scholarly journals Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine

2018 ◽  
Author(s):  
Wei Ding ◽  
Daniel P Higgins ◽  
Dilip K. Yadav ◽  
Read Pukklia-Worley ◽  
Amy K Walker
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Stress Responses ◽  
Chromatin Modification ◽  
Metabolic Gene ◽  
C Elegans ◽  
Genome Wide ◽  
Heat Shock Responses ◽  
Pathogen Response ◽  
H3k4 Methyltransferases

AbstractS-adenosylmethionine (SAM) is the methyl donor that modifies proteins such as histones, nucleic acids and produces phosphatidylcholine. Thus variations in SAM levels could affect processes from lipogenesis to epigenetic gene regulation. SAM is hypothesized to link metabolism and chromatin modification, however, its role in acute gene regulation is poorly understood. We recently found that Caenorhabditis elegans with reduced SAM had deficiencies in bacterial-induced H3K4 trimethylation at selected pathogen-response genes, decreasing their expression and limiting survival on the pathogen Pseudomonas aeruginosa. This led us to the hypothesis that SAM may be generally required stress-responsive transcription. Here we show that C. elegans with low SAM fail to activate genome-wide transcriptional programs when exposed to bacterial or xenotoxic stress. However, heat shock responses were unaffected. We also investigated the role of two H3K4 methyltransferases that use SAM, set-2/SET1, and set-16/MLL and found that set-2/SET1 has a specific requirement in bacterial stress responses, whereas set-16/MLL was required for survival in all three stresses. These results define a role for SAM and H3K4 methyltransferases in the acute genome-wide remodeling of gene expression in response to stress. Finally, we find that the ability to modify metabolic gene expression correlates with enhanced survival in stress conditions.

scholarly journals Histone H3K9 methylation promotes formation of genome compartments inCaenorhabditis elegansvia chromosome compaction and perinuclear anchoring

2020 ◽  
Vol 117 (21) ◽  
pp. 11459-11470 ◽  
Author(s):  
Qian Bian ◽  
Erika C. Anderson ◽  
Qiming Yang ◽  
Barbara J. Meyer
Keyword(s):  
Gene Expression ◽  
Nuclear Periphery ◽  
Chromosome Conformation ◽  
C Elegans ◽  
Genome Wide ◽  
Central Regions ◽  
In Trans ◽  
Genomic Regions ◽  
In Cis ◽  
Gene Expression Levels

Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explore mechanisms controlling genome compartment organization inCaenorhabditis elegansand investigate roles for compartments in regulating gene expression. Distal arms ofC. eleganschromosomes, which are enriched for heterochromatic histone modifications H3K9me1/me2/me3, interact with each other bothin cisandin trans,while interacting less frequently with central regions, leading to genome compartmentalization. Arms are anchored to the nuclear periphery via the nuclear envelope protein CEC-4, which binds to H3K9me. By performing genome-wide chromosome conformation capture experiments (Hi-C), we showed that eliminating H3K9me1/me2/me3 through mutations in the methyltransferase genesmet-2andset-25significantly impaired formation of inactive Arm and active Center compartments.cec-4mutations also impaired compartmentalization, but to a lesser extent. We found that H3K9me promotes compartmentalization through two distinct mechanisms: Perinuclear anchoring of chromosome arms via CEC-4 to promote theircisassociation, and an anchoring-independent mechanism that compacts individual chromosome arms. In bothmet-2 set-25andcec-4mutants, no dramatic changes in gene expression were found for genes that switched compartments or for genes that remained in their original compartment, suggesting that compartment strength does not dictate gene-expression levels. Furthermore, H3K9me, but not perinuclear anchoring, also contributes to formation of another prominent feature of chromosome organization, megabase-scale topologically associating domains on X established by the dosage compensation condensin complex. Our results demonstrate that H3K9me plays crucial roles in regulating genome organization at multiple levels.

scholarly journals Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 492 ◽  
Author(s):  
Buchberger ◽  
Reis ◽  
Lu ◽  
Posnien
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Evolutionary Biology ◽  
Phenotypic Evolution ◽  
Specific Expression ◽  
Expression Studies ◽  
Genome Wide ◽  
Key Driver ◽  
Context Dependent ◽  
Genome Wide Expression

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.

scholarly journals Nanoimpact in Plants: Lessons from the Transcriptome

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 751
Author(s):  
Susana García-Sánchez ◽  
Michal Gala ◽  
Gabriel Žoldák
Keyword(s):  
Gene Regulation ◽  
Abiotic Stress ◽  
Comparative Analysis ◽  
Drought Stress ◽  
Stress Responses ◽  
Specific Gene ◽  
Potential Toxicity ◽  
Transcriptional Responses ◽  
Regulatory Circuits ◽  
Pathogen Response

Transcriptomics studies are available to evaluate the potential toxicity of nanomaterials in plants, and many highlight their effect on stress-responsive genes. However, a comparative analysis of overall expression changes suggests a low impact on the transcriptome. Environmental challenges like pathogens, saline, or drought stress induce stronger transcriptional responses than nanoparticles. Clearly, plants did not have the chance to evolve specific gene regulation in response to novel nanomaterials; but they use common regulatory circuits with other stress responses. A shared effect with abiotic stress is the inhibition of genes for root development and pathogen response. Other works are reviewed here, which also converge on these results.

