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OsNAR2.1 induced endogenous nitrogen concentration variation affects transcriptional expression of miRNAs in rice

ABSTRACT: OsNAR2.1 induced endogenous nitrogen concentration variation affects transcriptional expression of miRNAs in rice

PROVIDER: PRJNA938571 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26277050.fastq.gz	Fastqsanger.gz
	SRR26277051.fastq.gz	Fastqsanger.gz
	SRR26277052.fastq.gz	Fastqsanger.gz

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Similar Datasets

OsNAR2.1 induced endogenous nitrogen concentration variation affects transcriptional expression of miRNAs in rice

2023-06-23 | GSE224933 | GEO

<i>OsNAR2.1</i> induced endogenous nitrogen concentration variation affects transcriptional expression of miRNAs in rice.

Project description:The studies of rice nitrogen concentration on the expression of miRNA so far are mostly limited to the exogenous nitrogen, leaving the effect of endogenous nitrogen largely unexplored. OsNAR2.1 is a high-affinity nitrate transporter partner protein which plays a central role in nitrate absorption and translocation in rice. The expression of OsNAR2.1 could influence the concentration of the endogenous nitrogen in rice. We showed that the expression and production of miRNA in rice can be influenced by manipulating the endogenous nitrogen concentration via OsNAR2.1 transgenic lines. The small RNA content, particularly 24 nucleotides small RNA, expressed differently in two transgenic rice lines (nitrogen efficient line with overexpression of OsNAR2.1 (Ov199), nitrogen-inefficient line with knockdown OsNAR2.1 by RNAi (RNAi)) compared to the wild-type (NP). Comparative hierarchical clustering expression pattern analysis revealed that the expression profiles of mature miRNA in both transgenic lines were different from NP. Several previously unidentified miRNAs were identified to be differentially expressed under different nitrogen concentrations, namely miR1874, miR5150, chr3-36147, chr4-27017 and chr5-21745. In conclusion, our findings suggest that the level of endogenous nitrogen concentration variation by overexpression or knockdown OsNAR2.1 could mediate the expression pattern and intensity of miRNA in rice, which is of high potential to be used in molecular breeding to improve the rice responses towards nitrogen utilization.

| S-EPMC9998545 | biostudies-literature

Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes

Project description:Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes

| PRJNA692223 | ENA

Endogenous Tau deletion affects sex-dependent outcome to traumatic brain injury in Drosophila

Project description:Endogenous Tau deletion affects sex-dependent outcome to traumatic brain injury in Drosophila

| PRJNA626587 | ENA

Aspergillus niger exposed to combinations of carbon source, nitrogen source, nitrogen concentration, and culture pH

Project description:Microarray analysis of Aspergillus niger under conditions with differing combinations of carbon source, nitrogen source, nitrogen concentration, and culture pH Fermentor cultures were grown in minimal medium (MM) at a constant temperature of 30 ± 0.5 ºC and with differing combinations of carbon source (either 277.5 mM glucose or 333.0 mM xylose), nitrogen source (NH4Cl or NaNO3) and nitrogen concentration (4x: 282.4 mM; 8x: 564.8 mM), and pH (pH4 or pH5) of the medium (M. Braaksma, A.K. Smilde, M.J. van der Werf, P.J. Punt, submitted for publication). At different time points samples were collected, quenched immediately in methanol at -45 ºC and centrifuged at -20 ºC to remove supernatant. Part of the biomass was frozen into liquid nitrogen and stored at -80 ºC for microarray analysis. For each of the 16 culture conditions one sample was selected for microarray analysis; samples were collected either around the time point carbon source depleted or a considerable time (~24 h) after carbon souce depletion. In addition some technical duplicates were included.

2010-04-08 | GSE17329 | GEO

Variation of salinity and nitrogen concentration affects the pentacyclic triterpenoid inventory of the haloalkaliphilic aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum.

