scholarly journals DNA Methylation Influences the Expression of DICER-LIKE4 Isoforms, Which Encode Proteins of Alternative Localization and Function

2016 ◽  
Vol 28 (11) ◽  
pp. 2786-2804 ◽  
Author(s):  
Nathan Pumplin ◽  
Alexis Sarazin ◽  
Pauline E. Jullien ◽  
Nicolas G. Bologna ◽  
Stefan Oberlin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
And Function

scholarly journals Impact of DNA methylation on 3D genome structure

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Diana Buitrago ◽  
Mireia Labrador ◽  
Juan Pablo Arcon ◽  
Rafael Lema ◽  
Oscar Flores ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Chromatin Structure ◽  
Chromatin Condensation ◽  
Genome Structure ◽  
Dna Methyltransferases ◽  
Model System ◽  
Structure And Function ◽  
3D Genome ◽  
Cellular Machinery ◽  
And Function

AbstractDetermining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, that lacks DNA methylation machinery making it a perfect model system to study the intrinsic role of DNA methylation in chromatin structure and function. We expressed the murine DNA methyltransferases in Saccharomyces cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. Despite lacking the machinery for positioning and reading methylation marks, induced DNA methylation follows a conserved pattern with low methylation levels at the 5’ end of the gene increasing gradually toward the 3’ end, with concentration of methylated DNA in linkers and nucleosome free regions, and with actively expressed genes showing low and high levels of methylation at transcription start and terminating sites respectively, mimicking the patterns seen in mammals. We also see that DNA methylation increases chromatin condensation in peri-centromeric regions, decreases overall DNA flexibility, and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal.

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 Gut Microbiota as Important Mediator Between Diet and DNA Methylation and Histone Modifications in the Host

Nutrients ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 597 ◽  
Author(s):  
Patrizia D’Aquila ◽  
Laurie Lynn Carelli ◽  
Francesco De Rango ◽  
Giuseppe Passarino ◽  
Dina Bellizzi
Keyword(s):  
Dna Methylation ◽  
Gut Microbiota ◽  
Histone Modifications ◽  
Molecular Mechanisms ◽  
Current Evidence ◽  
Long Term Effects ◽  
Metabolic Functions ◽  
Complex Ecosystem ◽  
Short And Long Term ◽  
And Function

The human gut microbiota is a complex ecosystem consisting of trillions of microorganisms that inhabit symbiotically on and in the human intestine. They carry out, through the production of a series of metabolites, many important metabolic functions that complement the activity of mammalian enzymes and play an essential role in host digestion. Interindividual variability of microbiota structure, and consequently of the expression of its genes (microbiome), was largely ascribed to the nutritional regime. Diet influences microbiota composition and function with short- and long-term effects. In spite of the vast literature, molecular mechanisms underlying these effects still remain elusive. In this review, we summarized the current evidence on the role exerted by gut microbiota and, more specifically, by its metabolites in the establishment of the host epigenome. The interest in this topic stems from the fact that, by modulating DNA methylation and histone modifications, the gut microbiota does affect the cell activities of the hosting organism.

scholarly journals Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation

2020 ◽  
Vol 178 (2) ◽  
pp. 325-337
Author(s):  
Matthew de Gannes ◽  
Chia-I Ko ◽  
Xiang Zhang ◽  
Jacek Biesiada ◽  
Liang Niu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Heart Development ◽  
Expression Patterns ◽  
Embryonic Stem Cell Line ◽  
Molecular Networks ◽  
Unknown Etiology ◽  
Postnatal Maturation ◽  
Complex Interactions ◽  
And Function

Abstract Congenital heart disease (CHD), the leading birth defect worldwide, has a largely unknown etiology, likely to result from complex interactions between genetic and environmental factors during heart development, at a time when the heart adapts to diverse physiological and pathophysiological conditions. Crucial among these is the regulation of cardiomyocyte development and postnatal maturation, governed by dynamic changes in DNA methylation. Previous work from our laboratory has shown that exposure to the environmental toxicant tetrachlorodibenzo-p-dioxin (TCDD) disrupts several molecular networks responsible for heart development and function. To test the hypothesis that the disruption caused by TCDD in the heart results from changes in DNA methylation and gene expression patterns of cardiomyocytes, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under control of the cardiomyocyte-specific Nkx2-5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte-specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 111 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue toward the elucidation of the complex interactions between genetic and epigenetic mechanisms after developmental TCDD exposure that may contribute to CHD.

scholarly journals Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

2015 ◽  
Vol 112 (22) ◽  
pp. 6800-6806 ◽  
Author(s):  
Benyam Kinde ◽  
Harrison W. Gabel ◽  
Caitlin S. Gilbert ◽  
Eric C. Griffith ◽  
Michael E. Greenberg
Keyword(s):  
Dna Methylation ◽  
Binding Protein ◽  
Cell Types ◽  
Cpg Methylation ◽  
Early Postnatal Development ◽  
Cpg Dinucleotides ◽  
Epigenetic Regulator ◽  
And Function ◽  
Syndrome Protein ◽  
The Brain

DNA methylation at CpG dinucleotides is an important epigenetic regulator common to virtually all mammalian cell types, but recent evidence indicates that during early postnatal development neuronal genomes also accumulate uniquely high levels of two alternative forms of methylation, non-CpG methylation and hydroxymethylation. Here we discuss the distinct landscape of DNA methylation in neurons, how it is established, and how it might affect the binding and function of protein readers of DNA methylation. We review studies of one critical reader of DNA methylation in the brain, the Rett syndrome protein methyl CpG-binding protein 2 (MeCP2), and discuss how differential binding affinity of MeCP2 for non-CpG and hydroxymethylation may affect the function of this methyl-binding protein in the nervous system.

