Researchers see popular herbicide (Atrazine) affecting health across generations

 First, the good news. Washington State University researchers have found that a rat exposed to a popular herbicide while in the womb developed no diseases and showed no apparent health effects aside from lower weight.
Now, the weird news. The grand-offspring of that rat did have more disease, as did a great-grand offspring third generation.

"The third generation had multiple diseases and much more frequently than the third generation of unexposed rats," said Michael Skinner, a Washington State University professor of biological sciences. At work, says Skinner, are epigenetic inheritance changes that turn genes on and off, often because of environmental influences.Writing this week in the journal PLOS ONE, Skinner reports exposing pregnant rats to atrazine, a commonly used herbicide on corn crops across the Midwest. Manufactured by Syngenta, the hormone-disrupting compound has been banned in Europe, where it was found contaminating water, while the Environmental Protection Agency permits its use in the U.S. It has been found in water systems serving 30 million Americans in 28 states, according to an Environmental Working Group survey of municipal water records.After Skinner and his colleagues exposed pregnant female rats to the herbicide, their first generation of offspring showed no ill effects but weighed less than rats in a control group. Rats bred from them had increased testis disease and altered sperm production, mammary tumors in both males and females, early-onset puberty in the males and lower-weight females. Their offspring—the great-grand offspring of the exposed rats—also had more testis disease, plus early onset puberty in females, hyperactivity and leaner male and female physiques.

When Skinner and his colleagues looked at sperm of the offspring, they found epimutations, or alterations in the methyl groups that stick to DNA and affect its activation.

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Related articles

• Burden of disease and costs of exposure to endocrine disrupting chemicals in the European Union: an updated analysis. - PubMed - NCBI

Prenatal unhealthy diet, insulin-like growth factor 2 gene (IGF2) methylation, and attention deficit hyperactivity disorder symptoms in youth with early-onset conduct problems Journal of Child Psychology and Psychiatry

Conduct problems (CP) and attention deficit hyperactivity disorder (ADHD) are often comorbid and have each been linked to ‘unhealthy diet’. Early-life diet also associates with DNA methylation of the insulin-like growth factor 2 gene (IGF2), involved in fetal and neural development. We investigated the degree to which prenatal high-fat and -sugar diet might relate to ADHD symptoms via IGF2 DNA methylation for early-onset persistent (EOP) versus low CP youth.
Methods

Participants were 164 youth with EOP (n = 83) versus low (n = 81) CP drawn from the Avon Longitudinal Study of Parents and Children. We assessed if the interrelationships between high-fat and -sugar diet (prenatal, postnatal), IGF2 methylation (birth and age 7, collected from blood), and ADHD symptoms (age 7–13) differed for EOP versus low CP youth.
Results

Prenatal ‘unhealthy diet’ was positively associated with IGF2 methylation at birth for both the EOP and low CP youth. For EOP only: (a) higher IGF2 methylation predicted ADHD symptoms; and (b) prenatal ‘unhealthy diet’ was associated with higher ADHD symptoms indirectly via higher IGF2 methylation.
Conclusions

Preventing ‘unhealthy diet’ in pregnancy might reduce the risk of ADHD symptoms in EOP youth via lower offspring IGF2 methylation."



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Epigenetic germline inheritance of diet-induced obesity and insulin resistance : Nature Genetics : Nature Publishing Group

"There is considerable controversy regarding epigenetic inheritance in mammalian gametes. Using in vitro fertilization to ensure exclusive inheritance via the gametes, we show that a parental high-fat diet renders offspring more susceptible to developing obesity and diabetes in a sex- and parent of origin–specific mode. The epigenetic inheritance of acquired metabolic disorders may contribute to the current obesity and diabetes pandemic."



