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Breaking the epigenetic code with MARCS: the Modification Atlas of Regulation by Chromatin States. 利用 MARCS：染色质状态调控修饰图谱破解表观遗传密码。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-09-04 DOI: 10.1080/17501911.2024.2387527
Andrey Tvardovskiy, Saulius Lukauskas, Till Bartke
{"title":"Breaking the epigenetic code with MARCS: the Modification Atlas of Regulation by Chromatin States.","authors":"Andrey Tvardovskiy, Saulius Lukauskas, Till Bartke","doi":"10.1080/17501911.2024.2387527","DOIUrl":"10.1080/17501911.2024.2387527","url":null,"abstract":"","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1061-1065"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An assessment of compositional methods for the analysis of DNA methylation-based deconvolution estimates. 评估用于分析基于 DNA 甲基化的解卷积估算的组成方法。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-08-02 DOI: 10.1080/17501911.2024.2379242
Alexander Alsup, Emily Nissen, Lucas A Salas, Annette M Molinaro, Alexander Reiner, Simin Liu, Tracy E Madsen, Longjian Liu, Paul L Auer, Brock C Christensen, John K Wiencke, Karl T Kelsey, Devin C Koestler
{"title":"An assessment of compositional methods for the analysis of DNA methylation-based deconvolution estimates.","authors":"Alexander Alsup, Emily Nissen, Lucas A Salas, Annette M Molinaro, Alexander Reiner, Simin Liu, Tracy E Madsen, Longjian Liu, Paul L Auer, Brock C Christensen, John K Wiencke, Karl T Kelsey, Devin C Koestler","doi":"10.1080/17501911.2024.2379242","DOIUrl":"10.1080/17501911.2024.2379242","url":null,"abstract":"<p><p>DNA methylation (DNAm)-based deconvolution estimates contain relative data, forming a composition, that standard methods (testing directly on cell proportions) are ill-suited to handle. In this study we examined the performance of an alternative method, analysis of compositions of microbiomes (ANCOM), for the analysis of DNAm-based deconvolution estimates. We performed two different simulation studies comparing ANCOM to a standard approach (two sample <i>t</i>-test performed directly on cell proportions) and analyzed a real-world data from the Women's Health Initiative to evaluate the applicability of ANCOM to DNAm-based deconvolution estimates. Our findings indicate that ANCOM can effectively account for the compositional nature of DNAm-based deconvolution estimates. ANCOM adequately controls the false discovery rate while maintaining statistical power comparable to that of standard methods.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1067-1080"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Potential epigenetic markers of clinical diagnostics/therapeutic targets in preeclampsia. 子痫前期临床诊断/治疗目标的潜在表观遗传标记。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-08-08 DOI: 10.1080/17501911.2024.2383558
Juliana de Oliveira Cruz, Marcelo Rizzatti Luizon
{"title":"Potential epigenetic markers of clinical diagnostics/therapeutic targets in preeclampsia.","authors":"Juliana de Oliveira Cruz, Marcelo Rizzatti Luizon","doi":"10.1080/17501911.2024.2383558","DOIUrl":"10.1080/17501911.2024.2383558","url":null,"abstract":"","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1057-1060"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
LINC01232 promotes ARNTL2 transcriptional activation and inhibits ferroptosis of CRC cells through p300/H3K27ac. LINC01232 通过 p300/H3K27ac 促进 ARNTL2 的转录激活并抑制 CRC 细胞的铁变态反应。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-09-13 DOI: 10.1080/17501911.2024.2387528
Shengwei Zhuang, Zhekun Huang, Hongkai Fan, Zhirong Wu, Han Liu
