scholarly journals Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana

2020 ◽  
Author(s):  
Andras Bittner ◽  
Jörn van Buer ◽  
Margarete Baier
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Cold Treatment ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
High Light ◽  
Cold Stimulus ◽  
Expression Of Genes ◽  
Specific Manner

Abstract Background: The majority of stress-sensitive genes responds to cold and high light in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory-based regulation is called priming. Here, we analyse the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and investigate if and how cold priming affects light regulation of gene expression.Results: Cold-priming affected cold and excess light regulation of a small subset of genes. In contrast to the strong gene co-regulation observed upon cold and light stress in not-primed plants, most priming-sensitive genes were regulated in a stressor-specific manner in cold-primed plant. Furthermore, almost as much genes were inversely regulated as co-regulated by a 24 h long 4 °C cold treatment and exposure to heat-filtered high light (800 µmol quanta m-2 s-1). Gene ontology enrichment analysis revealed that cold priming preferentially supports expression of genes involved in the defence against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defence genes in response to high light triggering. qPCR with independently cultivated and treated replicates confirmed the trends observed in the RNASeq guide experiment.Conclusion: A 24 h long priming cold stimulus activates a several days lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defence regulation in a stressor-specific manner.

scholarly journals Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana

2020 ◽  
Author(s):  
Andras Bittner ◽  
Jörn van Buer ◽  
Margarete Baier
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Cold Treatment ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
High Light ◽  
Cold Stimulus ◽  
Expression Of Genes ◽  
Specific Manner

Abstract Background: The majority of stress-sensitive genes responds to cold and high light in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory-based regulation is called priming. Here, we analyse the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and investigate if and how cold priming affects light regulation of gene expression.Results: Cold-priming affected cold and excess light regulation of a small subset of genes. In contrast to the strong gene co-regulation observed upon cold and light stress in not-primed plants, most priming-sensitive genes were regulated in a stressor-specific manner in cold-primed plant. Furthermore, almost as much genes were inversely regulated as co-regulated by a 24 h long 4 °C cold treatment and exposure to heat-filtered high light (800 µmol quanta m-2 s-1). Gene ontology enrichment analysis revealed that cold priming preferentially supports expression of genes involved in the defence against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defence genes in response to high light triggering. qPCR with independently cultivated and treated replicates confirmed the trends observed in the RNASeq guide experiment.Conclusion: A 24 h long priming cold stimulus activates a several days lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defence regulation in a stressor-specific manner.

scholarly journals Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana

2020 ◽  
Author(s):  
Andras Bittner ◽  
Jörn van Buer ◽  
Margarete Baier
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Cold Treatment ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
High Light ◽  
Cold Stimulus ◽  
Expression Of Genes ◽  
Specific Manner

Abstract Background The majority of stress-sensitive genes responds to cold and high light in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory-based regulation is called priming. Here, we show the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and analyse if and how cold priming affects light regulation of gene expression. Results 304 genes were differently regulated between cold-primed and non-primed plants after a second 24 h long 4 °C cold treatment. After triggering the plants with a heat-filtered high light stimulus (800 µmol quanta m -2 s -1 ), 1011 genes showed priming dependent regulation. Only 32 of the priming-sensitive genes responded similarly to cold and light triggering. The majority of the priming-sensitive genes were regulated in a stressor-specific manner. 29 genes were even inversely regulated by the two triggering stimuli. Cold priming preferentially supported expression of genes involved in the defence against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defence genes in response to high light triggering. qPCR of several independently cultivated and treated samples confirmed the trends observed by RNA-Sequencing. Conclusion The 24 h long priming cold stimulus activates a several days lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defence regulation in a stressor-specific manner.

scholarly journals Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana

2020 ◽  
Author(s):  
Andras Bittner ◽  
Jörn van Buer ◽  
Margarete Baier
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Cold Treatment ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
High Light ◽  
Cold Stimulus ◽  
Expression Of Genes ◽  
Specific Manner

Abstract Background The majority of stress-sensitive genes responds to cold and high light in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory-based regulation is called priming. Here, we analyse the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and investigate if and how cold priming affects light regulation of gene expression. Results Cold-priming affected cold and excess light regulation of a small subset of genes. In contrast to the strong gene co-regulation observed upon cold and light stress in not-primed plants, most priming-sensitive genes were regulated in a stressor-specific manner in cold-primed plant. Furthermore, almost as much genes were inversely regulated as co-regulated by a 24 h long 4 °C cold treatment and exposure to heat-filtered high light (800 µmol quanta m -2 s -1 ). Gene ontology enrichment analysis revealed that cold priming preferentially supports expression of genes involved in the defence against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defence genes in response to high light triggering. qPCR with independently cultivated and treated replicates confirmed the trends observed in the RNASeq guide experiment. Conclusion A 24 h long priming cold stimulus activates a several days lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defence regulation in a stressor-specific manner.