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Bacterial infection remodels the DNA methylation landscape of human dendritic cells

DNA methylation is an epigenetic mark thought to be robust
to environmental perturbations on a short time scale. Here, we challenge that
view by demonstrating that the infection of human dendritic cells (DCs) with a
live pathogenic bacteria is associated with rapid and active demethylation at
thousands of loci, independent of cell division. We performed an integrated
analysis of data on genome-wide DNA methylation, histone mark patterns,
chromatin accessibility, and gene expression, before and after infection. We
found that infection-induced demethylation rarely occurs at promoter regions
and instead localizes to distal enhancer elements, including those that
regulate the activation of key immune transcription factors. Active
demethylation is associated with extensive epigenetic remodeling, including the
gain of histone activation marks and increased chromatin accessibility, and is
strongly predictive of changes in the expression levels of nearby genes.
Collectively, our observations show that active, rapid changes in DNA
methylation in enhancers play a previously unappreciated role in regulating the
transcriptional response to infection, even in nonproliferating cells.

RNA Epigenetics | The Scientist Magazine®

 "For years, researchers described DNA and RNA as linear chains of four building blocks—the nucleotides A, G, C, and T for DNA; and A, G, C, and U for RNA. But these information molecules are much more than their core sequences. A variety of chemical modifications decorate the nucleic acids, increasing the alphabet of DNA to about a dozen known nucleotide variants. The alphabet of RNA is even more impressive, consisting of at least 140 alternative nucleotide forms. The different building blocks can affect the complementarity of the RNA molecules, alter their structure, and enable the binding of specific proteins that mediate various biochemical and cellular outcomes."



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Our epigenome is influenced by our habitat and lifestyle -- ScienceDaily

"Research on the genomes of Pygmy hunter-gatherer populations and Bantu farmers in Central Africa, carried out by scientists from the Institut Pasteur and the CNRS in cooperation with French and international teams(1), has shown for the first time that our habitat and lifestyle can have an impact on our epigenome -- the entire system that controls the expression of our genes without affecting their sequence. In this study, the scientists have shown that moving from a forest habitat to an urban environment has a profound impact on the epigenetic patterns of the immune response. Conversely, the different historical lifestyles of these populations -- sedentary farming or nomadic hunting and gathering -- are likely to affect more lasting functions, such as those associated with development, by modulating their genetic control via natural selection. This study is being published in the journal Nature Communications on November 30, 2015."



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Lead exposure in mothers can affect future generations -- ScienceDaily

It's a known fact that babies in the womb can be affected by low levels of lead exposure. If a pregnant woman is exposed to lead, the lead passes through the placenta into the baby's developing bones and other organs. Pregnant women with a past exposure to lead can also affect the unborn child's brain, causing developmental problems later in life. Previous research studies have suggested that exposure to heavy metal toxicants can influence a person's global DNA methylation profile.

In the recent Wayne State study led by Douglas Ruden, Ph.D., professor in the Department of Obstetrics & Gynecology and the Institute of Environmental Health Sciences, director of epigenomics, and program leader in the Center for Urban Responses to Environmental Stressors, he and his research team revealed that lead exposure can cause specific changes in DNA methylation, which can be detected in dried blood spots beyond one generation. The neonatal blood spots from both the mothers and children in this study were obtained from the Michigan Neonatal Biobank, a unique resource that has most of the neonatal dried blood spots from children born in Michigan since 1984.

Epigenetic Programming by Endocrine Disrupting Chemicals

The ‘developmental origins of adult health and disease’ (DOHaD) hypothesis postulates that adverse influences early in development can program the risks for adverse health outcomes in adult life. In modern societies, exposure to man-made environmental contaminants is a potential risk factor for developmental programming of chronic disease. Endocrine-disrupting chemicals (EDCs) are of specific concern. EDCs act by mimicking or inhibiting the actions of endogenous hormones, and can have estrogenic, anti-estrogenic, or even anti-androgenic activity. Most EDCs are synthetic chemicals that enter the environment and persist for long periods of time. Among them are many substances that are in widespread use, including dioxin, plastic-softening chemicals, agricultural pesticides, polychlorinated biphenyls, industrial solvents, and pharmaceuticals. Some evidence suggest that exposure to EDCs during early development can cause long-term health outcomes via mechanisms of epigenetic memory.

Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer: PNAS

During chronic inflammation, neutrophil-secreted
hypochlorous acid can damage nearby cells inducing the genomic accumulation of 5-chlorocytosine (5ClC), a known inflammation biomarker. Although 5ClC has been shown to promote epigenetic changes, it has been unknown heretofore if 5ClC directly perpetrates a mutagenic outcome within the cell. The present work shows that 5ClC is intrinsically mutagenic, both in vitro and, at a level of a
single molecule per cell, in vivo. Using biochemical and genetic approaches, we
have quantified the mutagenic and toxic properties of 5ClC, showing that this
lesion caused C→T transitions at frequencies ranging from 3–9% depending on the polymerase traversing the lesion. X-ray crystallographic studies provided a
molecular basis for the mutagenicity of 5ClC; a snapshot of human polymerase β
replicating across a primed 5ClC-containing template uncovered 5ClC engaged in a nascent base pair with an incoming dATP analog. Accommodation of the chlorine substituent in the template major groove enabled a unique interaction between 5ClC and the incoming dATP, which would facilitate mutagenic lesion bypass. The type of mutation induced by 5ClC, the C→T transition, has been previously shown to occur in substantial amounts both in tissues under inflammatory stress and in the genomes of many inflammation-associated cancers. In fact, many sequence-specific mutational signatures uncovered in sequenced cancer genomes feature C→T mutations. Therefore, the mutagenic ability of 5ClC documented in the present study may constitute a direct functional link between chronic inflammation and the genetic changes that enable and promote malignant transformation.

Correspondence of DNA Methylation Between Blood and Brain Tissue and its Application to Schizophrenia Research. - PubMed - NCBI

Given the difficulty of procuring human brain tissue, a key question in
molecular psychiatry concerns the extent to which epigenetic signatures
measured in more accessible tissues such as blood can serve as a
surrogate marker for the brain. Here, we aimed (1) to investigate the
blood-brain correspondence of DNA methylation using a within-subject
design and (2) to identify changes in DNA methylation of brain-related
biological pathways in schizophrenia.We obtained paired blood and
temporal lobe biopsy samples simultaneously from 12 epilepsy patients
during neurosurgical treatment. Using the Infinium 450K methylation
array we calculated similarity of blood and brain DNA methylation for
each individual separately. We applied our findings by performing gene
set enrichment analyses (GSEA) of peripheral blood DNA methylation data
(Infinium 27K) of 111 schizophrenia patients and 122 healthy controls
and included only Cytosine-phosphate-Guanine (CpG) sites that were
significantly correlated across tissues.Only 7.9% of CpG sites showed a
statistically significant, large correlation between blood and brain
tissue, a proportion that although small was significantly greater than
predicted by chance. GSEA analysis of schizophrenia data revealed
altered methylation profiles in pathways related to precursor
metabolites and signaling peptides.Our findings indicate that most DNA
methylation markers in peripheral blood do not reliably predict brain
DNA methylation status. However, a subset of peripheral data may proxy
methylation status of brain tissue. Restricting the analysis to these
markers can identify meaningful epigenetic differences in schizophrenia
and potentially other brain disorders.

