Environmental Epigenetics最新文献

{"title":"Erratum: Epigenome-wide association of father's smoking with offspring DNA methylation: a hypothesis-generating study.","authors":"G T Mørkve Knudsen,&nbsp;F I Rezwan,&nbsp;A Johannessen,&nbsp;S M Skulstad,&nbsp;R J Bertelsen,&nbsp;F G Real,&nbsp;S Krauss-Etschmann,&nbsp;V Patil,&nbsp;D Jarvis,&nbsp;S H Arshad,&nbsp;J W Holloway,&nbsp;C Svanes","doi":"10.1093/eep/dvz027","DOIUrl":"https://doi.org/10.1093/eep/dvz027","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/eep/dvz023.][This corrects the article DOI: 10.1093/eep/dvz023.].</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"6 1","pages":"dvz027"},"PeriodicalIF":3.8,"publicationDate":"2020-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/eep/dvz027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37630403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-CpG methylation biases bisulphite PCR towards low or unmethylated mitochondrial DNA: recommendations for the field.","authors":"Margaret J Morris,&nbsp;Luke B Hesson,&nbsp;Neil A Youngson","doi":"10.1093/eep/dvaa001","DOIUrl":"https://doi.org/10.1093/eep/dvaa001","url":null,"abstract":"<p><p>Mitochondrial DNA (mtDNA) is a circular genome of 16 kb that is present in multiple copies in mitochondria. mtDNA codes for genes that contribute to mitochondrial structure and function. A long-standing question has asked whether mtDNA is epigenetically regulated similarly to the nuclear genome. Recently published data suggest that unlike the nuclear genome where CpG methylation is the norm, mtDNA is methylated predominantly at non-CpG cytosines. This raises important methodological considerations for future investigations. In particular, existing bisulphite PCR techniques may be unsuitable due to primers being biased towards amplification from unmethylated mtDNA. Here, we describe how this may have led to previous studies underestimating the level of mtDNA methylation and reiterate methodological strategies for its accurate assessment.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"6 1","pages":"dvaa001"},"PeriodicalIF":3.8,"publicationDate":"2020-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/eep/dvaa001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37722613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenetic anticipation for food and reproduction.","authors":"Christelle Leung, Bernard Angers, Patrick Bergeron","doi":"10.1093/eep/dvz026","DOIUrl":"10.1093/eep/dvz026","url":null,"abstract":"<p><p>Physiological changes in anticipation of cyclic environmental events are common for the persistence of populations in fluctuating environments (e.g. seasons). However, dealing with sporadic resources such as the intermittent production of seed masting trees may be challenging unless reliable cues also make them predictable. To be adaptive, the anticipation of such episodic events would have to trigger the corresponding physiological response. Epigenetic modifications could result in such physiological anticipatory responses to future changes. The eastern chipmunk (<i>Tamias striatus</i>) is known to adjust its reproductive activity to match juvenile weaning with peak seed availability of masting trees, which are essential for their survival. We therefore expected that epigenetic changes would be linked to spring reproductive initiation in anticipation for beech seed availability in fall. We correlated the variation of DNA methylation profiles of 114 adult chipmunks captured in May with beech seeds abundance in September, over 4 years, for three distinct populations, as well as individuals sampled twice during reproductive and non-reproductive years. The significant correlation between spring epigenetic variation and the amount of food in the fall confirmed the phenotypic flexibility of individuals according to environmental fluctuations. Altogether, these results underlined the key role of epigenetic processes in anticipatory responses enabling organisms to persist in fluctuating environments.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"6 1","pages":"dvz026"},"PeriodicalIF":3.8,"publicationDate":"2020-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37607428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum to: Issue 6 (1)","authors":"","doi":"10.1093/eep/dvaa012","DOIUrl":"https://doi.org/10.1093/eep/dvaa012","url":null,"abstract":"","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"1 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/eep/dvaa012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46987856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"2019 environment, epigenetics and reproduction.","authors":"Michael K Skinner","doi":"10.1093/eep/dvz025","DOIUrl":"https://doi.org/10.1093/eep/dvz025","url":null,"abstract":"<p><p>A conference summary of the fourth 2018 biannual Kenya Africa Conference 'Environment, Epigenetics and Reproduction' is provided. A special Environmental Epigenetics issue containing a number of papers in Volume 5, Issue 3 and 4 are discussed.