Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation

2019 ◽  
Vol 70 (20) ◽  
pp. 5673-5686 ◽  
Author(s):  
Haidong Yan ◽  
Aureliano Bombarely ◽  
Bin Xu ◽  
Bingchao Wu ◽  
Taylor P Frazier ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Division ◽  
Flowering Time ◽  
Panicum Virgatum ◽  
Plant Evolution ◽  
Cellulose Biosynthesis ◽  
Auxin Response ◽  
Phenotypic Changes ◽  
First Time ◽  
Growth And Reproduction

Abstract Polyploidization is a significant source of genomic and organism diversification during plant evolution, and leads to substantial alterations in plant phenotypes and natural fitness. To help understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses of a synthesized autopolyploid accession of switchgrass (Panicum virgatum) in order to interpret the molecular and phenotypic changes. We found that mCHH levels were decreased in both genic and transposable element (TE) regions, and that TE methylation near genes was decreased as well. Among 142 differentially expressed genes involved in cell division, cellulose biosynthesis, auxin response, growth, and reproduction processes, 75 of them were modified by 122 differentially methylated regions, 10 miRNAs, and 15 siRNAs. In addition, up-regulated PvTOE1 and suppressed PvFT probably contribute to later flowering time of the autopolyploid. The expression changes were probably associated with modification of nearby methylation sites and siRNAs. We also experimentally demonstrated that expression levels of PvFT and PvTOE1 were regulated by DNA methylation, supporting the link between alterations in methylation induced by polyploidization and the phenotypic changes that were observed. Collectively, our results show epigenetic modifications in synthetic autopolyploid switchgrass for the first time, and support the hypothesis that polyploidization-induced methylation is an important cause of phenotypic alterations and is potentially important for plant evolution and improved fitness.

scholarly journals Photoperiodic stress induces genotype-specific shift in DNA methylation in Tartary buckwheat

2019 ◽  
Vol 70 (4) ◽  
pp. 278-285
Author(s):  
Muhammad Saad ◽  
Helen Mary ◽  
Umar Amjid ◽  
Ghulam Shabir ◽  
Kashif Aslam ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Flowering Time ◽  
Specific Pattern ◽  
Plant Response ◽  
Tartary Buckwheat ◽  
Genome Wide ◽  
Total Dna ◽  
First Time ◽  
Weight Data ◽  
Methylation Ratio

Tartary buckwheat, known for its rich source of health beneficial secondary metabolites, is cultivated in many areas of the world. Among different environmental factors, photoperiod strongly influence its growth, flowering time, and ultimately the yield. In this context, epigenetics could contribute significantly in the regulation of plant response against changing environment. Therefore, with the aim to study the involvement of DNA methylation in photoperiod mediated plant response, genome-wide DNA methylation analysis was performed in two accessions (A1 and A2) of Tartary buckwheat using three photoperiodic treatments, i.e., 10-hr light/day (T1), 12-hr light/day (T2), and 14-hr light/day (T3). Flowering time and plant fresh weight data revealed that accessions A1 and A2 prefer T1 and T2 treatments, respectively. Total DNA methylation ratio increased with the increase in photoperiod in accession A1 but decreased under same conditions in accession A2. Full methylation increased significantly while intensive decrease in hemimethylation was noted from T2 to T3 in A1, whereas full methylation strongly increased and hemimethylation strongly decreased from T1 to T2 in A2. Overall, the DNA methylation events appeared more frequently than demethylation events. This study reports for the first time an accession-/genotype specific pattern of shift in the DNA methylation under different photoperiodic treatments that will pave the way toward identification of specific genes involved in the regulation of plant response against photoperiodic stress.

scholarly journals Shadowing the Actions of a Predator: Backlit Fluorescent Microscopy Reveals Synchronous Nonbinary Septation of Predatory Bdellovibrio inside Prey and Exit through Discrete Bdelloplast Pores

