Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer

Kulis, Marta; Queirós, Ana C.; Beekman, Renée; Martín‐Subero, José I.

doi:10.1016/j.bbagrm.2013.08.001

Cited by 195 publications

(191 citation statements)

References 173 publications

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“…21 Whether DNA methylation changes precede the binding of transcription factors or are its consequence need to be understood. 39 Our data are consistent with these reports by others. In the present study, the HOMER algorithm 40 was used to detect the enriched consensus motifs for transcription factor binding sites in the SNL vs. control animals.…”

Section: Discussionsupporting

confidence: 94%

Plasticity of DNA methylation in a nerve injury model of pain

et al. 2015

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Section: Discussionsupporting

confidence: 94%

Plasticity of DNA methylation in a nerve injury model of pain

et al. 2015

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“…In this study, the methylation status of the promoter and exon1 region of FATP1 gene showed a negative relationship with expression of the FATP1 gene, which is consistent with the previous studies that show DNA methylation in the promoter negatively associated with gene expression (Jones, 2012;Kulis et al, 2013).…”

Section: Resultssupporting

confidence: 80%

“…As an important epigenetic modification, DNA methylation in the promoter is often negatively associated with gene expression, whereas the methylation status in the body of the same gene might be positively related to gene expression (Jones, 2012;Kulis et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Effect of Feeding Conditions on the Methylation Status of Fatp1 Gene in Chicken Breast Muscle

Gao

Zhao

et al. 2017

Rev. Bras. Cienc. Avic.

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The objective of this work was to investigate the effect of feeding conditions on methylation status of FATP1 gene, which is an important candidate gene of Intramuscular fat and important indicator of chicken meat quality. We selected Daninghe (DNH) and Qingjiaoma (QJM) chickens under scatter-feeding and captivity-feeding conditions as experimental animals, and detected the methylation status of FATP1 genes in chicken breast muscle using Bisulfite Sequencing PCR method. The results showed that the methylation level of FATP1 in scatter-fed chicken was lower than in captivity-fed conditions in DNH and QIM chicken breast tissues; DNA methylation in the promoter and exon1 region was demonstrated to negatively regulate the expression of the FATP1 gene. These results suggested that feeding conditions affect the methylation status and expression level of FATP1, thereby affecting the Intramuscular fat content in DNH and QJM chicken breast muscle.

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“…No correlation could be found between differential methylation of the central and 39 part of the gene body or sequences downstream of the gene. In animals, though, several studies of the methylome during the development of both somatic and cancer cells have indicated a correlation between intragenic methylation and gene expression (Kulis et al, 2013). No correlation could be observed between gene expression and differential methylation of the 39 part of the gene body or sequences downstream of the gene.…”

Section: Differential Methylation Targets 59 and 39 Edges Of Genic Rementioning

confidence: 97%

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

et al. 2014

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DNA methylation is an important and widespread epigenetic modification in plant genomes, mediated by DNA methyltransferases (DMTs). DNA methylation is known to play a role in genome protection, regulation of gene expression, and splicing and was previously associated with major developmental reprogramming in plants, such as vernalization and transition to flowering. Here, we show that DNA methylation also controls the growth processes of cell division and cell expansion within a growing organ. The maize (Zea mays) leaf offers a great tool to study growth processes, as the cells progressively move through the spatial gradient encompassing the division zone, transition zone, elongation zone, and mature zone. Opposite to de novo DMTs, the maintenance DMTs were transcriptionally regulated throughout the growth zone of the maize leaf, concomitant with differential CCGG methylation levels in the four zones. Surprisingly, the majority of differentially methylated sequences mapped on or close to gene bodies and not to repeat-rich loci. Moreover, especially the 59 and 39 regions of genes, which show overall low methylation levels, underwent differential methylation in a developmental context. Genes involved in processes such as chromatin remodeling, cell cycle progression, and growth regulation, were differentially methylated. The presence of differential methylation located upstream of the gene anticorrelated with transcript expression, while gene body differential methylation was unrelated to the expression level. These data indicate that DNA methylation is correlated with the decision to exit mitotic cell division and to enter cell expansion, which adds a new epigenetic level to the regulation of growth processes.DNA methylation is the covalent modification of nucleotides in DNA by the addition of a methyl group. In the nuclear genome of higher eukaryotes, 5-methylcytosine is the most important DNA modification (Goll and Bestor, 2005). It is a phenomenon of ancient origin predating plant-animal diversification. However, some differences exist between plant and animal methylome patterning and function, and DNA methylation has been found to be evolutionarily lost in a few species (Feng et al., 2010;Zemach et al., 2010). Eukaryotic DNA methylation is established by DNA methyltransferase (DMT) enzymes that transfer a methyl group from S-adenosyl Met to the fifth carbon of cytosine. These enzymes can largely be subdivided in maintenance and de novo DMTs, depending on whether the recognition site is already methylated or not. Maintenance DMTs conserve the methylation status of symmetrical (palindromic) sites after DNA replication, by recognizing the hemimethylated locus and methylating the newly synthesized strand. In plants, there are two types of maintenance DMTs: DNA METHYLTRANSFERASE (MET) and CHROMOMETHYLASE (CMT). The former methylates CG sites during DNA replication, whereas the latter methylates CHG (H = A, C, or T) sites located in chromatin in which histone 3 is dimethylated on Lys-9 (Goll and Bestor, 2005). De no...

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Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer

Cited by 195 publications

References 173 publications

Plasticity of DNA methylation in a nerve injury model of pain

Plasticity of DNA methylation in a nerve injury model of pain

Effect of Feeding Conditions on the Methylation Status of Fatp1 Gene in Chicken Breast Muscle

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

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