Bacterial remodelling of the host epigenome: functional role and evolution of effectors methylating host histones. - PubMed - NCBI

The modulation of the chromatin organization of eukaryotic cells plays
an important role in regulating key cellular processes including host
defence mechanisms against pathogens. Thus, to successfully survive in a
host cell, a sophisticated bacterial strategy is the subversion of
nuclear processes of the eukaryotic cell. Indeed, the number of
bacterial proteins that target host chromatin to remodel the host
epigenetic machinery is expanding. Some of the identified bacterial
effectors that target the chromatin machinery are "eukaryotic-like"
proteins as they mimic eukaryotic histone writers in carrying the same
enzymatic activities. The best-studied examples are the SET-domain
proteins that methylate histones to change the chromatin landscape. In
this review we will discuss SET-domain proteins identified in the
Legionella, Chlamydia and Bacillus genomes that encode enzymatic
activities targeting host histones. Moreover, we discuss their possible
origin as having evolved from prokaryotic ancestors or having been
acquired from their eukaryotic hosts during their co-evolution. The
characterization of such bacterial effectors as modifiers of the host
chromatin landscape is an exciting field of research as it elucidates
new bacterial strategies to manipulate host functions through histone
modifications but it also may identify new modifications of the
mammalian host cells not known before.

Borna Disease Virus Phosphoprotein Modulates Epigenetic Signaling in Neurons To Control Viral Replication

Understanding the modalities of interaction of neurotropic viruses with their target cells represents a major challenge that may improve our knowledge of many human neurological disorders for which viral origin is suspected. Borna disease virus (BDV) represents an ideal model to analyze the molecular mechanisms of viral persistence in neurons and its consequences for neuronal homeostasis. It is now established that BDV ensures its long-term maintenance in infected cells through a stable interaction of viral components with the host cell chromatin, in particular, with core histones. This has led to our hypothesis that such an interaction may trigger epigenetic changes in the host cell. Here, we focused on histone acetylation, which plays key roles in epigenetic regulation of gene expression, notably for neurons. We performed a comparative analysis of histone acetylation patterns of neurons infected or not infected by BDV, which revealed that infection decreases histone acetylation on selected lysine residues. We showed that the BDV phosphoprotein (P) is responsible for these perturbations, even when it is expressed alone independently of the viral context, and that this action depends on its phosphorylation by protein kinase C. We also demonstrated that BDV P inhibits cellular histone acetyltransferase activities. Finally, by pharmacologically manipulating cellular acetylation levels, we observed that inhibiting cellular acetyl transferases reduces viral replication in cell culture. Our findings reveal that manipulation of cellular epigenetics by BDV could be a means to modulate viral replication and thus illustrate a fascinating example of virus-host cell interaction. IMPORTANCE Persistent DNA viruses often subvert the mechanisms that regulate cellular chromatin dynamics, thereby benefitting from the resulting epigenetic changes to create a favorable milieu for their latent and persistent states. Here, we reasoned that Borna disease virus (BDV), the only RNA virus known to durably persist in the nucleus of infected cells, notably neurons, might employ a similar mechanism. In this study, we uncovered a novel modality of virus-cell interaction in which BDV phosphoprotein inhibits cellular histone acetylation by interfering with histone acetyltransferase activities. Manipulation of cellular histone acetylation is accompanied by a modulation of viral replication, revealing a perfect adaptation of this “ancient” virus to its host that may favor neuronal persistence and limit cellular damage.

Can An Infection Alter Your Epigenome? | What is Epigenetics?

Working in a cell-based culture system, researchers have been able to confirm that cells infected with the Toxoplasma parasite exhibit dramatic changes in gene expression. The parasite appears to modulate host gene expression through the activities of secreted proteins that it injects into the host cell. Toxoplasma can bewitch its host cell to arrest the cell cycle, block apoptosis, or, in the case of certain immune cells, cause them to become motile, thereby helping the parasite disseminate throughout the body.

So how might Toxoplasma hijack the host cell to do the parasite’s bidding? It has been shown that some of these parasite-secreted proteins alter signal transduction cascades that ultimately change gene expression, presumably through an epigenetic component. Recent studies lend support to this idea by showing how Toxoplasma infection has the potential to alter both DNA methylation and histone acetylation, modifications that repress or activate genes, respectively.

