPMC10030316 | biostudies-literature
Project description:Inulin- and neoseries-type fructans [fructooligosaccharides (FOS) and fructopolysaccharides] accumulate in storage roots of asparagus (Asparagus officinalis L.), which continue to grow throughout the lifespan of this perennial plant. However, little is known about the storage of fructans at the spatial level in planta, and the degree of control by the plant is largely uncertain. We have utilized mass spectrometry imaging (MSI) to resolve FOS distribution patterns in asparagus roots (inner, middle, and outer tissues). Fructan and proteome profiling were further applied to validate the differential abundance of various fructan structures and to correlate observed tissue-specific metabolite patterns with the abundance of related fructan biosynthesis enzymes. Our data revealed an increased abundance of FOS with higher degree of polymerization (DP > 5) and of fructopolysaccharides (DP11 to DP17) towards the inner root tissues. Three isoforms of fructan:fructan 6G-fructosyltransferase (6G-FFT), forming 6G-kestose with a β (2-6) linkage using sucrose as receptor and 1-kestose as donor, were similarly detected in all three root tissues. In contrast, one ß-fructofuranosidase, which likely exhibits fructan:fructan 1-fructosyltransferase (1-FFT) activity, showed very high abundance in the inner tissues and lower levels in the outer tissues. We concluded a tight induction of the biosynthesis of fructans with DP > 5, following a gradient from the outer root cortex to the inner vascular tissues, which also correlates with high levels of sucrose metabolism in inner tissues, observed in our study.
| S-EPMC7565981 | biostudies-literature