scholarly journals Massive Loss of DNA Methylation in Nitrogen-, but Not in Phosphorus-Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences

2018 ◽  
Vol 9 ◽  
Author(s):  
Svenja Mager ◽  
Uwe Ludewig
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zea Mays

scholarly journals DNA METHYLATION AND FESOD GENE EXPRESSION AFFECTED BY PLANT DENSITY IN ZEA MAYS L.

2019 ◽  
Vol 50 (Special) ◽  
Author(s):  
Shenawa & Alfalahi
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zea Mays ◽  
Zea Mays L ◽  
Plant Density ◽  
Maximum Level ◽  
Planting Density ◽  
Gene Copies ◽  
High Plant Density ◽  
Different Response

Methylation Sensitive Amplification Polymorphism (MSAP) was used to characterize the alterations in DNA methylation in maize (Zea mays L.) inbred lines and their half-daillels affected by plant densities (213333 plant h-1 and 13333 plant h-1). The two restriction was enzymes ( HpaII and MspI) succeeded in diagnosing a total of 23 specific loci, most of (22 loci) were Methylation Sensitive Loci (MSL), while the only one NML (No Methylated Loci) was monomorphic. Thirteen out of 22 MSL loci polymorphic, recording a were polymorphism percentage of 59%. Results of FeSOD gene expression cleared the different response of maize inbreds and hybrids to high plant density stress. Generally, the expression of  the targeted gene was increased in plants submitted to high plant density stress compared with low density. The inbred 3 and its single hybrid 1×3 achieved the highest level of gene expression under high planting density (5505.7 and 21098.6 copy, respectively), meanwhile, inbred 5 and it's single hybrid 4×5 gained the maximum level of FeSOD expression at the low plant density (8317.6 and 6862.1 copy, respectively). The response reached to its maximum limit in many of those genotypes, some other genotypes showed relatively steady performance along with higher stress, such as parent 1, that gave the lowest number of gene copies in both, high and low plant density (1375.8 and 1569.5 copy, respectively).

scholarly journals Herbicide stress-induced DNA methylation changes in two Zea mays inbred lines differing in Roundup® resistance

2021 ◽  
Author(s):  
Agata Tyczewska ◽  
Joanna Gracz-Bernaciak ◽  
Jakub Szymkowiak ◽  
Tomasz Twardowski
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zea Mays ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Differential Susceptibility ◽  
Inbred Lines ◽  
Specific Gene ◽  
Genes Encoding ◽  
Shock Proteins

AbstractDNA methylation plays a crucial role in the regulation of gene expression, activity of transposable elements, defense against foreign DNA, and inheritance of specific gene expression patterns. The link between stress exposure and sequence-specific changes in DNA methylation was hypothetical until it was shown that stresses can induce changes in the gene expression through hypomethylation or hypermethylation of DNA. To detect changes in DNA methylation under herbicide stress in two local Zea mays inbred lines exhibiting differential susceptibility to Roundup®, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation levels were determined at approximately 60% for both tested lines. The most significant changes were observed for the more sensitive Z. mays line, where 6 h after the herbicide application, a large increase in the level of DNA methylation (attributed to the increase in fully methylated bands (18.65%)) was noted. DNA sequencing revealed that changes in DNA methylation profiles occurred in genes encoding heat shock proteins, membrane proteins, transporters, kinases, lipases, methyltransferases, zinc-finger proteins, cytochromes, and transposons. Herbicide stress-induced changes depended on the Z. mays variety, and the large increase in DNA methylation level in the sensitive line resulted in a lower ability to cope with stress conditions.

scholarly journals Subtle perturbations of the maize methylome reveal genes and transposons silenced by DNA methylation

2017 ◽  
Author(s):  
Sarah N. Anderson ◽  
Greg Zynda ◽  
Jawon Song ◽  
Zhaoxue Han ◽  
Matthew Vaughn ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zea Mays ◽  
Natural Variation ◽  
Chromatin Modification ◽  
Inbred Lines ◽  
Specific Sequence ◽  
Number Of Genes ◽  
Context Specific ◽  
Mutant Lines

ABSTRACTDNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, providing evidence that context-specific DNA methylation directly regulates expression of a small number of genes. The analysis of a diverse set of inbred lines revealed that many genes regulated by CMTs exhibit natural variation for DNA methylation and gene expression. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm, highlighting the importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.

scholarly journals Direct and Indirect Transcriptional Effects of Abiotic Stress in Zea mays Plants Defective in RNA-Directed DNA Methylation