In a 2014 study, Hari Dass and Vyas noted diminished DNA methylation of the arginine vasopressin promoter in the medial amygdala of infected male rats, which may contribute to the loss of fear in response to cat odors. Interestingly, the aversion to cat odors in infected rats can be reversed with systemic hypermethylation.

Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort

Background: Epigenetic mechanisms such as
altered DNA methylation have been suggested to play a role in autism,
beginning with the classical
association of Prader-Willi syndrome, an imprinting
disorder, with autistic features.

Objectives: Here we tested for the relationship of paternal sperm DNA methylation with autism risk in offspring, examining an enriched-risk
cohort of fathers of autistic children.

Methods: We examined
genome-wide DNA methylation (DNAm) in paternal semen biosamples obtained
from an autism spectrum disorder (ASD)
enriched-risk pregnancy cohort, the Early Autism
Risk Longitudinal Investigation (EARLI) cohort, to estimate associations
between sperm DNAm and prospective ASD development,
using a 12-month ASD symptoms assessment, the Autism Observation Scale
for Infants (AOSI). We analysed methylation data
from 44 sperm samples run on the CHARM 3.0 array, which contains over 4
million
probes (over 7 million CpG sites), including 30
samples also run on the Illumina Infinium HumanMethylation450 (450K)
BeadChip
platform (∼485 000 CpG sites). We also examined
associated regions in an independent sample of post-mortem human brain
ASD
and control samples for which Illumina 450K DNA
methylation data were available.

Results: Using region-based statistical approaches, we identified 193 differentially methylated regions (DMRs) in paternal sperm with
a family-wise empirical P-value
[family-wise error rate (FWER)] <0.05 associated with performance on
the Autism Observational Scale for Infants (AOSI)
at 12 months of age in offspring. The DMRs
clustered near genes involved in developmental processes, including many
genes
in the SNORD family, within the
Prader-Willi syndrome gene cluster. These results were consistent among
the 75 probes on the Illumina
450K array that cover AOSI-associated DMRs from
CHARM. Further, 18 of 75 (24%) 450K array probes showed consistent
differences
in the cerebellums of autistic individuals compared
with controls.

Conclusions: These data
suggest that epigenetic differences in paternal sperm may contribute to
autism risk in offspring, and provide
evidence that directionally consistent, potentially
related epigenetic mechanisms may be operating in the cerebellum of
individuals
with autism.

The effects of in utero bisphenol A exposure on reproductive capacity in several generations of mice

In utero bisphenol A (BPA) exposure affects reproductive function in the
first generation (F1) of mice; however, not many studies have examined
the reproductive effects of BPA exposure on subsequent generations. In
this study, pregnant mice (F0) were orally dosed with vehicle, BPA (0.5,
20, and 50 μg/kg/day) or diethylstilbestrol (DES; 0.05 μg/kg/day) daily
from gestation day 11 until birth. F1 females were used to generate the
F2 generation, and F2 females were used to generate the F3 generation.
Breeding studies at the ages of 3, 6, and 9 months were conducted to
evaluate reproductive capacity over time. Further, studies were
conducted to evaluate pubertal onset, litter size, and percentage of
dead pups; and to calculate pregnancy rate, and mating, fertility, and
gestational indices. The results indicate that BPA exposure (0.5 and
50 μg/kg/day) significantly delayed the age at vaginal opening in the F3
generation compared to vehicle control. Both DES (0.05 μg/kg/day) and
BPA (50 μg/kg/day) significantly delayed the age at first estrus in the
F3 generation compared to vehicle control. BPA exposure reduced
gestational index in the F1 and F2 generations compared to control.
Further, BPA exposure (0.5 μg/kg/day) compromised the fertility index in
the F3 generation compared to control. Finally, in utero BPA exposure
reduced the ability of female mice to maintain pregnancies as they aged.
Collectively, these data suggest that BPA exposure affects reproductive
function in female mice and that some effects may be transgenerational
in nature.

