- Gene Body Methylation and Transcriptional Regulation: Statistical Modelling and More

2016 ◽  
pp. 225-243
Keyword(s):  
Transcriptional Regulation ◽  
Statistical Modelling ◽  
Gene Body ◽  
Gene Body Methylation

scholarly journals LPS-induced expression of CD14 in the TRIF pathway is epigenetically regulated by sulforaphane in porcine pulmonary alveolar macrophages

2016 ◽  
Vol 22 (8) ◽  
pp. 682-695 ◽  
Author(s):  
Qin Yang ◽  
Maren J Pröll ◽  
Dessie Salilew-Wondim ◽  
Rui Zhang ◽  
Dawit Tesfaye ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alveolar Macrophages ◽  
Methylation Status ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Tnf Α ◽  
Pulmonary Alveolar Macrophages ◽  
Cluster Of Differentiation ◽  
Cd14 Gene

Pulmonary alveolar macrophages (AMs) are important in defense against bacterial lung inflammation. Cluster of differentiation 14 (CD14) is involved in recognizing bacterial lipopolysaccharide (LPS) through MyD88-dependent and TRIF pathways of innate immunity. Sulforaphane (SFN) shows anti-inflammatory activity and suppresses DNA methylation. To identify CD14 epigenetic changes by SFN in the LPS-induced TRIF pathway, an AMs model was investigated in vitro. CD14 gene expression was induced by 5 µg/ml LPS at the time point of 12 h and suppressed by 5 µM SFN. After 12 h of LPS stimulation, gene expression was significantly up-regulated, including TRIF, TRAF6, NF-κB, TRAF3, IRF7, TNF-α, IL-1β, IL-6, and IFN-β. LPS-induced TRAM, TRIF, RIPK1, TRAF3, TNF-α, IL-1β and IFN-β were suppressed by 5 µM SFN. Similarly, DNMT3a expression was increased by LPS but significantly down-regulated by 5 µM SFN. It showed positive correlation of CD14 gene body methylation with in LPS-stimulated AMs, and this methylation status was inhibited by SFN. This study suggests that SFN suppresses CD14 activation in bacterial inflammation through epigenetic regulation of CD14 gene body methylation associated with DNMT3a. The results provide insights into SFN-mediated epigenetic down-regulation of CD14 in LPS-induced TRIF pathway inflammation and may lead to new methods for controlling LPS-induced inflammation in pigs.

scholarly journals On the origin and evolutionary consequences of gene body DNA methylation

2016 ◽  
Vol 113 (32) ◽  
pp. 9111-9116 ◽  
Author(s):  
Adam J. Bewick ◽  
Lexiang Ji ◽  
Chad E. Niederhuth ◽  
Eva-Maria Willing ◽  
Brigitte T. Hofmeister ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Recombinant Inbred Lines ◽  
Dna Methyltransferases ◽  
Inbred Lines ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Eutrema Salsugineum ◽  
And Function ◽  
Evolutionary Consequences

In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (gene body methylation; gbM), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, to our knowledge the first instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum. Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM, supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z, and various histone modifications in E. salsugineum and in Arabidopsis thaliana epigenetic recombinant inbred lines found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modification of chromatin over evolutionary timescales.

scholarly journals Gene body methylation mediates epigenetic inheritance of plant traits

2021 ◽  
Author(s):  
Zaigham Shahzad ◽  
Jonathan D. Moore ◽  
Daniel Zilberman
Keyword(s):  
Gene Expression ◽  
Flowering Time ◽  
Cytosine Methylation ◽  
Plant Traits ◽  
Phenotypic Diversity ◽  
Strong Association ◽  
Epigenetic Inheritance ◽  
Evolutionary Significance ◽  
Gene Body ◽  
Gene Body Methylation

AbstractCytosine methylation is an epigenetically heritable DNA modification common in plant and animal genes, but the functional and evolutionary significance of gene body methylation (gbM) has remained enigmatic. Here we show that gbM enhances gene expression in Arabidopsis thaliana. We also demonstrate that natural gbM variation influences drought and heat tolerance and flowering time by modulating gene expression, including that of Flowering Locus C (FLC). Notably, epigenetic variation accounts for as much trait heritability in natural populations as DNA sequence polymorphism. Furthermore, we identify gbM variation in numerous genes associated with environmental variables, including a strong association between flowering time, spring atmospheric NO2 – a by-product of fossil fuel burning – and FLC epialleles. Our study demonstrates that gbM is an important modulator of gene expression, and its natural variation fundamentally shapes phenotypic diversity in plant populations. Thus, gbM provides an epigenetic basis for adaptive evolution independent of genetic polymorphism.

scholarly journals DNA methylation is not a driver of gene expression reprogramming in young honey bee workers

2021 ◽  
Author(s):  
Carlos A. M. Cardoso-Junior ◽  
Boris Yagound ◽  
Isobel Ronai ◽  
Emily J. Remnant ◽  
Klaus Hartfelder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Honey Bee ◽  
Differential Gene Expression ◽  
Social Contexts ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Differential Gene ◽  
Honey Bee Workers ◽  
Methylation Patterns

AbstractIntragenic DNA methylation, also called gene body methylation, is an evolutionarily-conserved epigenetic mechanism in animals and plants. In social insects, gene body methylation is thought to contribute to behavioral plasticity, for example between foragers and nurse workers, by modulating gene expression. However, recent studies have suggested that the majority of DNA methylation is sequence-specific, and therefore cannot act as a flexible mediator between environmental cues and gene expression. To address this paradox, we examined whole-genome methylation patterns in the brains and ovaries of young honey bee workers that had been subjected to divergent social contexts: the presence or absence of the queen. Although these social contexts are known to bring about extreme changes in behavioral and reproductive traits through differential gene expression, we found no significant differences between the methylomes of workers from queenright and queenless colonies. In contrast, thousands of regions were differentially methylated between colonies, and these differences were not associated with differential gene expression in a subset of genes examined. Methylation patterns were highly similar between brain and ovary tissues and only differed in nine regions. These results strongly indicate that DNA methylation is not a driver of differential gene expression between tissues or behavioral morphs. Finally, despite the lack of difference in methylation patterns, queen presence affected the expression of all four DNA methyltransferase genes, suggesting that these enzymes have roles beyond DNA methylation. Therefore, the functional role of DNA methylation in social insect genomes remains an open question.

scholarly journals Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jered M Wendte ◽  
Yinwen Zhang ◽  
Lexiang Ji ◽  
Xiuling Shi ◽  
Rashmi R Hazarika ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Plant Species ◽  
Dna Methyltransferase ◽  
Constitutive Heterochromatin ◽  
De Novo ◽  
Flowering Plant ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Mechanistic Basis ◽  
Flowering Plant Species

In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H = A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. CMT3 expression reconstituted gbM through a progression of de novo CHG methylation on expressed genes, followed by the accumulation of CG methylation that could be inherited even following loss of the CMT3 transgene. Thus, gbM likely originates from the simultaneous targeting of loci by pathways that promote euchromatin and heterochromatin, which primes genes for the formation of stably inherited epimutations in the form of CG DNA methylation.

Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation

Nature Plants ◽  
2019 ◽  
Vol 5 (8) ◽  
pp. 846-855 ◽  
Author(s):  
Christiane Kiefer ◽  
Eva-Maria Willing ◽  
Wen-Biao Jiao ◽  
Hequan Sun ◽  
Mathieu Piednoël ◽  
...  
Keyword(s):  
Association Mapping ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Substitution Rates
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