2021 ◽  
Vol 12 ◽  
Author(s):  
Thelma F. Madzima ◽  
Stefania Vendramin ◽  
Jason S. Lynn ◽  
Phebe Lemert ◽  
Katherine C. Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zea Mays ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Water Deprivation ◽  
Regulation Of Gene Expression ◽  
Differentially Expressed ◽  
Dependent Manner ◽  
Transcriptional Responses

Plants respond to abiotic stress stimuli, such as water deprivation, through a hierarchical cascade that includes detection and signaling to mediate transcriptional and physiological changes. The phytohormone abscisic acid (ABA) is well-characterized for its regulatory role in these processes in response to specific environmental cues. ABA-mediated changes in gene expression have been demonstrated to be temporally-dependent, however, the genome-wide timing of these responses are not well-characterized in the agronomically important crop plant Zea mays (maize). ABA-mediated responses are synergistic with other regulatory mechanisms, including the plant-specific RNA-directed DNA methylation (RdDM) epigenetic pathway. Our prior work demonstrated that after relatively long-term ABA induction (8 h), maize plants homozygous for the mop1-1 mutation, defective in a component of the RdDM pathway, exhibit enhanced transcriptional sensitivity to the phytohormone. At this time-point, many hierarchically positioned transcription factors are differentially expressed resulting in primary (direct) and secondary (indirect) transcriptional outcomes. To identify more immediate and direct MOP1-dependent responses to ABA, we conducted a transcriptomic analysis using mop1-1 mutant and wild type plants treated with ABA for 1 h. One h of ABA treatment was sufficient to induce unique categories of differentially expressed genes (DEGs) in mop1-1. A comparative analysis between the two time-points revealed that distinct epigenetically-regulated changes in gene expression occur within the early stages of ABA induction, and that these changes are predicted to influence less immediate, indirect transcriptional responses. Homology with MOP1-dependent siRNAs and a gene regulatory network (GRN) were used to identify putative immediate and indirect targets, respectively. By manipulating two key regulatory networks in a temporal dependent manner, we identified genes and biological processes regulated by RdDM and ABA-mediated stress responses. Consistent with mis-regulation of gene expression, mop1-1 homozygous plants are compromised in their ability to recover from water deprivation. Collectively, these results indicate transcriptionally and physiologically relevant roles for MOP1-mediated regulation of gene expression of plant responses to environmental stress.

DNA Methylation Inhibites ANXA1 Gene Expression in Nasopharyngeal Carcinoma Cell Lines*

2009 ◽  
Vol 36 (10) ◽  
pp. 1319-1326 ◽  
Author(s):  
Shuang-Xiang TAN ◽  
Rui-Cheng HU ◽  
Ai-Guo DAI ◽  
Cen-E TANG ◽  
Hong YI ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Nasopharyngeal Carcinoma ◽  
Cell Lines ◽  
Carcinoma Cell ◽  
Nasopharyngeal Carcinoma Cell ◽  
Carcinoma Cell Lines

scholarly journals Epigenetic Changes During Mechanically Induced Osteogenic Lineage Commitment

2015 ◽  
Vol 137 (2) ◽  
Author(s):  
Julia C. Chen ◽  
Mardonn Chua ◽  
Raymond B. Bellon ◽  
Christopher R. Jacobs
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Shear Stress ◽  
Fluid Shear Stress ◽  
Methylation Status ◽  
Lineage Commitment ◽  
Fluid Shear ◽  
Osteogenic Lineage ◽  
Osteogenic Markers ◽  
Heterochromatin Structure

Osteogenic lineage commitment is often evaluated by analyzing gene expression. However, many genes are transiently expressed during differentiation. The availability of genes for expression is influenced by epigenetic state, which affects the heterochromatin structure. DNA methylation, a form of epigenetic regulation, is stable and heritable. Therefore, analyzing methylation status may be less temporally dependent and more informative for evaluating lineage commitment. Here we analyzed the effect of mechanical stimulation on osteogenic differentiation by applying fluid shear stress for 24 hr to osteocytes and then applying the osteocyte-conditioned medium (CM) to progenitor cells. We analyzed gene expression and changes in DNA methylation after 24 hr of exposure to the CM using quantitative real-time polymerase chain reaction and bisulfite sequencing. With fluid shear stress stimulation, methylation decreased for both adipogenic and osteogenic markers, which typically increases availability of genes for expression. After only 24 hr of exposure to CM, we also observed increases in expression of later osteogenic markers that are typically observed to increase after seven days or more with biochemical induction. However, we observed a decrease or no change in early osteogenic markers and decreases in adipogenic gene expression. Treatment of a demethylating agent produced an increase in all genes. The results indicate that fluid shear stress stimulation rapidly promotes the availability of genes for expression, but also specifically increases gene expression of later osteogenic markers.

Sign in / Sign up

Export Citation Format

Share Document