scholarly journals The impact of Piscirickettsia Salmonis infection on genome-wide DNA methylation profile in Atlantic Salmon

2021 ◽  
Author(s):  
Robert Mukiibi ◽  
Carolina Peñaloza ◽  
Alejandro Gutierrez ◽  
José M. Yáñez ◽  
Ross D. Houston ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Atlantic Salmon ◽  
Negative Correlation ◽  
Regulation Of Gene Expression ◽  
Head Kidney ◽  
Epigenetic Mechanism ◽  
Piscirickettsia Salmonis ◽  
The Impact

Salmon rickettsial septicaemia (SRS), caused by the intracellular bacteria Piscirickettsia Salmonis, generates significant mortalities to farmed Atlantic salmon, particularly in Chile. Due to its economic importance, a wealth of research has focussed on the biological mechanisms underlying pathogenicity of P. salmonis, the host response, and genetic variation in host resistance. DNA methylation is a fundamental epigenetic mechanism that influences almost every biological process via the regulation of gene expression and plays a key role in the response of an organism to stimuli. In the current study, the role of head kidney and liver DNA methylation in the response to P. salmonis infection was investigated in a commercial Atlantic salmon population. A total of 66 salmon were profiled using reduced representation bisulphite sequencing (RRBS), with head kidney and liver methylomes compared between infected animals (3 and 9 days post infection) and uninfected controls. These included groups of salmon with divergent (high or low) breeding values for resistance to P. salmonis infection, to examine the influence of genetic resistance. Head kidney and liver showed organ-specific global methylation patterns, but with similar distribution of methylation across gene features. Integration of methylation with RNA-Seq data revealed that methylation levels predominantly showed a negative correlation with gene expression, although positive correlations were also observed. Methylation within the first exon showed the strongest negative correlation with gene expression. A total of 911 and 813 differentially methylated CpG sites were identified between infected and control samples in the head kidney at 3 and 9 days respectively, whereas only 30 and 44 sites were differentially methylated in the liver. Differential methylation in the head kidney was associated with immunological processes such as actin cytoskeleton regulation, phagocytosis, endocytosis and pathogen associated pattern receptor signaling. We also identified 113 and 48 differentially methylated sites between resistant and susceptible fish in the head kidney and liver respectively. Our results contribute to the growing understanding of the role of methylation in regulation of gene expression and response to infectious diseases, and in particular reveal key immunological functions regulated by methylation in Atlantic salmon in response to P. salmonis.

Speciation and changes in male gene expression in Drosophila

Genome ◽  
2020 ◽  
pp. 1-11
Author(s):  
Bahar Patlar ◽  
Alberto Civetta
Keyword(s):  
Gene Expression ◽  
Reproductive Isolation ◽  
Potential Role ◽  
Regulation Of Gene Expression ◽  
Drosophila Model ◽  
Depth Analysis ◽  
The Impact ◽  
Plastic Responses ◽  
Male Gene

It has long been acknowledged that changes in the regulation of gene expression may account for major organismal differences. However, we still do not fully understand how changes in gene expression evolve and how do such changes influence organisms’ differences. We are even less aware of the impact such changes might have in restricting gene flow between species. Here, we focus on studies of gene expression and speciation in the Drosophila model. We review studies that have identified gene interactions in post-mating reproductive isolation and speciation, particularly those that modulate male gene expression. We also address studies that have experimentally manipulated changes in gene expression to test their effect in post-mating reproductive isolation. We highlight the need for a more in-depth analysis of the role of selection causing disrupted gene expression of such candidate genes in sterile/inviable hybrids. Moreover, we discuss the relevance to incorporate more routinely assays that simultaneously evaluate the potential effects of environmental factors and genetic background in modulating plastic responses in male genes and their potential role in speciation.

scholarly journals Nutrient-Dependent Changes of Protein Palmitoylation: Impact on Nuclear Enzymes and Regulation of Gene Expression

2018 ◽  
Vol 19 (12) ◽  
pp. 3820 ◽  
Author(s):  
Matteo Spinelli ◽  
Salvatore Fusco ◽  
Claudio Grassi
Keyword(s):  
Gene Expression ◽  
Protein Trafficking ◽  
Regulation Of Gene Expression ◽  
Cysteine Modification ◽  
Post Translational Modifications ◽  
Protein Palmitoylation ◽  
Physiological Phenomenon ◽  
The Impact ◽  
Protein Lipidation