{"title":"<i>LINC01232</i> promotes <i>ARNTL2</i> transcriptional activation and inhibits ferroptosis of CRC cells through p300/H3K27ac.","authors":"Shengwei Zhuang, Zhekun Huang, Hongkai Fan, Zhirong Wu, Han Liu","doi":"10.1080/17501911.2024.2387528","DOIUrl":"10.1080/17501911.2024.2387528","url":null,"abstract":"<p><p><b>Aim:</b> This study investigated the role of lncRNA <i>LINC01232</i> in ferroptosis of colorectal cancer (CRC).<b>Materials & methods:</b> Real time quantitative polymerase chain reaction or western blot experiments were performed to examine relevant mRNAs and proteins expression. The kit assays evaluated malondialdehyde, iron, Fe<sup>2+</sup> and glutathione levels. ROS levels were verified by flow cytometry. Chromatin immunoprecipitation and RNA immunoprecipitation analysis monitored the correlation among <i>LINC01232</i>, H3K27ac, p300 and ARNTL2.<b>Results:</b> <i>LINC01232</i> or <i>ARNTL2</i> knockdown facilitated erastin-induced ferroptosis. The interaction between <i>LINC01232</i> and p300 resulted in the enhancement of H3K27ac levels at <i>ARNTL2</i> promoter to promote <i>ARNTL2</i> transcriptional activity. <i>ARNTL2</i> overexpression reversed the promoting effect of <i>LINC01232</i> knockdown on ferroptosis.<b>Conclusion:</b> <i>LINC01232</i> inhibited the ferroptosis in CRC by epigenetically upregulating the transcriptional activity of <i>ARNTL2</i>.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":"16 15-16","pages":"1097-1115"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
From womb to wellness: early environmental exposures, cord blood DNA methylation and disease origins. 从子宫到健康：早期环境暴露、脐带血 DNA 甲基化和疾病起源。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-09-12 DOI: 10.1080/17501911.2024.2390823
Hooman Mirzakhani
{"title":"From womb to wellness: early environmental exposures, cord blood DNA methylation and disease origins.","authors":"Hooman Mirzakhani","doi":"10.1080/17501911.2024.2390823","DOIUrl":"10.1080/17501911.2024.2390823","url":null,"abstract":"<p><p>Fetal exposures can induce epigenetic modifications, particularly DNA methylation, potentially predisposing individuals to later health issues. Cord blood (CB) DNA methylation provides a unique window into the fetal epigenome, reflecting the intrauterine environment's impact. Maternal factors, including nutrition, smoking and toxin exposure, can alter CB DNA methylation patterns, associated with conditions from obesity to neurodevelopmental disorders. These epigenetic changes underscore prenatal exposures' enduring effects on health trajectories. Technical challenges include tissue specificity issues, limited coverage of current methylation arrays and confounding factors like cell composition variability. Emerging technologies, such as single-cell sequencing, promise to overcome some of these limitations. Longitudinal studies are crucial to elucidate exposure-epigenome interactions and develop prevention strategies. Future research should address these challenges, advance public health initiatives to reduce teratogen exposure and consider ethical implications of epigenetic profiling. Progress in CB epigenetics research promises personalized medicine approaches, potentially transforming our understanding of developmental programming and offering novel interventions to promote lifelong health from the earliest stages of life.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1175-1183"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of histone acetylation modification sites in the striatum of subchronically manganese-exposed rats. 亚慢性锰暴露大鼠纹状体组蛋白乙酰化修饰位点的鉴定
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-01-04 DOI: 10.2217/epi-2023-0364
Chunyan Ao, Shunfang Tang, Yue Yang, Ying Liu, Hua Zhao, Jiaqi Ban, Jun Li
