Epigenetics最新文献_第8页

Comparative genomic analyses reveal evidence for adaptive A-to-I RNA editing in insect Adar gene. 比较基因组分析揭示了昆虫 Adar 基因中适应性 A 到 I RNA 编辑的证据。

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-03-25 DOI: 10.1080/15592294.2024.2333665

Caiqing Zheng, Ling Ma, Fan Song, Li Tian, Wanzhi Cai, Hu Li, Yuange Duan

{"title":"Comparative genomic analyses reveal evidence for adaptive A-to-I RNA editing in insect Adar gene.","authors":"Caiqing Zheng, Ling Ma, Fan Song, Li Tian, Wanzhi Cai, Hu Li, Yuange Duan","doi":"10.1080/15592294.2024.2333665","DOIUrl":"10.1080/15592294.2024.2333665","url":null,"abstract":"Although A-to-I RNA editing leads to similar effects to A-to-G DNA mutation, nonsynonymous RNA editing (recoding) is believed to confer its adaptiveness by 'epigenetically' regulating proteomic diversity in a temporospatial manner, avoiding the pleiotropic effect of genomic mutations. Recent discoveries on the evolutionary trajectory of Ser>Gly auto-editing site in insect Adar gene demonstrated a selective advantage to having an editable codon compared to uneditable ones. However, apart from pure observations, quantitative approaches for justifying the adaptiveness of individual RNA editing sites are still lacking. We performed a comparative genomic analysis on 113 Diptera species, focusing on the Adar Ser>Gly auto-recoding site in Drosophila. We only found one species having a derived Gly at the corresponding site, and this occurrence was significantly lower than genome-wide random expectation. This suggests that the Adar Ser>Gly site is unlikely to be genomically replaced with G during evolution, and thus indicating the advantage of editable status over hardwired genomic alleles. Similar trends were observed for the conserved Ile>Met recoding in gene Syt1. In the light of evolution, we established a comparative genomic approach for quantitatively justifying the adaptiveness of individual editing sites. Priority should be given to such adaptive editing sites in future functional studies.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2333665"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10965108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar). 基因组环境决定了 DNA 甲基化对大西洋鲑（Salmo salar）肠道上皮细胞基因表达的影响。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-08-16 DOI: 10.1080/15592294.2024.2392049

Aikaterini Katirtzoglou, Søren B Hansen, Harald Sveier, Michael D Martin, Jaelle C Brealey, Morten T Limborg

{"title":"Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar).","authors":"Aikaterini Katirtzoglou, Søren B Hansen, Harald Sveier, Michael D Martin, Jaelle C Brealey, Morten T Limborg","doi":"10.1080/15592294.2024.2392049","DOIUrl":"10.1080/15592294.2024.2392049","url":null,"abstract":"The canonical view of DNA methylation, a pivotal epigenetic regulation mechanism in eukaryotes, dictates its role as a suppressor of gene activity, particularly within promoter regions. However, this view is being challenged as it is becoming increasingly evident that the connection between DNA methylation and gene expression varies depending on the genomic location and is therefore more complex than initially thought. We examined DNA methylation levels in the gut epithelium of Atlantic salmon (Salmo salar) using whole-genome bisulfite sequencing, which we correlated with gene expression data from RNA sequencing of the same gut tissue sample (RNA-seq). Assuming epigenetic signals might be pronounced between distinctive phenotypes, we compared large and small fish, finding 22 significant associations between 22 differentially methylated regions and 21 genes. We did not detect significant methylation differences between large and small fish. However, we observed a consistent signal of methylation levels around the transcription start sites (TSS), being negatively correlated with the expression levels of those genes. We found both negative and positive associations of methylation levels with gene expression further upstream or downstream of the TSS, revealing a more unpredictable pattern. The 21 genes showing significant methylation-expression correlations were involved in biological processes related to salmon health, such as growth and immune responses. Deciphering how DNA methylation affects the expression of such genes holds great potential for future applications. For instance, our results suggest the importance of genomic context in targeting epigenetic modifications to improve the welfare of aquaculture species like Atlantic salmon.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2392049"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11332636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141992224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Expression patterns and clinical value of key m6A RNA modification regulators in smoking patients with coronary artery disease. 主要 m6A RNA 修饰调节因子在吸烟冠心病患者中的表达模式和临床价值。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-08-21 DOI: 10.1080/15592294.2024.2392400

Huanwei Zhuang, Hua Ouyang, Yangfei Peng, Shuji Gong, Kun Xiang, Le Chen, Jinlan Chen