scholarly journals Network analysis links genome-wide phenotypic and transcriptional stress responses in a bacterial pathogen with a large pan-genome

2016 ◽  
Author(s):  
Paul A. Jensen ◽  
Zeyu Zhu ◽  
Tim van Opijnen
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Meta Analysis ◽  
Bacterial Pathogen ◽  
Metabolic Model ◽  
Genetic Network ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome ◽  
Response To Stress

ABSTRACTBackgroundBacteria modulate subcellular processes to handle stressful environments. Genome-wide profiling of gene expression (RNA-Seq) and fitness (Tn-Seq) allows two views of the same genetic network underlying these responses. However, it remains unclear how they combine, enabling a bacterium to overcome a perturbation.ResultsHere we generate RNA-Seq and Tn-Seq profiles in three strains of S. pneumoniae in response to stress defined by different levels of nutrient depletion. These profiles show that genes that change their expression and/or become phenotypically important come from a diverse set of functional categories, and genes that are phenotypically important tend to be highly expressed. Surprisingly, we find that expression and fitness changes rarely occur on the same gene, which we confirmed by over 140 validation experiments. To rationalize these unexpected results we built the first genome-scale metabolic model of S. pneumoniae showing that differential expression and phenotypic importance actually correlate between nearest neighbors, although they are distinctly partitioned into small subnetworks. Moreover, a meta-analysis of 234 S. pneumoniae gene expression studies reveals that essential genes and phenotypically important subnetworks rarely change expression, indicating that they are shielded from transcriptional fluctuations and that a clear distinction exists between transcriptional and phenotypic response networks.ConclusionsWe present a genome-wide computational/experimental approach that contextualizes changes that occur on transcriptomic and phenomic levels in response to stress. Importantly, this highlights the need to connect disparate response networks, for instance in antibiotic target identification, where preferred targets are phenotypically important genes that would be overlooked by transcriptomic analyses alone.

scholarly journals Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for the Evolution of Gene Expression

2019 ◽  
Author(s):  
Elisa Buchberger ◽  
Micael Reis ◽  
Ting-Hsuan Lu ◽  
Nico Posnien
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Evolutionary Biology ◽  
Expression Data ◽  
Regulatory Evolution ◽  
Specific Expression ◽  
Genome Wide ◽  
Key Driver ◽  
Context Dependent ◽  
Genome Wide Expression

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic variation. An exceptional contribution of cis-regulatory evolution has for instance been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and developmental stage-specific expression. We argue that the regulatory context must be considered when studying evolution of gene expression.

scholarly journals CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Fabio Gomez-Cano ◽  
Lisa Carey ◽  
Kevin Lucas ◽  
Tatiana García Navarrete ◽  
Eric Mukundi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Close Relative ◽  
Jet Fuels ◽  
Genome Wide ◽  
Reference Plant ◽  
Winter Cover Crop ◽  
One Stop ◽  
New Gene ◽  
Brassicaceae Family

Abstract Camelina is an annual oilseed plant from the Brassicaceae family that is gaining momentum as a biofuel winter cover crop. However, a significant limitation in further enhancing its utility as a producer of oils that can be used as biofuels, jet fuels or bio-based products is the absence of a repository for all the gene expression and regulatory information that is being rapidly generated by the community. Here, we provide CamRegBase (https://camregbase.org/) as a one-stop resource to access Camelina information on gene expression and co-expression, transcription factors, lipid associated genes and genome-wide orthologs in the close-relative reference plant Arabidopsis. We envision this as a resource of curated information for users, as well as a repository of new gene regulation information.

scholarly journals A global chromatin compaction pathway that represses germline gene expression during starvation

2021 ◽  
Vol 220 (9) ◽  
Author(s):  
Mezmur D. Belew ◽  
Emilie Chien ◽  
Matthew Wong ◽  
W. Matthew Michael
Keyword(s):  
Gene Expression ◽  
Topoisomerase Ii ◽  
Germline Gene ◽  
Regulate Gene Expression ◽  
Chromatin Compaction ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome ◽  
Energy Sensing ◽  
Heterochromatin Assembly

While much is known about how transcription is controlled at individual genes, comparatively little is known about how cells regulate gene expression on a genome-wide level. Here, we identify a molecular pathway in the C. elegans germline that controls transcription globally in response to nutritional stress. We report that when embryos hatch into L1 larvae, they sense the nutritional status of their environment, and if food is unavailable, they repress gene expression via a global chromatin compaction (GCC) pathway. GCC is triggered by the energy-sensing kinase AMPK and is mediated by a novel mechanism that involves the topoisomerase II/condensin II axis acting upstream of heterochromatin assembly. When the GCC pathway is inactivated, then transcription persists during starvation. These results define a new mode of whole-genome control of transcription.

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