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"5 4","pages":"dvz025"},"PeriodicalIF":3.8,"publicationDate":"2019-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/eep/dvz025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37498049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Folic acid supplementation reduces multigenerational sperm miRNA perturbation induced by <i>in utero</i> environmental contaminant exposure.","authors":"P M Herst,&nbsp;M Dalvai,&nbsp;M Lessard,&nbsp;P L Charest,&nbsp;P Navarro,&nbsp;C Joly-Beauparlant,&nbsp;A Droit,&nbsp;J M Trasler,&nbsp;S Kimmins,&nbsp;A J MacFarlane,&nbsp;M-O Benoit-Biancamano,&nbsp;J L Bailey","doi":"10.1093/eep/dvz024","DOIUrl":"https://doi.org/10.1093/eep/dvz024","url":null,"abstract":"<p><p>Persistent organic pollutants (POPs) can induce epigenetic changes in the paternal germline. Here, we report that folic acid (FA) supplementation mitigates sperm miRNA profiles transgenerationally following <i>in utero</i> paternal exposure to POPs in a rat model. Pregnant founder dams were exposed to an environmentally relevant POPs mixture (or corn oil) ± FA supplementation and subsequent F1-F4 male descendants were not exposed to POPs and were fed the FA control diet. Sperm miRNA profiles of intergenerational (F1, F2) and transgenerational (F3, F4) lineages were investigated using miRNA deep sequencing. Across the F1-F4 generations, sperm miRNA profiles were less perturbed with POPs+FA compared to sperm from descendants of dams treated with POPs alone. POPs exposure consistently led to alteration of three sperm miRNAs across two generations, and similarly one sperm miRNA due to POPs+FA; which was in common with one POPs intergenerationally altered sperm miRNA. The sperm miRNAs that were affected by POPs alone are known to target genes involved in mammary gland and embryonic organ development in F1, sex differentiation and reproductive system development in F2 and cognition and brain development in F3. When the POPs treatment was combined with FA supplementation, however, these same miRNA-targeted gene pathways were perturbed to a lesser extend and only in F1 sperm. These findings suggest that FA partially mitigates the effect of POPs on paternally derived miRNA in a intergenerational manner.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"5 4","pages":"dvz024"},"PeriodicalIF":3.8,"publicationDate":"2019-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/eep/dvz024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37471496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenome-wide association of father's smoking with offspring DNA methylation: a hypothesis-generating study.","authors":"G T Mørkve Knudsen,&nbsp;F I Rezwan,&nbsp;A Johannessen,&nbsp;S M Skulstad,&nbsp;R J Bertelsen,&nbsp;F G Real,&nbsp;S Krauss-Etschmann,&nbsp;V Patil,&nbsp;D Jarvis,&nbsp;S H Arshad,&nbsp;J W Holloway,&nbsp;C Svanes","doi":"10.1093/eep/dvz023","DOIUrl":"https://doi.org/10.1093/eep/dvz023","url":null,"abstract":"<p><p>Epidemiological studies suggest that father's smoking might influence their future children's health, but few studies have addressed whether paternal line effects might be related to altered DNA methylation patterns in the offspring. To investigate a potential association between fathers' smoking exposures and offspring DNA methylation using epigenome-wide association studies. We used data from 195 males and females (11-54 years) participating in two population-based cohorts. DNA methylation was quantified in whole blood using Illumina Infinium MethylationEPIC Beadchip. Comb-p was used to analyse differentially methylated regions (DMRs). Robust multivariate linear models, adjusted for personal/maternal smoking and cell-type proportion, were used to analyse offspring differentially associated probes (DMPs) related to paternal smoking. In sensitivity analyses, we adjusted for socio-economic position and clustering by family. Adjustment for inflation was based on estimation of the empirical null distribution in BACON. Enrichment and pathway analyses were performed on genes annotated to cytosine-phosphate-guanine (CpG) sites using the gometh function in missMethyl. We identified six significant DMRs (Sidak-corrected <i>P</i> values: 0.0006-0.0173), associated with paternal smoking, annotated to genes involved in innate and adaptive immunity, fatty acid synthesis, development and function of neuronal systems and cellular processes. DMP analysis identified 33 CpGs [false discovery rate (FDR)  < 0.05]. Following adjustment for genomic control (λ = 1.462), no DMPs remained epigenome-wide significant (FDR < 0.05). This hypothesis-generating study found that fathers' smoking was associated with differential methylation in their adolescent and adult offspring. Future studies are needed to explore the intriguing hypothesis that fathers' exposures might persistently modify their future offspring's epigenome.