{"title":"Expression patterns and clinical value of key m6A RNA modification regulators in smoking patients with coronary artery disease.","authors":"Huanwei Zhuang, Hua Ouyang, Yangfei Peng, Shuji Gong, Kun Xiang, Le Chen, Jinlan Chen","doi":"10.1080/15592294.2024.2392400","DOIUrl":"10.1080/15592294.2024.2392400","url":null,"abstract":"Even though N6-methyladenosine (m6A) RNA modifications are increasingly being implicated in human disease, their mechanisms are not fully understood in smokers with coronary artery disease (CAD). Thirty m6A-related regulators' expression (MRRE) in CAD individuals (smokers and non-smokers) were analyzed from GEO. Support Vector Machine, random forest, and nomogram models were constructed to assess its clinical value. Consensus clustering, principal component analysis, and ssGSEA were used to construct a full picture of m6A-related regulators in smokers with CAD. Oxygen-glucose deprivation (OGD) and qRT-PCR were used to validate hypoxia's effect on MRRE. A comparison between smokers with CAD and controls revealed lower expression levels of RBM15B, YTHDC2, and ZC3H13. Based on three key MRREs, all models showed good clinical value, and smokers with CAD were divided into two distinct molecular subgroups. The correlations were found between key MRRE and the degree of immune infiltration. Three key MRREs in HUVECs and FMC84 mouse cardiomyocytes were reduced in the OGD group. Through hypoxia, smoking might reduce the expression levels of RBM15B, YTHDC2, and ZC3H13 in smokers with CAD. Our findings provide an important theoretical basis for the treatment of smokers with CAD.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2392400"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11340747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

WGBS of embryonic gonads revealed that long non-coding RNAs in the MHM region might be involved in cell autonomous sex identity and female gonadal development in chickens. 胚胎性腺的WGBS表明，MHM区域的长链非编码rna可能参与了鸡细胞自主性别认同和雌性性腺发育。

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2023-12-01 DOI: 10.1080/15592294.2023.2283657

Ligen Chen, Yu Cheng, Guixin Zhang, Yang Zhou, Zhen Zhang, Qianhong Chen, Yanping Feng

{"title":"WGBS of embryonic gonads revealed that long non-coding RNAs in the MHM region might be involved in cell autonomous sex identity and female gonadal development in chickens.","authors":"Ligen Chen, Yu Cheng, Guixin Zhang, Yang Zhou, Zhen Zhang, Qianhong Chen, Yanping Feng","doi":"10.1080/15592294.2023.2283657","DOIUrl":"10.1080/15592294.2023.2283657","url":null,"abstract":"DNA methylation plays a key role in sex determination and differentiation in vertebrates. However, there are few studies on DNA methylation involved in chicken gonad development, and most focused on male hypermethylated regions (MHM). It is unclear whether there are specific differentially methylated regions (DMRs) in chicken embryonic gonads regulating sex determination and differentiation. Here, the DNA methylation maps showed that the difference of DNA methylation level between sexes was much higher at embryonic day 10 (E10) than that at embryonic day 6 (E6), and the significant differentially methylated regions at both stages were mainly distributed on the Z chromosome, including MHM1 and MHM2. The results of bisulphite sequencing PCR (BSP) and qRT-PCR showed hypomethylation of female MHM and upregulation of long non-coding RNAs (lncRNAs) whose promoter in the MHM region was consistent with the sequencing results, and similar results were in brain and muscle. In female sex-reversed gonads, the methylation pattern of MHM remained unchanged, and the expression levels of the three candidate lncRNAs were significantly decreased compared with those in females, but were significantly increased compared to males. The fluorescence in situ hybridization (FISH) results also showed that these lncRNAs were highly expressed in female embryonic gonads. The results of methyltransferase inhibitor and dual-luciferase reporter assay suggest that lncRNA expression may be regulated by DNA methylation within their promoters. Therefore, we speculated that MHM may be involved in cell-autonomous sex identity in chickens, and that lncRNAs regulated by MHM may be involved in female sexual differentiation.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2283657"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10761181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138458648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Generational stability of epigenetic transgenerational inheritance facilitates adaptation and evolution. 表观遗传的世代稳定性有利于适应和进化。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-08-05 DOI: 10.1080/15592294.2024.2380929