2010 ◽  
Vol 192 (24) ◽  
pp. 6329-6335 ◽  
Author(s):  
A. K. Fenton ◽  
M. Kanna ◽  
R. D. Woods ◽  
S.-I. Aizawa ◽  
R. E. Sockett
Keyword(s):  
Cell Division ◽  
Outer Membrane ◽  
Fluorescent Microscopy ◽  
Gram Negative Bacteria ◽  
Bacterial Cell Division ◽  
Prey Cell ◽  
Gram Negative ◽  
A Genome ◽  
Predatory Bacteria ◽  
First Time

ABSTRACT The Bdellovibrio are miniature “living antibiotic” predatory bacteria which invade, reseal, and digest other larger Gram-negative bacteria, including pathogens. Nutrients for the replication of Bdellovibrio bacteria come entirely from the digestion of the single invaded bacterium, now called a bdelloplast, which is bound by the original prey outer membrane. Bdellovibrio bacteria are efficient digesters of prey cells, yielding on average 4 to 6 progeny from digestion of a single prey cell of a genome size similar to that of the Bdellovibrio cell itself. The developmental intrabacterial cycle of Bdellovibrio is largely unknown and has never been visualized “live.” Using the latest motorized xy stage with a very defined z-axis control and engineered periplasmically fluorescent prey allows, for the first time, accurate return and visualization without prey bleaching of developing Bdellovibrio cells using solely the inner resources of a prey cell over several hours. We show that Bdellovibrio bacteria do not follow the familiar pattern of bacterial cell division by binary fission. Instead, they septate synchronously to produce both odd and even numbers of progeny, even when two separate Bdellovibrio cells have invaded and develop within a single prey bacterium, producing two different amounts of progeny. Evolution of this novel septation pattern, allowing odd progeny yields, allows optimal use of the finite prey cell resources to produce maximal replicated, predatory bacteria. When replication is complete, Bdellovibrio cells exit the exhausted prey and are seen leaving via discrete pores rather than by breakdown of the entire outer membrane of the prey.

scholarly journals Effects of Ration Levels on Growth and Reproduction from Larvae to First-Time Spawning in the Female Gambusia affinis

2015 ◽  
Vol 16 (12) ◽  
pp. 5604-5617 ◽  
Author(s):  
Zhiming Zhu ◽  
Xiangling Zeng ◽  
Xiaotao Lin ◽  
Zhongneng Xu ◽  
Jun Sun
Keyword(s):  
Gambusia Affinis ◽  
First Time ◽  
Growth And Reproduction

scholarly journals Discordant evolution of organellar genomes in peas (Pisum L.)

2020 ◽  
Author(s):  
Vera S. Bogdanova ◽  
Natalia V. Shatskaya ◽  
Anatoliy V. Mglinets ◽  
Oleg E. Kosterin ◽  
Gennadiy V. Vasiliev
Keyword(s):  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Plant Evolution ◽  
Hybrid Origin ◽  
Mitochondrial Genomes ◽  
North East ◽  
Plastid Genomes ◽  
First Time ◽  
Evolutionary Fate

AbstractPlastids and mitochondria have their own small genomes which do not undergo meiotic recombination and may have evolutionary fate different from each other and nuclear genome, thus highlighting interesting phenomena in plant evolution. We for the first time sequenced mitochondrial genomes of pea (Pisum L.), in 38 accessions mostly representing diverse wild germplasm from all over pea geographical range. Six structural types of pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Bayesian phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant implying not less than six events of hybridisation of diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles is supposed to have been driven by plastid-nuclear incompatibility, known to be widespread in pea wide crosses and apparently shaping the organellar phylogenies. The topology of a phylogenetic tree based on the nucleotide sequence of a nuclear gene His5 coding for a histone H1 subtype corresponds to the current taxonomy and resembles that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin resulting from crosses of peas similar to those presently inhabiting south-east and north-east Mediterranean in broad sense.

scholarly journals To Determine Pivotal Genes Driven by Methylated DNA in Obstructive Sleep Apnea Hypopnea Syndrome

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Yan Li ◽  
Yajuan Zhang
Keyword(s):  
Dna Methylation ◽  
Obstructive Sleep Apnea ◽  
Sleep Apnea ◽  
Molecular Mechanisms ◽  
Sleep Apnea Syndrome ◽  
Respiratory Dysfunction ◽  
Obstructive Sleep ◽  
Hypopnea Syndrome ◽  
First Time ◽  
Erbb2 Signaling