Borna disease virus phosphoprotein modulates epigenetic signaling in neurons to control viral replication.

Understanding the modalities
of interaction of neurotropic viruses with their target cells represents
a major challenge that may improve our knowledge of many human
neurological disorders for which viral origin is suspected. Borna
disease virus (BDV) represents an ideal model to analyze the molecular
mechanisms of viral persistence in neurons and its consequences for
neuronal homeostasis. It is now established that BDV ensures its
long-term maintenance in infected cells through a stable interaction of
viral components with the host cell chromatin, in particular with core
histones. This has led to our hypothesis that such an interaction may
trigger epigenetic changes in the host cell. Here, we focused on histone
acetylation, which play key roles in epigenetic regulation of gene
expression, notably for neurons. We performed a comparative analysis of
histone acetylation patterns of neurons infected or not by BDV, which
revealed that infection decreases histone acetylation on selected lysine
residues. We showed that the BDV phosphoprotein (P) is responsible for
these perturbations, even when expressed alone independently of the
viral context, and that this action depends on its phosphorylation by
protein kinase C. We also demonstrated that BDV P inhibits cellular
histone acetyl transferase activities. Finally, by pharmacologically
manipulating cellular acetylation levels, we observed that inhibiting
cellular acetyl transferases reduces viral replication in cell culture.
Our findings reveal that manipulation of cellular epigenetics by BDV
could be a mean to modulate viral replication and thus illustrate a
fascinating example of virus/host cell interaction.

IMPORTANCE:

Persistent
DNA viruses often subvert the mechanisms that regulate cellular
chromatin dynamics, thereby benefitting from the resulting epigenetic
changes to create a favorable milieu for their latent/persistent states.
Here, we reasoned that Borna Disease Virus (BDV), the only RNA virus
known to durably persist in the nucleus of infected cells, notably
neurons, might employ a similar mechanism. In this study, we uncover a
novel modality of virus/cell interaction in which BDV phosphoprotein
inhibits cellular histone acetylation by interfering with histone acetyl
transferase activities. Manipulation of cellular histone acetylation is
accompanied by a modulation of viral replication, revealing the perfect
adaptation of this "ancient" virus to its host that may favor neuronal
persistence and limit cellular damage.

Endocrine-disrupting chemicals can adversely affect reproduction of future generations of fish

Bisphenol A (BPA) is a chemical that is used in a variety of consumer
products, such as water bottles, dental composites and resins used to
line metal food and beverage containers. Often, aquatic environments
such as rivers and streams become reservoirs for contaminants, including
BPA. Now, University of Missouri researchers and U.S. Geological Survey
(USGS) scientists have determined that fish exposed to
endocrine-disrupting chemicals will pass adverse reproductive effects
onto their offspring as many as three generations later. These findings
suggest that BPA could have adverse reproductive effects for humans and
their offspring who are exposed to BPA as well.

Epigenetics and animal virus infections

Epigenetics, modifications of the genome, heritable during cell division, that do not involve changes in DNA sequences include several mechanisms mainly: histone modifications, DNA
methylation and related modifications, non-coding RNAs (ncRNAs) and
others that regulate gene expression.

The past two decades has seen an explosion of interest for revealing mechanisms that
control epigenetic modifications, mainly based on the influence they
have on chromatin structure and their impact in biological processes
such as programmed DNA rearrangements, imprinting, germ line silencing,
developmentally cued stem cell division, and overall chromosomal
stability and identity. It has also become obvious that epigenetics
changes are fundamental in the interplay between viruses and their host
cells. Generally speaking, when retroviruses and DNA viruses integrate
their genomes into the host genome, they can stay latent by silencing
their genes or can be productive by activating them, and viral gene
expression can be regulated just like as the host. In fact, viral DNA
uses host transcription factors as well as epigenetic regulators, in
such a way that the effect of viral epigenetic control of its own gene
expression also extends to regulate host gene expression. At the same
time cells use similar mechanisms, transcription factors and epigenetic
modifications, in order to try to eliminate viral infections. In
summary, epigenetic mechanisms are involved in most of the virus-cell
interactions.

