scholarly journals Differential requirement of MED14 and UVH6 for heterochromatin transcription upon destabilization of silencing

2018 ◽  
Author(s):  
Pierre Bourguet ◽  
Stève de Bossoreille ◽  
Leticia López-González ◽  
Marie-Noëlle Pouch-Pélissier ◽  
Ángeles Gómez-Zambrano ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Heat Stress ◽  
Environmental Changes ◽  
Constitutive Heterochromatin ◽  
Epigenetic Marks ◽  
Two Factors ◽  
Silencing Pathways ◽  
Heterochromatin Silencing ◽  
Insight Into ◽  
Chromatin Patterns

AbstractConstitutive heterochromatin is commonly associated with high levels of repressive epigenetic marks and is stably maintained transcriptionally silent by the concerted action of different, yet convergent, silencing pathways. Reactivation of heterochromatin transcription is generally associated with alterations in levels of these epigenetic marks. However, in mutants for particular epigenetic regulators, or upon particular environmental changes such as heat stress, heterochromatin-associated silencing is destabilized without noticeable changes in epigenetic marks. This suggests that transcription can occur in a non-permissive chromatin context, yet the factors involved remain poorly known. Here, we show that heat stress-induced transcription of heterochromatin depends on the TFIIH component UVH6 and the Mediator subunit MED14. Mutants for these two factors exhibit hypersensitivity to heat stress, and under these conditions, UVH6 and MED14 are required for transcription of a high number of loci. We further show that MED14, but not UVH6, is required for transcription when heterochromatin silencing is destabilized in the absence of stress. In this case, MED14 requires proper chromatin patterns of repressive epigenetic marks for its function. We also uncover that MED14 regulates non-CG DNA methylation at a subset of RNA-directed DNA methylation target loci. These findings provide insight into the control of heterochromatin transcription upon silencing destabilization and identify MED14 as a regulator of DNA methylation.

scholarly journals A role for MED14 and UVH6 in heterochromatin transcription upon destabilization of silencing

2018 ◽  
Vol 1 (6) ◽  
pp. e201800197 ◽  
Author(s):  
Pierre Bourguet ◽  
Stève de Bossoreille ◽  
Leticia López-González ◽  
Marie-Noëlle Pouch-Pélissier ◽  
Ángeles Gómez-Zambrano ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Environmental Changes ◽  
Constitutive Heterochromatin ◽  
Transcriptional Silencing ◽  
Epigenetic Marks ◽  
Transcriptional Changes ◽  
Heterochromatin Silencing ◽  
Insight Into

Constitutive heterochromatin is associated with repressive epigenetic modifications of histones and DNA which silence transcription. Yet, particular mutations or environmental changes can destabilize heterochromatin-associated silencing without noticeable changes in repressive epigenetic marks. Factors allowing transcription in this nonpermissive chromatin context remain poorly known. Here, we show that the transcription factor IIH component UVH6 and the mediator subunit MED14 are both required for heat stress–induced transcriptional changes and release of heterochromatin transcriptional silencing in Arabidopsis thaliana. We find that MED14, but not UVH6, is required for transcription when heterochromatin silencing is destabilized in the absence of stress through mutating the MOM1 silencing factor. In this case, our results raise the possibility that transcription dependency over MED14 might require intact patterns of repressive epigenetic marks. We also uncover that MED14 regulates DNA methylation in non-CG contexts at a subset of RNA-directed DNA methylation target loci. These findings provide insight into the control of heterochromatin transcription upon silencing destabilization and identify MED14 as a regulator of DNA methylation.

6 ALTERED CHROMATIN CONFORMATION IN BOVINE SPERMATOZOA PERTURBS DYNAMIC DNA METHYLATION IN THE MALE PRONUCLEUS AFTER FERTILIZATION IN VITRO

2013 ◽  
Vol 25 (1) ◽  
pp. 150 ◽  
Author(s):  
M. B. Rahman ◽  
M. M. Kamal ◽  
T. Rijsselaere ◽  
L. Vandaele ◽  
M. Shamsuddin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Heat Stress ◽  
De Novo ◽  
Chromatin Condensation ◽  
Sperm Chromatin ◽  
Chromatin Conformation ◽  
Epigenetic Marks ◽  
Time Points ◽  
Male Pronucleus ◽  
De Novo Methylation