Alexandra Korolenko, Michael K Skinner

{"title":"Generational stability of epigenetic transgenerational inheritance facilitates adaptation and evolution.","authors":"Alexandra Korolenko, Michael K Skinner","doi":"10.1080/15592294.2024.2380929","DOIUrl":"10.1080/15592294.2024.2380929","url":null,"abstract":"The epigenome and epigenetic inheritance were not included in the original modern synthesis theory or more recent extended evolutionary synthesis of evolution. In a broad range of species, the environment has been shown to play a significant role in natural selection, which more recently has been shown to occur through epigenetic alterations and epigenetic inheritance. However, even with this evidence, the field of epigenetics and epigenetic inheritance has been left out of modern evolutionary synthesis, as well as other current evolutionary models. Epigenetic mechanisms can direct the regulation of genetic processes (e.g. gene expression) and also can be directly changed by the environment. In contrast, DNA sequence cannot be directly altered by the environment. The goal of this review is to present the evidence of how epigenetics and epigenetic inheritance can alter phenotypic variation in numerous species. This can occur at a significantly higher frequency than genetic change, so correlates with the frequency of evolutionary change. In addition, the concept and importance of generational stability of transgenerational inheritance is incorporated into evolutionary theory. For there to be a better understanding of evolutionary biology, we must incorporate all aspects of molecular (e.g. genetics and epigenetics) and biological sciences (e.g. environment and adaptation).","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2380929"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11305060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141893150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic architecture of epigenetic cortical clock age in brain tissue from older individuals: alterations in CD46 and other loci. 老年人脑组织表观遗传皮层时钟年龄的遗传结构：CD46 和其他位点的改变。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-08-22 DOI: 10.1080/15592294.2024.2392050

Francine Grodstein, Bernardo Lemos, Jingyun Yang, Katia de Paiva Lopes, Ricardo A Vialle, Nicholas Seyfried, Yanling Wang, Gemma Shireby, Eilis Hannon, Alan Thomas, Keeley Brookes, Jonathan Mill, Philip L De Jager, David A Bennett

{"title":"Genetic architecture of epigenetic cortical clock age in brain tissue from older individuals: alterations in CD46 and other loci.","authors":"Francine Grodstein, Bernardo Lemos, Jingyun Yang, Katia de Paiva Lopes, Ricardo A Vialle, Nicholas Seyfried, Yanling Wang, Gemma Shireby, Eilis Hannon, Alan Thomas, Keeley Brookes, Jonathan Mill, Philip L De Jager, David A Bennett","doi":"10.1080/15592294.2024.2392050","DOIUrl":"10.1080/15592294.2024.2392050","url":null,"abstract":"The cortical epigenetic clock was developed in brain tissue as a biomarker of brain aging. As one way to identify mechanisms underlying aging, we conducted a GWAS of cortical age. We leveraged postmortem cortex tissue and genotyping array data from 694 participants of the Rush Memory and Aging Project and Religious Orders Study (ROSMAP; 11000,000 SNPs), and meta-analysed ROSMAP with 522 participants of Brains for Dementia Research (5,000,000 overlapping SNPs). We confirmed results using eQTL (cortical bulk and single nucleus gene expression), cortical protein levels (ROSMAP), and phenome-wide association studies (clinical/neuropathologic phenotypes, ROSMAP). In the meta-analysis, the strongest association was rs4244620 (p = 1.29 × 10-7), which also exhibited FDR-significant cis-eQTL effects for CD46 in bulk and single nucleus (microglia, astrocyte, oligodendrocyte, neuron) cortical gene expression. Additionally, rs4244620 was nominally associated with lower cognition, faster slopes of cognitive decline, and greater Parkinsonian signs (n ~ 1700 ROSMAP with SNP/phenotypic data; all p ≤ 0.04). In ROSMAP alone, the top SNP was rs4721030 (p = 8.64 × 10-8) annotated to TMEM106B and THSD7A. Further, in ROSMAP (n = 849), TMEM106B and THSD7A protein levels in cortex were related to many phenotypes, including greater AD pathology and lower cognition (all p ≤ 0.0007). Overall, we identified converging evidence of CD46 and possibly TMEM106B/THSD7A for potential roles in cortical epigenetic clock age.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2392050"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Circ-0006332 stimulates cardiomyocyte pyroptosis via the miR-143/TLR2 axis to promote doxorubicin-induced cardiac damage. Circ-0006332通过miR-143/TLR2轴刺激心肌细胞热解，促进多柔比星诱导的心脏损伤。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-07-17 DOI: 10.1080/15592294.2024.2380145

Ping Zhang, Yuanyuan Liu, Yuliang Zhan, Pengtao Zou, Xinyong Cai, Yanmei Chen, Liang Shao