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"5 4","pages":"dvz023"},"PeriodicalIF":3.8,"publicationDate":"2019-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/eep/dvz023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37450074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mothers' and fathers' cognitive and affective responses to epigenetics concepts.","authors":"Brittany M Hollister,&nbsp;Haley E Yaremych,&nbsp;Megan R Goldring,&nbsp;Susan Persky","doi":"10.1093/eep/dvz021","DOIUrl":"https://doi.org/10.1093/eep/dvz021","url":null,"abstract":"<p><p>Advances in our understanding of epigenetics present new opportunities to improve children's health through the counseling of parents about epigenetics concepts. However, it is important to first evaluate how parents respond to this type of information and determine the consequences of educating parents about epigenetics. We have taken an initial step toward this goal by assessing parental responses to an epigenetics learning module. Parents (<i>n</i> = 190, 126 mothers) responded to pre- and post-module survey questions. Prior to the module, parents reported that mothers' lifestyles prior to conception were more important for children's health than fathers' lifestyles prior to conception (<i>t</i> = 4.49, df = 316.5, <i>P</i> < 0.0001). However, after the module, there was no difference between ratings of the importance of mothers' and fathers' preconception lifestyles (<i>t</i> = 1.18, df = 319.8, <i>P</i> = NS). Furthermore, after viewing the module, parents increased their ratings of the importance of both mothers' (<i>t</i> = -5.65, df = 294.8, <i>P</i> < 0.0001) and father's (<i>t</i> = -9.01, df = 287.2, <i>P</i> < 0.0001) preconception lifestyles for child health. After viewing the module, most parents reported feelings of guilt and negativity regarding epigenetics (78 and 55%, respectively). When compared with lean parents, parents with overweight more often reported feelings of guilt (<i>χ</i> ² =10.27, <i>P</i> = 0.001). This work represents an important first step in evaluating parental responses to epigenetics concepts.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"5 4","pages":"dvz021"},"PeriodicalIF":3.8,"publicationDate":"2019-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/eep/dvz021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38648759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regional epigenetic variation in asexual snail populations among urban and rural lakes","authors":"Jennifer L. M. Thorson, Mark W. Smithson, Ingrid Sadler‐Riggleman, Daniel Beck, M. Dybdahl, M. Skinner","doi":"10.1093/eep/dvz020","DOIUrl":"https://doi.org/10.1093/eep/dvz020","url":null,"abstract":"Abstract Epigenetic variation has the potential to influence environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the capacity to respond through epigenetic variation. An epigenetic response could be even more important in a population when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories. Snails were collected from a more pristine rural Lake 1 (Lake Lytle), and two urban lakes, Lake 2 (Capitol Lake) and Lake 3 (Lake Washington) on the Northwest Pacific coast. DNA methylation was assessed for each sample population using methylated DNA immunoprecipitation, MeDIP, followed by next-generation sequencing. The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2, and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. The presence of site-specific differences between each of these lake populations suggest an epigenetic response to varied environmental factors. The results do not support an effect of geographic distance in these populations. The role of dispersal distance among lakes, population history, environmental pollution and stably inherited methylation versus environmentally triggered methylation in producing the observed epigenetic variation are discussed. Observations support the proposal that epigenetic alterations may associate with phenotypic variation and environmental factors and history of the different lakes.","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/eep/dvz020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49282167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The epigenetic legacy of illicit drugs: developmental exposures and late-life phenotypes","authors":"N. Wanner, Mathia Colwell, Christopher D. Faulk","doi":"10.1093/eep/dvz022","DOIUrl":"https://doi.org/10.1093/eep/dvz022","url":null,"abstract":"Abstract The effects of in utero exposure to illicit drugs on adult offspring are a significant and widespread but understudied global health concern, particularly in light of the growing opioid epidemic and emerging therapeutic uses for cannabis, ketamine, and MDMA. Epigenetic mechanisms including DNA methylation, histone modifications, and expression of non-coding RNAs provide a mechanistic link between the prenatal environment and health consequences years beyond the original exposure, and shifts in the epigenome present in early life or adolescence can lead to disease states only appearing during adulthood. The current review summarizes the literature assessing effects of perinatal illicit drug exposure on adult disease phenotypes as mediated by perturbations of the epigenome. Both behavioral and somatic phenotypes are included and studies reporting clinical data in adult offspring, epigenetic readouts in offspring of any age, or both phenotypic and epigenetic measures are prioritized. Studies of licit substances of abuse (i.e. alcohol, nicotine) are excluded with a focus on cannabis, psychostimulants, opioids, and psychedelics; current issues in the field and areas of interest for further investigation are also discussed.","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/eep/dvz022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47731037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}