Diet is the main environmental stimulus chronically impinging on the organism throughout the entire life. Nutrients impact cells via a plethora of mechanisms including the regulation of both protein post-translational modifications and gene expression. Palmitoylation is the most-studied protein lipidation, which consists of the attachment of a molecule of palmitic acid to residues of proteins. S-palmitoylation is a reversible cysteine modification finely regulated by palmitoyl-transferases and acyl-thioesterases that is involved in the regulation of protein trafficking and activity. Recently, several studies have demonstrated that diet-dependent molecules such as insulin and fatty acids may affect protein palmitoylation. Here, we examine the role of protein palmitoylation on the regulation of gene expression focusing on the impact of this modification on the activity of chromatin remodeler enzymes, transcription factors, and nuclear proteins. We also discuss how this physiological phenomenon may represent a pivotal mechanism underlying the impact of diet and nutrient-dependent signals on human diseases.

scholarly journals 5-Azacytidine: A Promoter of Epigenetic Changes in the Quest to Improve Plant Somatic Embryogenesis

2018 ◽  
Vol 19 (10) ◽  
pp. 3182 ◽  
Author(s):  
Pedro Osorio-Montalvo ◽  
Luis Sáenz-Carbonell ◽  
Clelia De-la-Peña
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Somatic Embryogenesis ◽  
Regulation Of Gene Expression ◽  
Culture Conditions ◽  
Short Time ◽  
Time Frames ◽  
Different Sources

Somatic embryogenesis (SE) is a widely studied process due to its biotechnological potential to generate large quantities of plants in short time frames and from different sources of explants. The success of SE depends on many factors, such as the nature of the explant, the microenvironment generated by in vitro culture conditions, and the regulation of gene expression, among others. Epigenetics has recently been identified as an important factor influencing SE outcome. DNA methylation is one of the most studied epigenetic mechanisms due to its essential role in gene expression, and its participation in SE is crucial. DNA methylation levels can be modified through the use of drugs such as 5-Azacytidine (5-AzaC), an inhibitor of DNA methylation, which has been used during SE protocols. The balance between hypomethylation and hypermethylation seems to be the key to SE success. Here, we discuss the most prominent recent research on the role of 5-AzaC in the regulation of DNA methylation, highlighting its importance during the SE process. Also, the molecular implications that this inhibitor might have for the increase or decrease in the embryogenic potential of various explants are reviewed.

scholarly journals Epigenetic Basis of Molecular Changes in Animal Cells with Particular Regard to Embryonic Development – A Review / Epigenetyczne Podstawy Przemian Molekularnych Zachodzących W Komórkach Zwierzęcych, Ze Szczególnym Uwzględnieniem Rozwoju Embrionalnego – Artykuł Przeglądowy

2013 ◽  
Vol 13 (4) ◽  
pp. 675-685
Author(s):  
Joanna Romanek
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Embryonic Development ◽  
De Novo ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Epigenetic Mechanism ◽  
Animal Cells ◽  
Molecular Changes ◽  
De Novo Methylation

Abstract Regulation of gene expression is a complex process. Epigenetics is the study of heritable changes in gene expression independently of DNA sequence. Epigenetic control of gene transcription is based on two main processes. The first is reversible DNA methylation, primarily of cytosine at position C5, rarely in position N3, or of adenine at position C6 (Xu et al., 2010). The second process is the change in chromatin structure and function by chemical modification of histones, including mainly methylation, acetylation, and phosphorylation of histone amino acids (Zamudio et al., 2008). During development and differentiation of cells, changes occur in DNA methylation of genes. After fertilization there are dynamic histone modifications and changes in DNA methylation in zygotes. Use of methylation sensitive restriction enzymes causes a global demethylation in the early embryonic stage (Sulewska et al., 2007 b). De novo methylation of CpG sites is followed by embryo implantation. Next, during gastrulation most genes are methylated except the tissue-specific genes. The last wave of de novo methylation takes place during the gametogenesis and is dependent on sex (Sulewska et al., 2007 b). The aim of this work is to review the current knowledge about epigenetic mechanism of molecular changes in animal cells with particular regard to embryonic development.

scholarly journals The role of epigenetic regulation in adaptive phenotypic plasticity of plants

2021 ◽  
Vol 78 (5) ◽  
pp. 347-359
Author(s):  
E.L. Kordyum ◽  
◽  
D.V. Dubyna ◽  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Phenotypic Plasticity ◽  
Epigenetic Regulation ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Model Species ◽  
Wide Range ◽  
Adaptive Phenotypic Plasticity

