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 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 On the origin and evolutionary consequences of gene body DNA methylation

2016 ◽  
Vol 113 (32) ◽  
pp. 9111-9116 ◽  
Author(s):  
Adam J. Bewick ◽  
Lexiang Ji ◽  
Chad E. Niederhuth ◽  
Eva-Maria Willing ◽  
Brigitte T. Hofmeister ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Recombinant Inbred Lines ◽  
Dna Methyltransferases ◽  
Inbred Lines ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Eutrema Salsugineum ◽  
And Function ◽  
Evolutionary Consequences

In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (gene body methylation; gbM), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, to our knowledge the first instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum. Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM, supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z, and various histone modifications in E. salsugineum and in Arabidopsis thaliana epigenetic recombinant inbred lines found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modification of chromatin over evolutionary timescales.

scholarly journals Natural variation of DNA methylation and gene expression may determine local adaptations of Scots pine populations

2018 ◽  
Vol 69 (21) ◽  
pp. 5293-5305 ◽  
Author(s):  
Emmi Alakärppä ◽  
Heikki M Salo ◽  
Luis Valledor ◽  
Maria Jesús Cañal ◽  
Hely Häggman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Scots Pine ◽  
Natural Variation ◽  
Local Adaptations

scholarly journals Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

2016 ◽  
Vol 311 (6) ◽  
pp. L1245-L1258 ◽  
Author(s):  
Isaac K. Sundar ◽  
Irfan Rahman
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Dna Methylation ◽  
Cigarette Smoke ◽  
Histone Modifications ◽  
Expression Patterns ◽  
Chromatin Modification ◽  
Gene Expression Patterns ◽  
Validation Data ◽  
Histone Marks

Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb. We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.

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 Identification of DNA methylated regions by using methylated DNA immunoprecipitation sequencing in Brassica rapa

2018 ◽  
Vol 69 (1) ◽  
pp. 107 ◽  
Author(s):  
Satoshi Takahashi ◽  
Naoki Fukushima ◽  
Kenji Osabe ◽  
Etsuko Itabashi ◽  
Motoki Shimizu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Brassica Rapa ◽  
Inbred Lines ◽  
Methylated Dna ◽  
Transcriptional Suppression ◽  
Genome Wide ◽  
Transposon Silencing ◽  
Lower Expression ◽  
Model Based Analysis

DNA methylation is an epigenetic gene regulatory mechanism that plays an essential role in gene expression, transposon silencing, genome imprinting and plant development. We investigated the influence of DNA methylation on gene expression in Brassica rapa L., to understand whether epigenetic differences exist between inbred lines. Genome-wide DNA methylation was analysed by methylated DNA immunoprecipitation sequencing (MeDIP-seq) of 14-day-old first and second leaves from two inbred lines of Chinese cabbage, one susceptible and one resistant to fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans. MACS (model-based analysis for ChIP-seq) identified DNA methylation peaks in genic regions including 2 kb upstream, exon, intron and 2 kb downstream. More than 65% of genes showed similar patterns of DNA methylation in the genic regions in the two inbred lines. DNA methylation states of the two inbred lines were compared with their transcriptome. Genes having DNA methylation in the intron and in the 200 bp upstream and downstream regions were associated with a lower expression level in both lines. A small number of genes showed a negative correlation between differences in DNA methylation levels and differences in transcriptional levels in the two inbred lines, suggesting that DNA methylation in these genes results in transcriptional suppression.

scholarly journals Characterization of histone modifications associated with DNA damage repair genes upon exposure to gamma rays in Arabidopsis seedlings

2016 ◽  
Vol 57 (6) ◽  
pp. 646-654 ◽  
Author(s):  
Suvendu Mondal ◽  
Young Sam Go ◽  
Seung Sik Lee ◽  
Byung Yeoup Chung ◽  
Jin-Hong Kim
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Gamma Irradiation ◽  
Histone Modifications ◽  
Gamma Rays ◽  
Regulation Of Gene Expression ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Marker Genes ◽  
Transcription Start Sites