Soon after fertilization, mammalian zygotes need proper DNA methylation reprogramming, at which time the epigenetic marks that the oocyte and sperm have acquired during gametogenesis are erased to allow totipotent zygotic development. Aberrant epigenetic marks in the paternal genome are thought to be associated with altered chromatin condensation in spermatozoa of suboptimal quality. We have recently reported that heat stress on bulls during germ cell development, especially at the spermiogenesis stage, altered sperm chromatin condensation. The objective of this study was to investigate dynamic DNA methylation reprogramming in the male pronucleus after fertilization of oocytes with sperm known to have altered chromatin conformation. To evaluate dynamic DNA methylation reprogramming, zygotes collected at 3 different time points [i.e. 12, 18, and 24 h post-insemination (hpi)] were immunocytochemically investigated using an antibody against 5-methylcytosine (5mC). The total fluorescence intensity of the male pronuclei (n = 89, ≥25 in each group) was measured by ImageJ and data were analyzed by ANOVA. The DNA methylation pattern in male pronuclei when oocytes were fertilized with heat-stressed sperm did not change between time points (P > 0.05), whereas control zygotes clearly showed demethylation and de novo methylation at 18 and 24 hpi, respectively. The results of this study indicated that dynamic DNA methylation reprogramming patterns such as DNA demethylation followed by de novo methylation in the male pronucleus soon after fertilization were altered when oocytes were fertilized with heat-stressed sperm. In conclusion, altered sperm chromatin conformation due to heat stress perturbs dynamic DNA methylation reprogramming in the male pronucleus, which may hamper nuclear totipotency and embryo survival.

DNA Methylation of Seed in Response to Heat Stress in Brassica rapa L.

2011 ◽  
Vol 37 (9) ◽  
pp. 1597-1604 ◽  
Author(s):  
Gui-Zhen GAO ◽  
Fei YING ◽  
Bi-Yun CHEN ◽  
Hao LI ◽  
Xiao-Dan LÜ ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Heat Stress ◽  
Brassica Rapa

scholarly journals The tepary bean genome provides insight into evolution and domestication under heat stress

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Samira Mafi Moghaddam ◽  
Atena Oladzad ◽  
Chushin Koh ◽  
Larissa Ramsay ◽  
John P. Hart ◽  
...  
Keyword(s):  
Heat Stress ◽  
Common Bean ◽  
Sonoran Desert ◽  
Climate Adaptation ◽  
Human Consumption ◽  
Disease Resistance Gene ◽  
Gene Repertoire ◽  
Tepary Bean ◽  
Hot Environments ◽  
Insight Into

AbstractTepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Here, we report on the tepary genome including exploration of possible mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid and hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.

scholarly journals Identification of Putative Virulence Genes by DNA Methylation Studies in the Cereal Pathogen Fusarium graminearum

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1192
Author(s):  
Francesco Tini ◽  
Giovanni Beccari ◽  
Gianpiero Marconi ◽  
Andrea Porceddu ◽  
Micheal Sulyok ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Fusarium Graminearum ◽  
Environmental Changes ◽  
Virulent Strain ◽  
Fungal Virulence ◽  
Wheat Seedlings ◽  
Wide Range ◽  
Conidia Production ◽  
Natural Hosts

DNA methylation mediates organisms’ adaptations to environmental changes in a wide range of species. We investigated if a such a strategy is also adopted by Fusarium graminearum in regulating virulence toward its natural hosts. A virulent strain of this fungus was consecutively sub-cultured for 50 times (once a week) on potato dextrose agar. To assess the effect of subculturing on virulence, wheat seedlings and heads (cv. A416) were inoculated with subcultures (SC) 1, 23, and 50. SC50 was also used to re-infect (three times) wheat heads (SC50×3) to restore virulence. In vitro conidia production, colonies growth and secondary metabolites production were also determined for SC1, SC23, SC50, and SC50×3. Seedling stem base and head assays revealed a virulence decline of all subcultures, whereas virulence was restored in SC50×3. The same trend was observed in conidia production. The DNA isolated from SC50 and SC50×3 was subject to a methylation content-sensitive enzyme and double-digest, restriction-site-associated DNA technique (ddRAD-MCSeEd). DNA methylation analysis indicated 1024 genes, whose methylation levels changed in response to the inoculation on a healthy host after subculturing. Several of these genes are already known to be involved in virulence by functional analysis. These results demonstrate that the physiological shifts following sub-culturing have an impact on genomic DNA methylation levels and suggest that the ddRAD-MCSeEd approach can be an important tool for detecting genes potentially related to fungal virulence.

scholarly journals Precise regulation of the relative rates of surface area and volume synthesis in bacterial cells growing in dynamic environments

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Handuo Shi ◽  
Yan Hu ◽  
Pascal D. Odermatt ◽  
Carlos G. Gonzalez ◽  
Lichao Zhang ◽  
...  
Keyword(s):  
Growth Rate ◽  
Time Delay ◽  
Surface Area ◽  
Environmental Changes ◽  
Volume Ratio ◽  
Dynamic Environments ◽  
Bacterial Cells ◽  
Bacterial Growth Rate ◽  
State Size ◽  
Insight Into

