Impact of AtNHX1, a vacuolar Na+/H+ antiporter, upon gene expression during short- and long-term salt stress in Arabidopsis thaliana

It is well established among interdisciplinary researchers that there is an urgent need to address the negative impacts that accompany climate change. One such negative impact is the increased prevalence of unfavorable environmental conditions that significantly contribute to reduced agricultural yield. Plant microRNAs (miRNAs) are key gene expression regulators that control development, defense against invading pathogens and adaptation to abiotic stress. Arabidopsis thaliana (Arabidopsis) can be readily molecularly manipulated, therefore offering an excellent experimental system to alter the profile of abiotic stress responsive miRNA/target gene expression modules to determine whether such modification enables Arabidopsis to express an altered abiotic stress response phenotype. Towards this goal, high throughput sequencing was used to profile the miRNA landscape of Arabidopsis whole seedlings exposed to heat, drought and salt stress, and identified 121, 123 and 118 miRNAs with a greater than 2-fold altered abundance, respectively. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) was next employed to experimentally validate miRNA abundance fold changes, and to document reciprocal expression trends for the target genes of miRNAs determined abiotic stress responsive. RT-qPCR also demonstrated that each miRNA/target gene expression module determined to be abiotic stress responsive in Arabidopsis whole seedlings was reflective of altered miRNA/target gene abundance in Arabidopsis root and shoot tissues post salt stress exposure. Taken together, the data presented here offers an excellent starting platform to identify the miRNA/target gene expression modules for future molecular manipulation to generate plant lines that display an altered response phenotype to abiotic stress.

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Short- and long-term changes in gene expression mediated by the activation of TLR9

Molecular Immunology ◽

10.1016/j.molimm.2009.11.014 ◽

2010 ◽

Vol 47 (6) ◽

pp. 1317-1324 ◽

Cited By ~ 30

Author(s):

Sven Klaschik ◽

Debra Tross ◽

Hidekazu Shirota ◽

Dennis M. Klinman

Keyword(s):

Gene Expression ◽

Long Term Changes ◽

Short And Long Term

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Short- and long-term dynamic responses of the metabolic network and gene expression in yeast to a transient change in the nutrient environment

Molecular BioSystems ◽

10.1039/c2mb05443d ◽

2012 ◽

Vol 8 (6) ◽

pp. 1760 ◽

Cited By ~ 6

Author(s):

Duygu Dikicioglu ◽

Warwick B. Dunn ◽

Douglas B. Kell ◽

Betul Kirdar ◽

Stephen G. Oliver

Keyword(s):

Gene Expression ◽

Metabolic Network ◽

Dynamic Responses ◽

Transient Change ◽

Nutrient Environment ◽

Short And Long Term

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Short- and long-term swimming exercise training increases myocardial insulin-like growth factor-I gene expression

Growth Hormone & IGF Research ◽

10.1016/s1096-6374(02)00137-5 ◽

2003 ◽

Vol 13 (1) ◽

pp. 19-25 ◽

Cited By ~ 31

Author(s):

M. Scheinowitz ◽

G. Kessler-Icekson ◽

S. Freimann ◽

R. Zimmermann ◽

W. Schaper ◽

...

Keyword(s):

Gene Expression ◽

Growth Factor ◽

Exercise Training ◽

Swimming Exercise ◽

Insulin Like Growth Factor ◽

Factor I ◽

Short And Long Term ◽

Growth Factor I ◽

I Gene

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Comparative Analysis of Short- and Long-Term Changes in Gene Expression Caused by Low Water Potential in Potato (Solanum tuberosum) Cell-Suspension Cultures

PLANT PHYSIOLOGY ◽

10.1104/pp.106.2.703 ◽

1994 ◽

Vol 106 (2) ◽

pp. 703-712 ◽

Cited By ~ 31

Author(s):

A. Leone ◽

A. Costa ◽

M. Tucci ◽

S. Grillo

Keyword(s):

Gene Expression ◽

Solanum Tuberosum ◽

Comparative Analysis ◽

Water Potential ◽

Cell Suspension ◽

Cell Suspension Cultures ◽

Suspension Cultures ◽

Long Term Changes ◽

Short And Long Term

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Effects of Short and Long-Term Soy Protein Isolate Intake on Hepatic Cytochrome P450 Expression in Obese Zucker Rats