Abstract Dynamic histone modifications play an important role in controlling gene expression in response to various environmental cues. This mechanism of regulation of gene expression is important for sessile organisms, like land plants. We have previously reported consistent upregulation of various marker genes in response to gamma rays at various post-irradiation times. In the present study, we performed various chromatin modification analyses at selected loci using the standard chromatin immunoprecipitation procedure, and demonstrate that upregulation of these genes is associated with histone H3 lysine 4 tri-methylation (H3K4me3) at the gene body or transcription start sites of these loci. Further, at specific AtAgo2 loci, both H3K4me3 and histone H3 lysine 9 acetylation (H3K9ac) are important in controlling gene expression in response to gamma irradiation. There was no change in DNA methylation in these selected loci. We conclude that specific histone modification such as H3K4me3 and H3K9ac may be more important in activating gene expression in these selected loci in response to gamma irradiation than a change in DNA methylation.

scholarly journals Mu killer Causes the Heritable Inactivation of the Mutator Family of Transposable Elements in Zea mays

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 781-797
Author(s):  
R Keith Slotkin ◽  
Michael Freeling ◽  
Damon Lisch
Keyword(s):  
Dna Methylation ◽  
Zea Mays ◽  
Transposable Elements ◽  
Plant Development ◽  
Epigenetic Silencing ◽  
The Other ◽  
Transcript Levels ◽  
Transposon Silencing ◽  
Number Of Genes

Abstract Mutations in a number of genes responsible for the maintenance of transposon silencing have been reported. However, the initiation of epigenetic silencing of transposable elements is poorly characterized. Here, we report the identification of a single dominant locus, Mu killer (Muk), that acts to silence MuDR, the autonomous regulatory transposon of the Mutator family of transposable elements in maize. Muk results in the methylation of MuDR TIRs and is competent to silence one or several active MuDR elements. Silencing by Muk is not dependent on the position of the MuDR element and occurs gradually during plant development. Transcript levels of the MuDR transposase, mudrA, decrease substantially when Muk is present. The other transcript encoded by MuDR, mudrB, also fails to accumulate in the poly(A) RNA fraction when MuDR and Muk are combined. Additionally, plants undergoing MuDR silencing produce small, mudrA-homologous ∼26-nt RNAs, suggesting a role for RNA-directed DNA methylation in MuDR silencing. MuDR elements silenced by Muk remain silenced even in plants that do not inherit Muk, suggesting that Muk is required for the initiation of MuDR silencing but not for its maintenance.

scholarly journals Maize DNA Methylation in Response to Drought Stress Is Involved in Target Gene Expression and Alternative Splicing

2021 ◽  
Vol 22 (15) ◽  
pp. 8285
Author(s):  
Qi Wang ◽  
Jie Xu ◽  
Xuemei Pu ◽  
Haozhe Lv ◽  
Yanjun Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Alternative Splicing ◽  
Genotyping By Sequencing ◽  
Inbred Lines ◽  
Sequencing Data ◽  
Positive Correlation ◽  
Differentially Methylated Genes ◽  
Maize Roots ◽  
Interfering Rna

DNA methylation is important for plant growth, development, and stress response. To understand DNA methylation dynamics in maize roots under water stress (WS), we reanalyzed DNA methylation sequencing data to profile DNA methylation and the gene expression landscape of two inbred lines with different drought sensitivities, as well as two of their derived recombination inbred lines (RILs). Combined with genotyping-by-sequencing, we found that the inheritance pattern of DNA methylation between RILs and parental lines was sequence-dependent. Increased DNA methylation levels were observed under WS and the methylome of drought-tolerant inbred lines were much more stable than that of the drought-sensitive inbred lines. Distinctive differentially methylated genes were found among diverse genetic backgrounds, suggesting that inbred lines with different drought sensitivities may have responded to stress in varying ways. Gene body DNA methylation showed a negative correlation with gene expression but a positive correlation with exon splicing events. Furthermore, a positive correlation of a varying extent was observed between small interfering RNA (siRNA) and DNA methylation, which at different genic regions. The response of siRNAs under WS was consistent with the differential DNA methylation. Taken together, our data can be useful in deciphering the roles of DNA methylation in plant drought-tolerance variations and in emphasizing its function in alternative splicing.

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