scholarly journals Tying Metabolic Branches With Histone Tails Using Systems Biology

2019 ◽  
Vol 12 ◽  
pp. 251686571986968
Author(s):  
Sriram Chandrasekaran
Keyword(s):  
Gene Expression ◽  
Systems Biology ◽  
Histone Modifications ◽  
Metabolic Pathways ◽  
Cellular Mechanism ◽  
Histone Tails ◽  
Metabolic Fluxes ◽  
Adenosyl Methionine ◽  
The Impact ◽  
Influence Gene Expression

Histone modifications represent an innate cellular mechanism to link nutritional status to gene expression. Metabolites such as acetyl-CoA and S-adenosyl methionine influence gene expression by serving as substrates for modification of histones. Yet, we lack a predictive model for determining histone modification levels based on cellular metabolic state. The numerous metabolic pathways that intersect with histone marks makes it highly challenging to understand their interdependencies. Here, we highlight new systems biology tools to unravel the impact of nutritional cues and metabolic fluxes on histone modifications.

scholarly journals The Interplay between Immunity and Microbiota at Intestinal Immunological Niche: The Case of Cancer

2019 ◽  
Vol 20 (3) ◽  
pp. 501 ◽  
Author(s):  
Rossella Cianci ◽  
Laura Franza ◽  
Giovanni Schinzari ◽  
Ernesto Rossi ◽  
Gianluca Ianiro ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune System ◽  
Gut Microbiota ◽  
Special Role ◽  
Microbiota Composition ◽  
Cancer Treatments ◽  
Microbial Composition ◽  
Different Types ◽  
The Impact ◽  
Influence Gene Expression

The gut microbiota is central to the pathogenesis of several inflammatory and autoimmune diseases. While multiple mechanisms are involved, the immune system clearly plays a special role. Indeed, the breakdown of the physiological balance in gut microbial composition leads to dysbiosis, which is then able to enhance inflammation and to influence gene expression. At the same time, there is an intense cross-talk between the microbiota and the immunological niche in the intestinal mucosa. These interactions may pave the way to the development, growth and spreading of cancer, especially in the gastro-intestinal system. Here, we review the changes in microbiota composition, how they relate to the immunological imbalance, influencing the onset of different types of cancer and the impact of these mechanisms on the efficacy of traditional and upcoming cancer treatments.

scholarly journals Slower development of lower canopy beans produces better coffee

2020 ◽  
Vol 71 (14) ◽  
pp. 4201-4214 ◽  
Author(s):  
Bing Cheng ◽  
Heather E Smyth ◽  
Agnelo Furtado ◽  
Robert J Henry
Keyword(s):  
Gene Expression ◽  
Metabolic Pathways ◽  
Global Gene Expression ◽  
Coffee Production ◽  
High Quality ◽  
Development Stages ◽  
Expression Of Genes ◽  
Coffee Beans ◽  
The Impact ◽  
Selection Of

Abstract The production of high-quality coffee is being challenged by changing climates in coffee-growing regions. The coffee beans from the upper and lower canopy at different development stages of the same plants were analyzed to investigate the impact of the microenvironment on gene expression and coffee quality. Compared with coffee beans from the upper canopy, lower canopy beans displayed more intense aroma with higher caffeine, trigonelline, and sucrose contents, associated with greater gene expression in the representative metabolic pathways. Global gene expression indicated a longer ripening in the lower canopy, resulting from higher expression of genes relating to growth inhibition and suppression of chlorophyll degradation during early bean ripening. Selection of genotypes or environments that enhance expression of the genes slowing bean development may produce higher quality coffee beans, allowing coffee production in a broader range of available future environments.

scholarly journals Divergent patterns of selection on metabolite levels and gene expression

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Alexander F. Kern ◽  
Grace Xiaolu Yang ◽  
Neil M. Khosla ◽  
Roy Moh Lik Ang ◽  
Michael P. Snyder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Pathways ◽  
Antifungal Drugs ◽  
Ergosterol Biosynthesis ◽  
Expression Data ◽  
Yeast Strains ◽  
Genetic Cross ◽  
Polygenic Adaptation ◽  
Trait Locus ◽  
The Impact

Abstract Background Natural selection can act on multiple genes in the same pathway, leading to polygenic adaptation. For example, adaptive changes were found to down-regulate six genes involved in ergosterol biosynthesis—an essential pathway targeted by many antifungal drugs—in some strains of the yeast Saccharomyces cerevisiae. However, the impact of this polygenic adaptation on metabolite levels was unknown. Here, we performed targeted mass spectrometry to measure the levels of eight metabolites in this pathway in 74 yeast strains from a genetic cross. Results Through quantitative trait locus (QTL) mapping we identified 19 loci affecting ergosterol pathway metabolite levels, many of which overlap loci that also impact gene expression within the pathway. We then used the recently developed v-test, which identified selection acting upon three metabolite levels within the pathway, none of which were predictable from the gene expression adaptation. Conclusions These data showed that effects of selection on metabolite levels were complex and not predictable from gene expression data. This suggests that a deeper understanding of metabolism is necessary before we can understand the impacts of even relatively straightforward gene expression adaptations on metabolic pathways.

scholarly journals An Efficient Chromatin Immunoprecipitation (ChIP) Protocol for Studying Histone Modifications in Peach Reproductive Tissues

2021 ◽  
Author(s):  
Monica Canton ◽  
Silvia Farinati ◽  
Cristian Forestan ◽  
Justin Joseph ◽  
Claudio Bonghi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Histone H3 ◽  
Fruit Trees ◽  
Fruit Growth ◽  
Bud Dormancy ◽  
Chromatin States ◽  
Reproductive Tissues ◽  
The Impact

Abstract BackgroundPerennial fruit trees display a perennial growth behaviour characterized by an annual cycling between growth and dormancy, with complex physiological features. Rosaceae fruit trees represent excellent models for studying not only the fruit growth/patterning, but also the progression of the reproductive cycle depending upon the impact of climate conditions. In addition, the current development of high‐throughput technologies is starting to have an important impact on Rosaceae tree research for investigating genome structure and function as well as (epi)genetic mechanisms involved in important developmental and environmental response processes during fruit tree growth. Among the epigenetic mechanisms, chromatin remodelling mediated by both histone modifications and other chromatin-related processes play a crucial role in gene modulation, controlling gene expression process. A very useful technique to investigate the chromatin states in plants and their dynamics is chromatin immunoprecipitation (ChIP), generally applied for studies on chromatin states and enrichment in post transcriptional modifications (PTMs) of histone proteins. Results Because peach is a model in Rosaceae family for studies in bud formation, dormancy and organ differentiation for climacteric fruits, in our work, we primarily established specific protocols for chromatin extraction and immunoprecipitation in reproductive tissues of peach Prunus persica. Subsequently focused our investigations on the role of two chromatin marks, namely trimethylation of histone H3 at lysine in position 4 (H3K4me3) and trimethylation of histone H3 at lysine 27 (H3K27me3) on modulating specific gene expression. Bud dormancy and fruit growth were investigated in a nectarine genotype called Fantasia as a model system. ConclusionsHere we presented general strategies to systematically optimize ChIP protocols for buds and mesocarp tissues and analyzed the correlation between gene expression and chromatin mark enrichment/depletion. Confirming like histone modifications are implicated in regulating bud dormancy progression and the core ripening genes.

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