scholarly journals Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana

2020 ◽  
Author(s):  
Andras Bittner ◽  
Jörn van Buer ◽  
Margarete Baier
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Growth Regulation ◽  
Plant Pathogens ◽  
Cold Treatment ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
Cold Stimulus ◽  
Expression Of Genes ◽  
Specific Manner

Abstract Background The majority of stress-sensitive genes responds to cold and highlight in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory based regulation is called priming. Here, we show the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and test if and how cold priming effects light regulation of gene expression. Results 304 genes were differently regulated between cold-primed and non-primed plants after a second 24 h long 4 °C cold treatment. After triggering the plants with a heat-filtered highlight stimulus (800 µmol quanta m -2 s -1 ), 1011 genes showed priming dependent regulation. Only 32 of the priming-sensitive genes responded similarly to cold and light triggering. The majority of the priming-sensitive genes were regulated in a stressor-specific manner. 29 genes were even inversely regulated by the two triggering stimuli. Cold priming preferentially supported expression of genes involved in the defense against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defense genes in response to highlight triggering. qPCR in several independently cultivated and treated samples confirmed the trends observed by RNA-Sequencing. Conclusion The 24 h long priming cold stimulus activates a several day lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defense regulation in a stressor-specific manner.

Cytokinin Regulation of Gene Expression in the AHP Gene Family in Arabidopsis thaliana

2007 ◽  
Vol 26 (3) ◽  
pp. 229-244 ◽  
Author(s):  
Jana Hradilová ◽  
Jiří Malbeck ◽  
Břetislav Brzobohatý
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Regulation Of Gene Expression

scholarly journals Circadian variations in gene expression in rat abdominal adipose tissue and relationship to physiology

2010 ◽  
Vol 42A (2) ◽  
pp. 141-152 ◽  
Author(s):  
Siddharth Sukumaran ◽  
Bai Xue ◽  
William J. Jusko ◽  
Debra C. DuBois ◽  
Richard R. Almon
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Circadian Rhythms ◽  
Regulation Of Gene Expression ◽  
Gene Array ◽  
Circadian Oscillation ◽  
Peripheral Tissues ◽  
Physiological Processes ◽  
Expression Of Genes ◽  
Rat Adipose Tissue

Circadian rhythms occur in all levels of organization from expression of genes to complex physiological processes. Although much is known about the mechanism of the central clock in the suprachiasmatic nucleus, the regulation of clocks present in peripheral tissues as well as the genes regulated by those clocks is still unclear. In this study, the circadian regulation of gene expression was examined in rat adipose tissue. A rich time series involving 54 animals euthanized at 18 time points within the 24-h cycle (12:12 h light-dark) was performed. mRNA expression was examined with Affymetrix gene array chips and quantitative real-time PCR, along with selected physiological measurements. Transcription factors involved in the regulation of central rhythms were examined, and 13 showed circadian oscillations. Mining of microarray data identified 190 probe sets that showed robust circadian oscillations. Circadian regulated probe sets were further parsed into seven distinct temporal clusters, with >70% of the genes showing maximum expression during the active/dark period. These genes were grouped into eight functional categories, which were examined within the context of their temporal expression. Circadian oscillations were also observed in plasma leptin, corticosterone, insulin, glucose, triglycerides, free fatty acids, and LDL cholesterol. Circadian oscillation in these physiological measurements along with the functional categorization of these genes suggests an important role for circadian rhythms in controlling various functions in white adipose tissue including adipogenesis, energy metabolism, and immune regulation.

scholarly journals Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits

2018 ◽  
Author(s):  
Heather E. Wheeler ◽  
Sally Ploch ◽  
Alvaro N. Barbeira ◽  
Rodrigo Bonazzola ◽  
Angela Andaleon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Complex Traits ◽  
Target Gene ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Nucleic Acid Binding ◽  
Expression Of Genes ◽  
Gene Associations ◽  
Made In

AbstractRegulation of gene expression is an important mechanism through which genetic variation can affect complex traits. A substantial portion of gene expression variation can be explained by both local (cis) and distal (trans) genetic variation. Much progress has been made in uncovering cis-acting expression quantitative trait loci (cis-eQTL), but trans-eQTL have been more difficult to identify and replicate. Here we take advantage of our ability to predict the cis component of gene expression coupled with gene mapping methods such as PrediXcan to identify high confidence candidate trans-acting genes and their targets. That is, we correlate the cis component of gene expression with observed expression of genes in different chromosomes. Leveraging the shared cis-acting regulation across tissues, we combine the evidence of association across all available GTEx tissues and find 2356 trans-acting/target gene pairs with high mappability scores. Reassuringly, trans-acting genes are enriched in transcription and nucleic acid binding pathways and target genes are enriched in known transcription factor binding sites. Interestingly, trans-acting genes are more significantly associated with selected complex traits and diseases than target or background genes, consistent with percolating trans effects. Our scripts and summary statistics are publicly available for future studies of trans-acting gene regulation.