AbstractThe steady-state size of bacterial cells correlates with nutrient-determined growth rate. Here, we explore how rod-shaped bacterial cells regulate their morphology during rapid environmental changes. We quantify cellular dimensions throughout passage cycles of stationary-phase cells diluted into fresh medium and grown back to saturation. We find that cells exhibit characteristic dynamics in surface area to volume ratio (SA/V), which are conserved across genetic and chemical perturbations as well as across species and growth temperatures. A mathematical model with a single fitting parameter (the time delay between surface and volume synthesis) is quantitatively consistent with our SA/V experimental observations. The model supports that this time delay is due to differential expression of volume and surface-related genes, and that the first division after dilution occurs at a tightly controlled SA/V. Our minimal model thus provides insight into the connections between bacterial growth rate and cell shape in dynamic environments.

scholarly journals Individuals Diagnosed with Binge-Eating Disorder Have DNA Hypomethylated Sites in Genes of the Metabolic System: A Pilot Study

Nutrients ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1413
Author(s):  
Mariana Lizbeth Rodríguez-López ◽  
José Jaime Martínez-Magaña ◽  
David Ruiz-Ramos ◽  
Ana Rosa García ◽  
Laura Gonzalez ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Eating Disorder ◽  
Protein Kinase ◽  
Binge Eating ◽  
Binge Eating Disorder ◽  
Environmental Changes ◽  
Diagnostic Category ◽  
The Body ◽  
Metabolic System ◽  
Genome Wide

Binge-eating disorder, recently accepted as a diagnostic category, is differentiated from bulimia nervosa in that the former shows the presence of binge-eating episodes and the absence of compensatory behavior. Epigenetics is a conjunct of mechanisms (like DNA methylation) that regulate gene expression, which are dependent on environmental changes. Analysis of DNA methylation in eating disorders shows that it is reduced. The present study aimed to analyze the genome-wide DNA methylation differences between individuals diagnosed with BED and BN. A total of 46 individuals were analyzed using the Infinium Methylation EPIC array. We found 11 differentially methylated sites between BED- and BN-diagnosed individuals, with genome-wide significance. Most of the associations were found in genes related to metabolic processes (ST3GAL4, PRKAG2, and FRK), which are hypomethylated genes in BED. Cg04781532, located in the body of the PRKAG2 gene (protein kinase AMP-activated non-catalytic subunit gamma 2), was hypomethylated in individuals with BED. Agonists of PRKAG2, which is the subunit of AMPK (AMP-activated protein kinase), are proposed to treat obesity, BED, and BN. The present study contributes important insights into the effect that BED could have on PRKAG2 activation.

scholarly journals Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Guillaume Wos ◽  
Rimjhim Roy Choudhury ◽  
Filip Kolář ◽  
Christian Parisod
Keyword(s):  
Transposable Elements ◽  
Environmental Changes ◽  
Common Garden ◽  
Elevational Gradient ◽  
Mountain Regions ◽  
Transcriptomic Response ◽  
Genetic Lineages ◽  
Two Factors ◽  
Arabidopsis Arenosa ◽  
Expression Response

Abstract Background Plant genomes can respond rapidly to environmental changes and transposable elements (TEs) arise as important drivers contributing to genome dynamics. Although some elements were reported to be induced by various abiotic or biotic factors, there is a lack of general understanding on how environment influences the activity and diversity of TEs. Here, we combined common garden experiment with short-read sequencing to investigate genomic abundance and expression of 2245 consensus TE sequences (containing retrotransposons and DNA transposons) in an alpine environment in Arabidopsis arenosa. To disentangle general trends from local differentiation, we leveraged four foothill-alpine population pairs from different mountain regions. Seeds of each of the eight populations were raised under four treatments that differed in temperature and irradiance, two factors varying with elevation. RNA-seq analysis was performed on leaves of young plants to test for the effect of elevation and subsequently of temperature and irradiance on expression of TE sequences. Results Genomic abundance of the 2245 consensus TE sequences varied greatly between the mountain regions in line with neutral divergence among the regions, representing distinct genetic lineages of A. arenosa. Accounting for intraspecific variation in abundance, we found consistent transcriptomic response for some TE sequences across the different pairs of foothill-alpine populations suggesting parallelism in TE expression. In particular expression of retrotransposon LTR Copia (e.g. Ivana and Ale clades) and LTR Gypsy (e.g. Athila and CRM clades) but also non-LTR LINE or DNA transposon TIR MuDR consistently varied with elevation of origin. TE sequences responding specifically to temperature and irradiance belonged to the same classes as well as additional TE clades containing potentially stress-responsive elements (e.g. LTR Copia Sire and Tar, LTR Gypsy Reina). Conclusions Our study demonstrated that the A. arenosa genome harbours a considerable diversity of TE sequences whose abundance and expression response varies across its native range. Some TE clades may contain transcriptionally active elements responding to a natural environmental gradient. This may further contribute to genetic variation between populations and may ultimately provide new regulatory mechanisms to face environmental challenges.

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