In recent decades, knowledge about the role of epigenetic regulation of gene expression in plant responses to external stimuli and in adaptation of plants to adverse environmental fluctuations have extended significantly. DNA methylation is considered as the main molecular mechanism that provides genomic information and contributes to the understanding of the molecular basis of phenotypic variations based on epigenetic modifications. Unfortunately, the vast majority of research in this area has been performed on the model species Arabidopsis thaliana. The development of the methylation-sensitive amplified polymorphism (MSAP) method has made it possible to implement the large-scale detection of DNA methylation alterations in wild non-model and agricultural plants with large and highly repetitive genomes in natural and manipulated habitats. The article presents current information on DNA methylation in species of natural communities and crops and its importance in plant development and adaptive phenotypic plasticity, along with brief reviews of current ideas about adaptive phenotypic plasticity and epigenetic regulation of gene expression. The great potential of further studies of the epigenetic role in phenotypic plasticity of a wide range of non-model species in natural populations and agrocenoses for understanding the molecular mechanisms of plant existence in the changing environment in onto- and phylogeny, directly related to the key tasks of forecasting the effects of global warming and crop selection, is emphasized. Specific taxa of the Ukrainian flora, which, in authors’ opinion, are promising and interesting for this type of research, are recommended.

scholarly journals DNA Methylation, Epigenetics, and Evolution in Vertebrates: Facts and Challenges

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Annalisa Varriale
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Environmental Influence ◽  
Epigenetic Modification ◽  
Regulation Of Gene Expression ◽  
Entire Genome ◽  
Phenotypic Differences ◽  
Methylation Patterns ◽  
And Control

DNA methylation is a key epigenetic modification in the vertebrate genomes known to be involved in biological processes such as regulation of gene expression, DNA structure and control of transposable elements. Despite increasing knowledge about DNA methylation, we still lack a complete understanding of its specific functions and correlation with environment and gene expression in diverse organisms. To understand how global DNA methylation levels changed under environmental influence during vertebrate evolution, we analyzed its distribution pattern along the whole genome in mammals, reptiles and fishes showing that it is correlated with temperature, independently on phylogenetic inheritance. Other studies in mammals and plants have evidenced that environmental stimuli can promote epigenetic changes that, in turn, might generate localized changes in DNA sequence resulting in phenotypic effects. All these observations suggest that environment can affect the epigenome of vertebrates by generating hugely different methylation patterns that could, possibly, reflect in phenotypic differences. We are at the first steps towards the understanding of mechanisms that underlie the role of environment in molding the entire genome over evolutionary times. The next challenge will be to map similarities and differences of DNA methylation in vertebrates and to associate them with environmental adaptation and evolution.

Epigenetic regulation mechanisms of microRNA expression

2017 ◽  
Vol 8 (5-6) ◽  
pp. 203-212 ◽  
Author(s):  
Sara Morales ◽  
Mariano Monzo ◽  
Alfons Navarro
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cell Proliferation ◽  
Epigenetic Regulation ◽  
Regulation Of Gene Expression ◽  
Transcriptional Level ◽  
Regulate Gene Expression ◽  
Regulation Mechanisms ◽  
Regulate Gene

AbstractMicroRNAs (miRNAs) are single-stranded RNAs of 18–25 nucleotides that regulate gene expression at the post-transcriptional level. They are involved in many physiological and pathological processes, including cell proliferation, apoptosis, development and carcinogenesis. Because of the central role of miRNAs in the regulation of gene expression, their expression needs to be tightly controlled. Here, we summarize the different mechanisms of epigenetic regulation of miRNAs, with a particular focus on DNA methylation and histone modification.

scholarly journals Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1059
Author(s):  
Alice Shwe ◽  
Tone-Kari Knutsdatter Østbye ◽  
Aleksei Krasnov ◽  
Sigmund Ramberg ◽  
Rune Andreassen
Keyword(s):  
Gene Expression ◽  
Atlantic Salmon ◽  
Target Genes ◽  
Sea Water ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Head Kidney ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Small Rna Sequencing

Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression during smoltification and the adaption to seawater is largely unknown. Here, small RNA sequencing of materials from head kidney before, during smoltification and post seawater transfer were used to study expression dynamics of miRNAs, while microarray analysis was applied to study mRNA expression dynamics. Comparing all timepoints, 71 miRNAs and 2709 mRNAs were identified as differentially expressed (DE). Hierarchical clustering analysis of the DE miRNAs showed three major clusters with characteristic expression changes. Eighty-one DE mRNAs revealed negatively correlated expression patterns to DE miRNAs in Cluster I and III. Furthermore, 42 of these mRNAs were predicted as DE miRNA targets. Gene enrichment analysis of negatively correlated target genes showed they were enriched in gene ontology groups hormone biosynthesis, stress management, immune response, and ion transport. The results strongly indicate that post-transcriptional regulation of gene expression by miRNAs is important in smoltification and sea water adaption, and this study identifies several putative miRNA-target pairs for further functional studies.

Cellular Reprogramming Erases Aberrant DNA Methylation and the Malignant Phenotype in Chronic Myeloid Leukemia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 4524-4524
Author(s):  
Giovanni Amabile ◽  
Annalisa Di Ruscio ◽  
Fabian Muller ◽  
Robert S Welner ◽  
Henry Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Chronic Myeloid Leukemia ◽  
Tyrosine Kinase ◽  
Myeloid Leukemia ◽  
Regulation Of Gene Expression ◽  
Cellular Reprogramming ◽  
Genetic Event ◽  
Aberrant Dna Methylation ◽  
The Impact

Abstract Chronic Myeloid Leukemia (CML) is a myeloproliferative disorder characterized by the presence of the Philadelphia chromosome deriving from the genetic translocation t(9;22)(q34;q11.2) that encodes for the BCR-ABL fusion gene. BCR-ABL is a constitutively active tyrosine kinase believed to be the primary genetic event driving CML development (Daley and Baltimore, 1988; Huettner et al., 2000). Tyrosine Kinase Inhibitors (TKI) targeting the BCR-ABL kinase have revolutionized CML therapy, however, they fail to fully eradicate the disease due to the presence of a drug-resistant stem cell pool that sustains continued growth of the malignant cells. Indeed, discontinuation of TKI results in relapse and/or disease progression. It has been shown that the emergence of leukemic clones resistant to TKI and responsible for CML evolution is correlated with aberrant DNA methylation (Machova Polakova et al., 2013). DNA methylation is a key epigenetic signature implicated in regulation of gene expression (Robertson, 2001), that occurs predominantly within CpG dinucleotides. CpG-rich regions (namely CpG islands) are frequently located within promoter regions (~70%) of human protein-coding genes (Illingworth et al., 2010). Methylation of CpG-rich promoters negatively correlates with gene expression levels and it is considered an important regulatory mechanism for long-term gene silencing (Herman and Baylin, 2003). Although numerous studies have established a link between aberrant promoter DNA methylation and cancer (Costello et al., 2000; Feinberg et al., 2006), the impact of DNA methylation in CML is still poorly understood (Yamazaki et al., 2012), particularly due to the lack of the specific animal models. In this study we tested the functional relevance of aberrant methylome in CML development and investigated the possibility that BCR-ABL oncogene triggers DNA methylation changes leading to an aggressive leukemic phenotype. To this end, we have combined cellular reprogramming (Amabile and Meissner, 2009; Carette et al., 2010; Kumano et al., 2012; Miyoshi et al., 2010; Takahashi et al., 2007), due to its ability to erase tissue-specific DNA methylation and to re-establish an embryonic stem-like DNA methylation state (Mikkelsen et al., 2008), with a previously developed BCR-ABL inducible murine model (Koschmieder et al., 2005). Using this approach, we demonstrate that the presence of a single genetic aberration is sufficient to trigger DNA methylation changes and leads to an aggressive leukemic phenotype. We show that by resetting the normal DNA methylation profile of primary human CML cells through cellular reprogramming, we are able to re-establish normal myeloid differentiation, despite the persistence of the native genetic lesion. Finally, by combining a comprehensive genome-scale methylation analysis with cellular reprogramming of leukemic cells, we elucidate the sequential events driving leukemogenesis and reveal the reciprocal interplay of genetic and epigenetic mechanisms during malignant transformation. In conclusion, these results dissect the role of DNA methylation alterations in CML development and warrant an application of demethylating agents such as 5-azacytidine as adjuvant treatment in therapeutic approaches to CML. Disclosures Martinelli: Novartis: Speakers Bureau; Bristol Myers Squibb: Speakers Bureau; Pfizer: Speakers Bureau.

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