{"title":"Circ-0006332 stimulates cardiomyocyte pyroptosis via the miR-143/TLR2 axis to promote doxorubicin-induced cardiac damage.","authors":"Ping Zhang, Yuanyuan Liu, Yuliang Zhan, Pengtao Zou, Xinyong Cai, Yanmei Chen, Liang Shao","doi":"10.1080/15592294.2024.2380145","DOIUrl":"10.1080/15592294.2024.2380145","url":null,"abstract":"Doxorubicin (DOX)-mediated cardiotoxicity can impair the clinical efficacy of chemotherapy, leading to heart failure (HF). Given the importance of circRNAs and miRNAs in HF, this paper intended to delineate the mechanism of the circular RNA 0006332 (circ -0,006,332)/microRNA (miR)-143/Toll-like receptor 2 (TLR2) axis in doxorubicin (DOX)-induced HF. The binding of miR-143 to circ -0,006,332 and TLR2 was assessed with the dual-luciferase assay, and the binding between miR-143 and circ -0,006,332 was determined with FISH, RIP, and RNA pull-down assays. miR-143 and/or circ -0,006,332 were overexpressed in rats and cardiomyocytes, followed by DOX treatment. In cardiomyocytes, miR-143 and TLR2 expression, cell viability, LDH release, ATP contents, and levels of IL-1β, IL-18, TNF-α, and pyroptosis-related molecules were examined. In rats, cardiac function, serum levels of cardiac enzymes, apoptosis, myocardial fibrosis, and levels of IL-1β, IL-18, TNF-α, TLR2, and pyroptosis-related molecules were detected. miR-143 diminished TLR2 expression by binding to TLR2, and circ -0,006,332 bound to miR-143 to downregulate miR-143 expression. miR-143 expression was reduced and TLR2 expression was augmented in DOX-induced cardiomyocytes. miR-143 inhibited DOX-induced cytotoxicity by suppressing pyroptosis in H9C2 cardiomyocytes. In DOX-induced rats, miR-143 reduced cardiac dysfunction, myocardial apoptosis, myocardial fibrosis, TLR2 levels, and pyroptosis. Furthermore, overexpression of circ -0,006,332 blocked these effects of miR-143 on DOX-induced cardiomyocytes and rats. Circ -0,006,332 stimulates cardiomyocyte pyroptosis by downregulating miR-143 and upregulating TLR2, thus promoting DOX-induced cardiac injury.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2380145"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11259061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Novel DNA methylation changes in mouse lungs associated with chronic smoking. 与长期吸烟有关的小鼠肺部 DNA 甲基化新变化

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-03-04 DOI: 10.1080/15592294.2024.2322386

Chinonye Doris Onuzulu, Samantha Lee, Sujata Basu, Jeannette Comte, Yan Hai, Nikho Hizon, Shivam Chadha, Maria Shenna Fauni, Andrew J Halayko, Christopher D Pascoe, Meaghan J Jones

{"title":"Novel DNA methylation changes in mouse lungs associated with chronic smoking.","authors":"Chinonye Doris Onuzulu, Samantha Lee, Sujata Basu, Jeannette Comte, Yan Hai, Nikho Hizon, Shivam Chadha, Maria Shenna Fauni, Andrew J Halayko, Christopher D Pascoe, Meaghan J Jones","doi":"10.1080/15592294.2024.2322386","DOIUrl":"10.1080/15592294.2024.2322386","url":null,"abstract":"Smoking is a potent cause of asthma exacerbations, chronic obstructive pulmonary disease (COPD) and many other health defects, and changes in DNA methylation (DNAm) have been identified as a potential link between smoking and these health outcomes. However, most studies of smoking and DNAm have been done using blood and other easily accessible tissues in humans, while evidence from more directly affected tissues such as the lungs is lacking. Here, we identified DNAm patterns in the lungs that are altered by smoking. We used an established mouse model to measure the effects of chronic smoke exposure first on lung phenotype immediately after smoking and then after a period of smoking cessation. Next, we determined whether our mouse model recapitulates previous DNAm patterns observed in smoking humans, specifically measuring DNAm at a candidate gene responsive to cigarette smoke, Cyp1a1. Finally, we carried out epigenome-wide DNAm analyses using the newly released Illumina mouse methylation microarrays. Our results recapitulate some of the phenotypes and DNAm patterns observed in human studies but reveal 32 differentially methylated genes specific to the lungs which have not been previously associated with smoking. The affected genes are associated with nicotine dependency, tumorigenesis and metastasis, immune cell dysfunction, lung function decline, and COPD. This research emphasizes the need to study CS-mediated DNAm signatures in directly affected tissues like the lungs, to fully understand mechanisms underlying CS-mediated health outcomes.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2322386"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10913724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140021232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Parental arsenic exposure and tissue-specific DNA methylation in Bangladeshi infants with spina bifida. 孟加拉脊柱裂婴儿的父母砷暴露和组织特异性 DNA 甲基化。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-10-19 DOI: 10.1080/15592294.2024.2416345