scholarly journals DNA modifications in the mammalian brain

2014 ◽  
Vol 369 (1652) ◽  
pp. 20130512 ◽  
Author(s):  
Jaehoon Shin ◽  
Guo-li Ming ◽  
Hongjun Song
Keyword(s):  
Dna Methylation ◽  
Brain Development ◽  
Genomic Imprinting ◽  
Mammalian Brain ◽  
Epigenetic Mark ◽  
Mammalian Development ◽  
Dna Modifications ◽  
Dna Elements ◽  
And Function ◽  
Neuronal Functions

DNA methylation is a crucial epigenetic mark in mammalian development, genomic imprinting, X-inactivation, chromosomal stability and suppressing parasitic DNA elements. DNA methylation in neurons has also been suggested to play important roles for mammalian neuronal functions, and learning and memory. In this review, we first summarize recent discoveries and fundamental principles of DNA modifications in the general epigenetics field. We then describe the profiles of different DNA modifications in the mammalian brain genome. Finally, we discuss roles of DNA modifications in mammalian brain development and function.

scholarly journals DNA methylation and methyl-CpG binding proteins: developmental requirements and function

Chromosoma ◽  
2009 ◽  
Vol 118 (5) ◽  
pp. 549-565 ◽  
Author(s):  
Ozren Bogdanović ◽  
Gert Jan C. Veenstra
Keyword(s):  
Dna Methylation ◽  
Binding Proteins ◽  
And Function

scholarly journals Surface IgM expression and function are associated with clinical behavior, genetic abnormalities, and DNA methylation in CLL

Blood ◽  
2016 ◽  
Vol 128 (6) ◽  
pp. 816-826 ◽  
Author(s):  
Annalisa D’Avola ◽  
Samantha Drennan ◽  
Ian Tracy ◽  
Isla Henderson ◽  
Laura Chiecchio ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Clinical Outcome ◽  
Behavior Genetic ◽  
Clinical Behavior ◽  
Genetic Abnormalities ◽  
Key Points ◽  
Key Factor ◽  
And Function

Key Points High sIgM level is a potential key factor associated with poorer clinical outcome in CLL. Genetic and epigenetic features influence sIgM levels and function in CLL.

scholarly journals Diverse roles of MeCP2 in the specification and maintenance of midbrain dopamine phenotype.

2021 ◽  
Author(s):  
Xi-Biao He ◽  
Fang Guo
Keyword(s):  
Dna Methylation ◽  
Tyrosine Hydroxylase ◽  
Dna Binding ◽  
Psychiatric Disorders ◽  
Binding Sites ◽  
Neuronal Phenotype ◽  
Midbrain Dopamine ◽  
And Function ◽  
Determining Factor

Midbrain dopamine (DA) neurons are associated with locomotor and psychiatric disorders. DA neuronal phenotype is specified in ancestral progenitors and maintained throughout differentiation. Here we demonstrate that premature MeCP2 expression prevents DA progenitors from acquiring DA phenotype through interfering NURR1 transactivation. By contrast, the maintenance of DA phenotype is not affected by MeCP2 overexpression in DA neurons. By analyzing the DNA methylation and MeCP2 binding to the promoter of DA phenotype gene tyrosine hydroxylase (Th) along differentiation, we show that Th expression is determined by TET1-mediated de-methylation of NURR1 binding sites within Th promoter. Premature MeCP2 dominates the DNA binding of these sites thereby blocking TET1 function in DA progenitors, whereas TET1 prevents excessive MeCP2 binding in DA neurons. Finally, we show that targeted de-methylation in DA progenitors protects phenotype specification from premature MeCP2 expression, whereas targeted methylation disturbs phenotype maintenance in MeCP2-overexpressed DA neurons. These findings demonstrate MeCP2 as a novel determining factor for DA neuronal phenotype and function.

scholarly journals Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum genome

2017 ◽  
Author(s):  
Jacob L. Steenwyk ◽  
James St. Denis ◽  
Jacqueline M. Dresch ◽  
Denis A. Larochelle ◽  
Robert A. Drewell
Keyword(s):  
Dna Methylation ◽  
Dictyostelium Discoideum ◽  
Dna Methyltransferase ◽  
Model Organism ◽  
Epigenetic Mark ◽  
Whole Genome ◽  
Protein Coding ◽  
Genome Bisulfite Sequencing ◽  
Chromatin Structural ◽  
And Function

AbstractDNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the slime mold Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methyl-cytosine in the genome is unclear. Here we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage, replicate sequencing of bisulfite converted gDNA extracted from post-starvation cells. We find an overall very low level of DNA methylation, occurring at only 462 out of the ~7.5 million (0.006%) cytosines in the genome. Despite this sparse profile, significant methylation can be detected at 51 of these sites in replicate experiments, suggesting they are robust targets for DNA methylation. These 5-methyl-cytosines are associated with a broad range of protein-coding genes, tRNA-encoding genes and retrotransposable elements. Our data provides evidence of a minimal, but functional, methylome in Dictyostelium, thereby making Dictyostelium a candidate model organism to further investigate the evolutionary function of DNA methylation.

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