The goal of this special issue is to bring
together key experimental and theoretical research linking
state-of-the-art knowledge of epigenetic mechanisms involved in
regulating virus-cell interactions.

Mining for viral fragments in methylation enriched sequencing data.

Most next generation sequencing experiments generate more data than is usable for the experimental set up. For example, methyl-CpG binding domain (MBD) affinity purification based sequencing is often used for DNA-methylation profiling, but up to 30% of the sequenced fragments cannot be mapped uniquely to the reference genome. Here we present and evaluate a methodology for the identification of viruses in these otherwise unused paired-end MBD-seq data. Viral detection is accomplished by mapping non-reference alignable reads to a comprehensive set of viral genomes. As viruses play an important role in epigenetics and cancer development, 92 (pre)malignant and benign samples, originating from two different collections of cervical samples and related cell lines, were used in this study. These samples include primary carcinomas (n = 22), low- and high-grade cervical intraepithelial neoplasia (CIN1 and CIN2/3 - n = 2/n = 30) and normal tissue (n = 20), as well as control samples (n = 17). Viruses that were detected include phages, adenoviruses, herpesviridae and HPV. HPV, which causes virtually all cervical cancers, was identified in 95% of the carcinomas, 100% of the CIN2/3 samples, both CIN1 samples and in 55% of the normal samples. Comparing the amount of mapped fragments on HPV for each HPV-infected sample yielded a significant difference between normal samples and carcinomas or CIN2/3 samples (adjusted p-values resp. <10(-5), <10(-5)), reflecting different viral loads and/or methylation degrees in non-normal samples. Fragments originating from different HPV types could be distinguished and were independently validated by PCR-based assays in 71% of the detections. In conclusion, although limited by the a priori knowledge of viral reference genome sequences, the proposed methodology can provide a first confined but substantial insight into the presence, concentration and types of methylated viral sequences in MBD-seq data at low additional cost.

Short-term diesel exhaust inhalation in a controlled human crossover study is associated with changes in DNA methylation of circulating mononuclear cells in asthmatics

Background

Changes in DNA methylation have been associated with traffic-related air pollution in observational studies, but the specific mechanisms and temporal dynamics therein have not been explored in a controlled study of asthmatics. In this study, we investigate short-term effects of diesel exhaust inhalation on DNA methylation levels at CpG sites across the genome in circulating blood in asthmatics.

Methods

A double-blind crossover study of filtered air and diesel exhaust exposures was performed on sixteen non-smoking asthmatic subjects. Blood samples were collected pre-exposure, and then 6 and 30 hours post-exposure. Peripheral blood mononuclear cell DNA methylation was interrogated using the Illumina Infinium HumanMethylation450 Array. Exposure-related changes in DNA methylation were identified. In addition, CpG sites overlapping with Alu or LINE1 repetitive elements and candidate microRNA loci were also analyzed.

Results

DNA methylation at 2827 CpG sites were affected by exposure to diesel exhaust but not filtered air; these sites enriched for genes involved in protein kinase and NFkB pathways. CpG sites with significant changes in response to diesel exhaust exposure primarily became less methylated, with a site residing within GSTP1 being among the significant hits. Diesel exhaust-associated change was also found for CpG sites overlapping with Alu and LINE1 elements as well as for a site withinmiR-21.

Conclusion

Short-term exposure to diesel exhaust resulted in DNA methylation changes at CpG sites residing in genes involved in inflammation and oxidative stress response, repetitive elements, and microRNA. This provides plausibility for the role of DNA methylation in pathways by which airborne particulate matter impacts gene expression and offers support for including DNA methylation analysis in future efforts to understand the interactions between environmental exposures and biological systems.