scholarly journals The Use of Natural Products of Epigenetic Modulators in Anti-Cancer Drug Studies

Proceedings ◽  
2019 ◽  
Vol 40 (1) ◽  
pp. 41
Author(s):  
Demokan
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Natural Products ◽  
Cancer Treatment ◽  
Tumor Cells ◽  
Histone Modifications ◽  
Regulation Of Gene Expression ◽  
Epigenetic Mechanisms ◽  
Expression Of Genes ◽  
Anti Cancer

The natural products obtained from plants, bacteria, fungi and marine have been used in the treatment of human diseases throughout the centuries. These compounds of them also interfere with the expression of genes by influencing epigenetic mechanisms. Recent researches showed significant outcomes suggesting that epigenetic silencing of the main regulatory genesis a sign of cancer onset and its progression. Epigenetic mechanisms that regulate expression of genes without mutation in the DNA are carried through DNA methylation, histone modification, chromatin remodeling and RNA interference. DNA methylation observed in the promoter regions of genes and prevents binding of the transcription factors by suppressing gene expression or by altering the nucleosome package of DNA, and may also directly inhibit transcription. Plant based products, such as curcumin, flavonoids, genistein, have been shown to exhibit cytostatic and apoptotic activities by influencing DNA methylation-based gene expression regulation in tumor cells. Additionally, natural products such as sulforaphane, retinoic acid, cucurbitacin B, casein Q, parthenolide, folate, cobalamin, pyridoxine and methionine also are used as anti-cancer agents based on DNA methylation. On the other hand, microRNAs (miRNAs) play a particular role in the epigenetic regulation of gene expression in post-transcription and post-translation processes. Quercetin, tryptolide, and honokiol are the natural compounds used in miRNA based agents. Histone modifications, which also affect the chromatin structure, play an important role in the initiation and progression of carcinogenesis as well as regulation of gene expression. As expected particular inhibitors of histone acetyltransferases (HATs) and histone deacetylase (HDAC) enzymes which are responsible of histone modifications have been developed for epigenetic intervention in cancer treatment. Numerous natural compounds are known to affect histone-modifying enzymes; such as romidepsin, epigallocatechingallate (EGCG), daidzein, sulphorafane, glucoraphanin, parthenolide, triptolide, sinapinic acid. Natural epigenetic modulators developed for epigenetic mechanisms enable the destruction of apoptotic, necrotic or autophagic pathways of tumor cells. Beside epigenetic mechanisms, these products exert their effects through influencing the cell cycle, DNA repair, and epigenetic mechanisms which modulate gene expression. More extensive in vitro and in vivo studies are required to investigate the effect of natural product-based epigenetic agents which seems to be very promising for future cancer treatment approaches.

Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana

2021 ◽  
Author(s):  
Fanli Meng ◽  
Hainan Zhao ◽  
Bo Zhu ◽  
Tao Zhang ◽  
Mingyu Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcriptional Repression ◽  
Regulation Of Gene Expression ◽  
Fine Tuning ◽  
Specific Gene ◽  
Open Chromatin ◽  
Floral Tissue ◽  
Deletion Lines ◽  
A Genome

Abstract Enhancers located in introns are abundant and play a major role in the regulation of gene expression in mammalian species. By contrast, the functions of intronic enhancers in plants have largely been unexplored and only a handful of plant intronic enhancers have been reported. We performed a genome-wide prediction of intronic enhancers in Arabidopsis thaliana using open chromatin signatures based on DNase I sequencing. We identified 941 candidate intronic enhancers associated with 806 genes in seedling tissue and 1,271 intronic enhancers associated with 1,069 genes in floral tissue. We validated the function of 15 of 21 (71%) of the predicted intronic enhancers in transgenic assays using a reporter gene. We also created deletion lines of three intronic enhancers associated with two different genes using CRISPR/Cas. Deletion of these enhancers, which span key transcription factor binding sites, did not abolish gene expression but caused varying levels of transcriptional repression of their cognate genes. Remarkably, the transcriptional repression of the deletion lines occurred at specific developmental stages and resulted in distinct phenotypic effects on plant morphology and development. Clearly, these three intronic enhancers are important in fine-tuning tissue- and development-specific expression of their cognate genes.

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