The role of epigenetic regulation in adaptive phenotypic plasticity of plants

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.

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Epigenetic regulation mechanisms of microRNA expression

BioMolecular Concepts ◽

10.1515/bmc-2017-0024 ◽

2017 ◽

Vol 8 (5-6) ◽

pp. 203-212 ◽

Cited By ~ 39

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.

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The Role of Translation Initiation Regulation in Haematopoiesis

Comparative and Functional Genomics ◽

10.1155/2012/576540 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10 ◽

Cited By ~ 7

Author(s):

Godfrey Grech ◽

Marieke von Lindern

Keyword(s):

Gene Expression ◽

Translation Initiation ◽

Translational Control ◽

Molecular Mechanisms ◽

Rna Binding ◽

Regulation Of Gene Expression ◽

Mrna Translation ◽

Translation Control ◽

Haematological Disorders

Organisation of RNAs into functional subgroups that are translated in response to extrinsic and intrinsic factors underlines a relatively unexplored gene expression modulation that drives cell fate in the same manner as regulation of the transcriptome by transcription factors. Recent studies on the molecular mechanisms of inflammatory responses and haematological disorders indicate clearly that the regulation of mRNA translation at the level of translation initiation, mRNA stability, and protein isoform synthesis is implicated in the tight regulation of gene expression. This paper outlines how these posttranscriptional control mechanisms, including control at the level of translation initiation factors and the role of RNA binding proteins, affect hematopoiesis. The clinical relevance of these mechanisms in haematological disorders indicates clearly the potential therapeutic implications and the need of molecular tools that allow measurement at the level of translational control. Although the importance of miRNAs in translation control is well recognised and studied extensively, this paper will exclude detailed account of this level of control.

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Role of Iron in Epigenetic Regulation of Gene Expression

Nutrition and Epigenetics ◽

10.1201/b17530-14 ◽

2014 ◽

pp. 274-293 ◽

Cited By ~ 3

Keyword(s):

Gene Expression ◽

Epigenetic Regulation ◽

Regulation Of Gene Expression

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Epigenetic Influences on Plant Responses to the Environment [University of Wisconsin - Oshkosh]

Journal of Student Research ◽

10.47611/jsr.vi.624 ◽

2019 ◽

Author(s):

Angela L Vickman ◽

Travis Smith ◽

Hayley Vandenboom ◽

Lisa A. Dorn

Keyword(s):

Gene Expression ◽

Phenotypic Plasticity ◽

Molecular Mechanisms ◽

Molecular Level ◽

Physical Structure ◽

Plant Responses ◽

Appropriate Behavior ◽

Stressful Environment ◽

University Of Wisconsin

Plants and animals may respond to changes in the environment at the molecular level by changing the amount of a gene product (a protein) to generate the appropriate behavior or physical structure (a phenotype) for that environment. For example, an extremely stressful environment can cause plants to reproduce immediately rather than waiting for conditions to improve. The molecular mechanisms for changing phenotype with environment (phenotypic plasticity) are not clear, however previous studies have shown plasticity may be the result of failing to change expression to maintain a phenotype or a deliberate change in expression altering the phenotype. To explore the molecular mechanisms underlying phenotypic plasticity, I am using a minION sequencing apparatus to re-sequence three inbred lines of Arabidopsis thaliana with extreme phenotypic plasticity differences and gene expression differences with the environment. I will specifically explore the role of methylated cytosines and adenines in gene expression.

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Epigenetic Regulation of Myogenesis: Focus on the Histone Variants

International Journal of Molecular Sciences ◽

10.3390/ijms222312727 ◽

2021 ◽

Vol 22 (23) ◽

pp. 12727

Author(s):

Joana Esteves de Lima ◽

Frédéric Relaix

Keyword(s):

Gene Expression ◽

Cell Fate ◽

Epigenetic Regulation ◽

Muscle Development ◽

Regulation Of Gene Expression ◽

Histone Variants ◽

Myoblast Differentiation ◽

Post Translational Modifications ◽

Differentiation Status

Skeletal muscle development and regeneration rely on the successive activation of specific transcription factors that engage cellular fate, promote commitment, and drive differentiation. Emerging evidence demonstrates that epigenetic regulation of gene expression is crucial for the maintenance of the cell differentiation status upon division and, therefore, to preserve a specific cellular identity. This depends in part on the regulation of chromatin structure and its level of condensation. Chromatin architecture undergoes remodeling through changes in nucleosome composition, such as alterations in histone post-translational modifications or exchange in the type of histone variants. The mechanisms that link histone post-translational modifications and transcriptional regulation have been extensively evaluated in the context of cell fate and differentiation, whereas histone variants have attracted less attention in the field. In this review, we discuss the studies that have provided insights into the role of histone variants in the regulation of myogenic gene expression, myoblast differentiation, and maintenance of muscle cell identity.

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

10.1101/2021.12.20.473279 ◽

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.

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The biological characteristics of transcription factors AP-2α and AP-2γ and their importance in various types of cancers

Bioscience Reports ◽

10.1042/bsr20181928 ◽

2019 ◽

Vol 39 (3) ◽

Cited By ~ 4

Author(s):

Damian Kołat ◽

Żaneta Kałuzińska ◽

Andrzej K. Bednarek ◽

Elżbieta Płuciennik

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcription Factors ◽

Molecular Mechanisms ◽

Regulation Of Gene Expression ◽

Cancer Tissue ◽

Diagnostic Biomarkers ◽

Oncological Patients ◽

Wide Range ◽

Non Coding Rnas

Abstract The Activator Protein 2 (AP-2) transcription factor (TF) family is vital for the regulation of gene expression during early development as well as carcinogenesis process. The review focusses on the AP-2α and AP-2γ proteins and their dualistic regulation of gene expression in the process of carcinogenesis. Both AP-2α and AP-2γ influence a wide range of physiological or pathological processes by regulating different pathways and interacting with diverse molecules, i.e. other proteins, long non-coding RNAs (lncRNA) or miRNAs. This review summarizes the newest information about the biology of two, AP-2α and AP-2γ, TFs in the carcinogenesis process. We emphasize that these two proteins could have either oncogenic or suppressive characteristics depending on the type of cancer tissue or their interaction with specific molecules. They have also been found to contribute to resistance and sensitivity to chemotherapy in oncological patients. A better understanding of molecular network of AP-2 factors and other molecules may clarify the atypical molecular mechanisms occurring during carcinogenesis, and may assist in the recognition of new diagnostic biomarkers.

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

International Journal of Molecular Sciences ◽

10.3390/ijms19103182 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3182 ◽

Cited By ~ 12

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.

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