Project description:The occurrence and activity of aerobic methanotrophs are influenced by environmental conditions, including pH, temperature, salinity, methane and oxygen concentrations, and nutrient availability. Aerobic methanotrophs synthesize a variety of lipids important for cell functions. However, culture-based experiments studying the influence of environmental parameters on lipid production by aerobic methanotrophs are scarce. Such information is crucial to interpret lipid patterns of methanotrophic bacteria in the environment. In this study, the alkaliphilic strain Methylotuvimicrobium alcaliphilum was cultivated under different salinities and different nitrate concentrations to assess the effect of changing conditions on the inventory of pentacyclic triterpenoids. The results indicate that hopanoid abundance is enhanced at lower salinity and higher nitrate concentration. The production of most pentacyclic triterpenoids was favored at low salinity, especially for aminotriol. Interestingly, 3-methyl-aminotetrol and tetrahymanol were favored at higher salinity. Bacteriohopanepolyols (BHPs), particularly aminotriol and 3-methyl-aminotriol, increased considerably at higher nitrate concentrations. Four novel N-containing BHPs-aminodiol, 3-methyl-aminodiol, and isomers of aminotriol and 3-methyl-aminotriol-were identified. This study highlights the significance of environmental factors for bacterial lipid production and documents the need for cultivation studies under variable conditions to utilize the full potential of the biomarker concept.

| S-EPMC8102298 | biostudies-literature

OsPHR3 affects the traits governing nitrogen homeostasis in rice.

Project description:BackgroundPhosphate (Pi) and Nitrogen (N) are essential macronutrients required for plant growth and development. In Arabidopsis thaliana (Arabidopsis), the transcription factor PHR1 acts as a Pi central regulator. PHL1 is a homolog of PHR1 and also plays a role in maintaining Pi homeostasis. In rice (Oryza sativa), OsPHR1-4 are the orthologs of PHR1 and have been implicated in regulating sensing and signaling cascades governing Pi homeostasis.ResultsHere the role of OsPHR3 was examined in regulating the homeostasis of N under different Pi regimes. Deficiencies of different variants of N exerted attenuating effects on the relative expression levels of OsPHR3 in a tissue-specific manner. For the functional characterization of OsPHR3, its Tos17 insertion homozygous mutants i.e., osphr3-1, osphr3-2, and osphr3-3 were compared with the wild-type for various morphophysiological and molecular traits during vegetative (hydroponics with different regimes of N variants) and reproductive (pot soil) growth phases. During vegetative growth phase, compared with the wild-type, OsPHR3 mutants showed significant variations in the adventitious root development, influx rates of 15N-NO3- and 15N-NH4+, concentrations of total N, NO3- and NH4+ in different tissues, and the relative expression levels of OsNRT1.1a, OsNRT2.4, OsAMT1;1, OsNia1 and OsNia2. The effects of the mutation in OsPHR3 was also explicit on the seed-set and grain yield during growth in a pot soil. Although Pi deficiency affected total N and NO3- concentration, the lateral root development and the relative expression levels of some of the NO3- and NH4+ transporter genes, its availability did not exert any notable regulatory influences on the traits governing N homeostasis.ConclusionsOsPHR3 plays a pivotal role in regulating the homeostasis of N independent of Pi availability.

| S-EPMC6192161 | biostudies-literature

Physiological concentration changes of intracellular spermine activates DNA methyltransferase 3A and 3B and affects gene methylation

Project description:Physiological concentration changes of intracellular spermine activates DNA methyltransferase 3A and 3B and affects gene methylation

| PRJNA438224 | ENA

Cis-regulatory variation affects gene expression dynamics

Project description:Cis-regulatory variation affects gene expression dynamics

| PRJNA695016 | ENA

Transcriptomic response of rice leaves to 30% CO2 concentration

Project description:Analysis of rice leaves (V2 stage) in response to a short treatment with very high CO2 concentration in the dark, using standard atmosphere as control. Results provide insight into molecular mechanisms occurring in response to these extreme conditions, which are often used in the food industry.

2016-07-01 | GSE70840 | GEO

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