Obstructive sleep apnea syndrome (OSAHS) is a widespread respiratory dysfunction that has attracted more and more attention in recent years. Recently, a large number of studies have shown that abnormal DNA methylation epigenetically silences genes necessary for the pathogenesis of human diseases. However, the exact mechanism of abnormal DNA methylation in OSAHS is still elusive. In this study, we downloaded the OSAHS data from the GEO database. Our data for the first time revealed 520 hypermethylated genes and 889 hypomethylated genes in OSAHS. Bioinformatics analysis revealed that these abnormal methylated genes exhibited an association with the regulation of angiogenesis, apoptosis, Wnt, and ERBB2 signaling pathways. PPI network analysis displayed the interactions among these genes and validated several hub genes, such as GPSM2, CCR8, TAS2R20, TAS2R4, and TAS2R5, which were related to regulating liganded Gi-activating GPCR and the transition of mitotic metaphase/anaphase. In conclusion, our study offers a new hint of understanding the molecular mechanisms in OSAHS progression and will provide OSAHS with newly generated innovative biomarkers.

scholarly journals Validation and characterization of a DNA methylation alcohol biomarker across the life course

2019 ◽  
Author(s):  
Paul Darius Yousefi ◽  
Rebecca Richmond ◽  
Ryan Langdon ◽  
Andrew Ness ◽  
Chunyu Liu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Parents And Children ◽  
Average Alcohol ◽  
Alcohol Biomarker ◽  
Audit Score ◽  
Potential Applications ◽  
The Life Course ◽  
Offspring Generation ◽  
First Time

AbstractRecently, an alcohol predictor was developed using DNA methylation at 144 CpG sites (DNAm-Alc) as a biomarker for improved clinical or epidemiologic assessment of alcohol-related ill health. We validate the performance and characterize the drivers of this DNAm-Alc for the first time in independent populations. In N=1,049 parents from the Avon Longitudinal Study of Parents and Children (ALSPAC) Accessible Resource for Integrated Epigenomic Studies (ARIES) at midlife, we found DNAm-Alc explained 7.6% of the variation in alcohol intake, roughly half of what had been reported previously, and interestingly explained a larger 9.8% of AUDIT score, a scale of alcohol use disorder. Explanatory capacity in participants from the offspring generation of ARIES measured during adolescence was much lower. However, DNAm-Alc explained 14.3% of the variation in replication using the Head and Neck 5000 (HN5000) clinical cohort that had higher average alcohol consumption. To investigate whether this relationship was being driven by genetic and/or earlier environment confounding we examined how earlier vs. concurrent DNAm-Alc measures predicted AUDIT scores. In both ARIES parental and offspring generations, we observed associations between AUDIT and concurrent, but not earlier DNAm-Alc, suggesting independence from genetic and stable environmental contributions. The stronger relationship between DNAm-Alcs and AUDIT in parents at midlife compared to adolescents despite similar levels of consumption suggests that DNAm-Alc likely reflects long-term patterns of alcohol abuse. Such biomarkers may have potential applications for biomonitoring and risk prediction, especially in cases where reporting bias is a concern.

Search for Pharmacoepigenetic Correlations in Type 2 Diabetes Under Sulfonylurea Treatment

2018 ◽  
Vol 127 (04) ◽  
pp. 226-233 ◽  
Author(s):  
Makrina Karaglani ◽  
Georgia Ragia ◽  
Maria Panagopoulou ◽  
Ioanna Balgkouranidou ◽  
Evangelia Nena ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Promoter ◽  
Katp Channels ◽  
Protective Role ◽  
Gene Promoters ◽  
Specific Pcr ◽  
Abcc8 Gene ◽  
First Time ◽  
E23k Polymorphism