Gwen Tindula, Sudipta Kumer Mukherjee, Sheikh Muhammad Ekramullah, D M Arman, Joynul Islam, Subrata Kumar Biswas, Benjamin C Warf, David C Christiani, Bernardo Lemos, Liming Liang, Andres Cardenas, Maitreyi Mazumdar

{"title":"Parental arsenic exposure and tissue-specific DNA methylation in Bangladeshi infants with spina bifida.","authors":"Gwen Tindula, Sudipta Kumer Mukherjee, Sheikh Muhammad Ekramullah, D M Arman, Joynul Islam, Subrata Kumar Biswas, Benjamin C Warf, David C Christiani, Bernardo Lemos, Liming Liang, Andres Cardenas, Maitreyi Mazumdar","doi":"10.1080/15592294.2024.2416345","DOIUrl":"10.1080/15592294.2024.2416345","url":null,"abstract":"An emerging hypothesis linking arsenic toxicity involves altered epigenetic mechanisms, such as DNA methylation. In this study, we examined the relationship between parents' arsenic exposure and DNA methylation in tissues obtained from 28 infants with spina bifida from Bangladesh. We analyzed arsenic in parents' toenails using inductively coupled plasma mass spectrometry (ICP-MS). DNA methylation was measured in infants' dural tissue, buccal swabs, and whole blood using the Illumina Infinium MethylationEPIC BeadChip. We performed epigenome-wide association analyses (EWAS) and tested differentially methylated regions (DMRs). In EWAS, DNA methylation at cg24039697 in dural tissue was positively associated (β = 0.59, p = 7.6 × 10-9) with father's toenail arsenic concentrations, adjusting for covariates. We did not identify any CpG sites related to father's arsenic exposure in the other tissues, or any CpG sites related to mother's arsenic exposure. Gene ontology analysis identified many biological pathways of interest, including the Wnt signaling pathways. We identified several DMRs across the tissues related to arsenic exposure that included probes mapping to genes that have previously been identified in studies of neural tube defects. This study emphasizes the potential impact of arsenic exposure in fathers, often understudied in epidemiological studies, on DNA methylation in a unique neurological tissue specific to spina bifida.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2416345"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11492674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142460921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The one-carbon metabolism as an underlying pathway for placental DNA methylation - a systematic review. 作为胎盘 DNA 甲基化潜在途径的一碳代谢--系统综述。

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-03-14 DOI: 10.1080/15592294.2024.2318516

Marjolein M van Vliet, Sam Schoenmakers, Joost Gribnau, Régine P M Steegers-Theunissen

{"title":"The one-carbon metabolism as an underlying pathway for placental DNA methylation - a systematic review.","authors":"Marjolein M van Vliet, Sam Schoenmakers, Joost Gribnau, Régine P M Steegers-Theunissen","doi":"10.1080/15592294.2024.2318516","DOIUrl":"10.1080/15592294.2024.2318516","url":null,"abstract":"Epigenetic modifications, including DNA methylation, are proposed mechanisms explaining the impact of parental exposures to foetal development and lifelong health. Micronutrients including folate, choline, and vitamin B12 provide methyl groups for the one-carbon metabolism and subsequent DNA methylation processes. Placental DNA methylation changes in response to one-carbon moieties hold potential targets to improve obstetrical care. We conducted a systematic review on the associations between one-carbon metabolism and human placental DNA methylation. We included 22 studies. Findings from clinical studies with minimal ErasmusAGE quality score 5/10 (n = 15) and in vitro studies (n = 3) are summarized for different one-carbon moieties. Next, results are discussed per study approach: (1) global DNA methylation (n = 9), (2) genome-wide analyses (n = 4), and (3) gene specific (n = 14). Generally, one-carbon moieties were not associated with global methylation, although conflicting outcomes were reported specifically for choline. Using genome-wide approaches, few differentially methylated sites associated with S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), or dietary patterns. Most studies taking a gene-specific approach indicated site-specific relationships depending on studied moiety and genomic region, specifically in genes involved in growth and development including LEP, NR3C1, CRH, and PlGF; however, overlap between studies was low. Therefore, we recommend to further investigate the impact of an optimized one-carbon metabolism on DNA methylation and lifelong health.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2318516"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10950272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140131045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0