Current Developments in Nutrition ◽

10.1093/cdn/nzab055_035 ◽

2021 ◽

Vol 5 (Supplement_2) ◽

pp. 1225-1225

Author(s):

Melisa Kozaczek ◽

Walter Bottje ◽

Reza Hakkak

Keyword(s):

Gene Expression ◽

Soy Protein ◽

Soy Protein Isolate ◽

Global Gene Expression ◽

Protein Isolate ◽

Zucker Rats ◽

Z Score ◽

Short And Long Term ◽

Obese Zucker Rats

Abstract Objectives To determine the effects feeding for 8 (short-term) and 16 weeks (long-term) soy protein isolate on hepatic CYP gene expression. Methods 7-weeks old rats were randomly assigned to either a casein (CAS) or a soy protein isolate (SPI) diet. They were provided the diets ad libitum for 8 and 16 weeks. Rats were euthanized and livers were stored at − 80°C. RNA was extracted from liver samples, and sequenced to obtain transcriptomic data (RNAseq). Ingenuity Pathway Analysis software (IPA, Qiagen, CA) was used in the analysis of global gene expression data. This analysis includes predictions of activation or inhibition of molecules or upstream regulators and functions based on a generated z-score and p-value of overlap (P = 0.05). Z-scores were consider significant when > 2 (activation) and < −2 (inhibition). Results Comparing short- vs long-term feeding revealed an increase in the number of down-regulated CYP genes from only 3 at 8 weeks of SPI diet to 10 at 16 weeks of same diet (P < 0.05). In contrast, upregulated CYP gene numbers showed a small increase in long-term SPI diet compared to short-term, from 14 genes at 8 weeks to 17 genes at 16 weeks (P < 0.05). In addition, we present a predicted activation of the transcription factor Aryl hydrocarbon receptor (AHR, activation z-score = 2.146, P = 4.20E-11), linked to the subsequent activation or up-regulation of various CYPs genes, indirectly leading to the activation and inhibition of two main metabolic functions under SPI feeding: conversion of lipid (lipid metabolism) –predicted to be activated (z-score = 2.089, P = 2.77E-08), and recruitment of phagocytes (inflammatory response) –predicted to be inhibited (z-score = −2.311, P = 2.10E-05). Conclusions Through global gene expression analysis we showed that gene expression of drug-metabolizing cytochrome P450 genes was modified in genetically obese Zucker rats after being fed a soy-based diet for short- and long-term, and that this change could have an important role in attenuation of liver steatosis. Further research is needed to corroborate these results. Funding Sources This study was supported in part by the College of Medicine's University Medical Group (RH) and the Arkansas Biosciences Institute (WB, RH).

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Variation, Variegation and Heritable Gene Repression in S. cerevisiae

Frontiers in Genetics ◽

10.3389/fgene.2021.630506 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kholoud Shaban ◽

Safia Mahabub Sauty ◽

Krassimir Yankulov

Keyword(s):

Gene Expression ◽

Current Knowledge ◽

Regulatory Circuits ◽

Epigenetic Diversity ◽

Short And Long Term ◽

Unstructured Proteins ◽

Gene Regulatory ◽

Gene Regulatory Circuits ◽

Insight Into

Phenotypic heterogeneity provides growth advantages for a population upon changes of the environment. In S. cerevisiae, such heterogeneity has been observed as “on/off” states in the expression of individual genes in individual cells. These variations can persist for a limited or extended number of mitotic divisions. Such traits are known to be mediated by heritable chromatin structures, by the mitotic transmission of transcription factors involved in gene regulatory circuits or by the cytoplasmic partition of prions or other unstructured proteins. The significance of such epigenetic diversity is obvious, however, we have limited insight into the mechanisms that generate it. In this review, we summarize the current knowledge of epigenetically maintained heterogeneity of gene expression and point out similarities and converging points between different mechanisms. We discuss how the sharing of limiting repression or activation factors can contribute to cell-to-cell variations in gene expression and to the coordination between short- and long- term epigenetic strategies. Finally, we discuss the implications of such variations and strategies in adaptation and aging.

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