AbstractSulfonylureas are insulin secretagogues which act in pancreatic β cells by blocking the KATP channels encoded by KCNJ11 and ABCC8 genes. In the present study, a pharmacoepigenetic approach was applied for the first time, investigating the correlation of KCNJ11 and ABCC8 gene promoter methylation with sulfonylureas-induced mild hypoglycemic events as well as the KCNJ11 E23K genotype. Sodium bisulfite-treated genomic DNA of 171 sulfonylureas treated T2DM patients previously genotyped for KCNJ11 E23K, including 88 that had experienced drug-associated hypoglycemia and 83 that had never experienced hypoglycemia, were analyzed for DNA methylation of KCNJ11 and ABCC8 gene promoters via quantitative Methylation-Specific PCR. KCNJ11 methylation was detected in 19/88 (21.6%) of hypoglycemic and in 23/83 (27.7%) of non-hypoglycemic patients (p=0.353), while ABCC8 methylation in 6/83 (7.2%) of non-hypoglycemic and none (0/88) of the hypoglycemic patients (p=0.012). Methylation in at least one promoter (KCNJ11 or ABCC8) was significantly associated with non-hypoglycemic patients who are carriers of KCNJ11 EK allele (p=0.030). Our data suggest that ABCC8 but not KCNJ11 methylation is associated to hypoglycemic events in sulfonylureas-treated T2DM patients. Furthermore, it is demonstrated that the KCNJ11 E23K polymorphism in association to either of the two genes’ DNA methylation may have protective role against sulfonylurea-induced hypoglycemia.

DNA methylation versus gene expression

Development ◽  
1984 ◽  
Vol 83 (Supplement) ◽  
pp. 31-40
Author(s):  
Adrian P. Bird
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cell Division ◽  
Methylation Pattern ◽  
Current Evidence ◽  
Evolutionary Perspective ◽  
Cell Type ◽  
Versus Gene ◽  
Daughter Cells ◽  
The Relationship

Vertebrate DNA is methylated at a high proportion of cytosine residues in the sequence CpG, and it has been suggested that the distribution of methylated and non-methylated CpGs in a given cell type influences the pattern of gene expression in those cells. Since a DNA methylation pattern is normally transmitted faithfully to daughter cells via cell division, this idea suggests an origin for stable, clonally inherited patterns of gene expression. This article discusses some of the current evidence for a relationship between DNA methylation and gene expression. Although the evidence is incomplete, it appears already that the relationship is variable: transcription of some genes is repressed by the presence of 5-methylcytosine at certain CpGs, and may be controlled by methylation, while transcription of other genes is indifferent to methylation. In attempting to explain this variability it is helpful to adopt an evolutionary perspective.

scholarly journals Aging and Caloric Restriction Modulate the DNA Methylation Profile of the Ribosomal RNA Locus in Human and Rat Liver

Nutrients ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 277 ◽  
Author(s):  
Noémie Gensous ◽  
Francesco Ravaioli ◽  
Chiara Pirazzini ◽  
Roberto Gramignoli ◽  
Ewa Ellis ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Caloric Restriction ◽  
Ribosomal Rna ◽  
Tissue Specificity ◽  
Rdna Locus ◽  
Nutritional Interventions ◽  
Age Related ◽  
Dna Methylation Profile ◽  
Main Determinants ◽  
First Time

A growing amount of evidence suggests that the downregulation of protein synthesis is an adaptive response during physiological aging, which positively contributes to longevity and can be modulated by nutritional interventions like caloric restriction (CR). The expression of ribosomal RNA (rRNA) is one of the main determinants of translational rate, and epigenetic modifications finely contribute to its regulation. Previous reports suggest that hypermethylation of ribosomal DNA (rDNA) locus occurs with aging, although with some species- and tissue- specificity. In the present study, we experimentally measured DNA methylation of three regions (the promoter, the 5′ of the 18S and the 5′ of 28S sequences) in the rDNA locus in liver tissues from rats at two, four, 10, and 18 months. We confirm previous findings, showing age-related hypermethylation, and describe, for the first time, that this gain in methylation also occurs in human hepatocytes. Furthermore, we show that age-related hypermethylation is enhanced in livers of rat upon CR at two and 10 months, and that at two months a trend towards the reduction of rRNA expression occurs. Collectively, our results suggest that CR modulates age-related regulation of methylation at the rDNA locus, thus providing an epigenetic readout of the pro-longevity effects of CR.

Sign in / Sign up

Export Citation Format

Share Document