{"title":"Identification of histone acetylation modification sites in the striatum of subchronically manganese-exposed rats.","authors":"Chunyan Ao, Shunfang Tang, Yue Yang, Ying Liu, Hua Zhao, Jiaqi Ban, Jun Li","doi":"10.2217/epi-2023-0364","DOIUrl":"10.2217/epi-2023-0364","url":null,"abstract":"<p><p><b>Aim:</b> To explore the specific histone acetylation sites and oxidative stress-related genes that are associated with the pathogenesis of manganese toxicity. <b>Methods:</b> We employed liquid chromatography-tandem mass spectrometry and bioinformatics analysis to identify acetylated proteins in the striatum of subchronic manganese-intoxicated rats. <b>Results:</b> We identified a total of 12 differentially modified histone acetylation sites: H3K9ac, H3K14ac, H3K18ac, H3K56ac and H3K79ac were upregulated and H3K27ac, H3K36ac, H4K91ac, H4K79ac, H4K31ac, H2BK16ac and H2BK20ac were downregulated. Additionally, we found that <i>CAT</i>, <i>SOD1</i> and <i>SOD2</i> might be epigenetically regulated and involved in the pathogenesis of manganism. <b>Conclusion:</b> This study identified histone acetylation sites and oxidative stress-related genes associated with the pathogenesis of manganese toxicity, and these findings are useful in the search for potential epigenetic targets for manganese toxicity.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"5-21"},"PeriodicalIF":3.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139086372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
LINC00513 promotes colorectal cancer malignant progression by binding with IGF2BP1 to enhance the stability of connective tissue growth factor mRNA. LINC00513 通过与 IGF2BP1 结合，增强结缔组织生长因子 mRNA 的稳定性，从而促进结直肠癌的恶性进展。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-07-29 DOI: 10.1080/17501911.2024.2373686
Weijian Lun, Xiaobin Zhang, Yinsheng Hong, Canhua Luo, Yongjia Liu
{"title":"<i>LINC00513</i> promotes colorectal cancer malignant progression by binding with IGF2BP1 to enhance the stability of connective tissue growth factor mRNA.","authors":"Weijian Lun, Xiaobin Zhang, Yinsheng Hong, Canhua Luo, Yongjia Liu","doi":"10.1080/17501911.2024.2373686","DOIUrl":"10.1080/17501911.2024.2373686","url":null,"abstract":"<p><p><b>Aim:</b> This study aimed to investigate the role of <i>LINC00513</i> in colorectal cancer (CRC) progression.<b>Materials & methods:</b> Cell proliferation was evaluated using Cell Counting Kit-8. Cell migration was detected with transwell assay. RNA pull-down was applied for verifying the interactions between <i>LINC00513</i>, IGF2BP1 and connective tissue growth factor (<i>CTGF</i>).<b>Results:</b> <i>LINC00513</i>, IGF2BP1 and <i>CTGF</i> levels were upregulated in CRC. Knockdown of <i>LINC00513</i> significantly inhibited the malignant behavior of CRC cells. <i>LINC00513</i> increased <i>CTGF</i> mRNA stability by binding with IGF2BP1. Furthermore, overexpression of IGF2BP1 or <i>CTGF</i> reversed the inhibitory effect of <i>LINC00513</i> shRNA on CRC progression.<b>Conclusion:</b> <i>LINC00513</i> promoted CRC cell malignant behaviors through IGF2BP1/<i>CTGF</i>.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"985-998"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141787657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Epigenetic landscape of intestinal cell line HT29 cocultured with Lacticaseibacillus. 与乳酸杆菌共培养的肠细胞株 HT29 的表观遗传学特征。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-07-29 DOI: 10.1080/17501911.2024.2377949
Anunay Sinha, Sanjeev Khosla
{"title":"Epigenetic landscape of intestinal cell line HT29 cocultured with <i>Lacticaseibacillus</i>.","authors":"Anunay Sinha, Sanjeev Khosla","doi":"10.1080/17501911.2024.2377949","DOIUrl":"10.1080/17501911.2024.2377949","url":null,"abstract":"<p><p><b>Aim:</b> To investigate the changes in epigenetic landscape of HT29 cells upon coculture with the <i>Lacticaseibacillus.</i><b>Materials & methods:</b> Histone and m6A mRNA modifications were examined by biochemical and NGS-based methods including western blotting, colorimetric assays, ChIP-Seq and direct mRNA sequencing. LC-MS was performed to identify <i>Lacticaseibacillus</i> secretome.<b>Results:</b> In cocultured HT29 cells global enrichment of H3K9ac and H3K4me3 and depletion of H3K9me3 mark was observed; mean genic positional signals showed depletion of H3K9ac and H3K4me3 at the TSS but enrichment in the upstream region; m6A methylation was altered in mRNAs corresponding to specific gene pathways; <i>Lacticaseibacillus</i> HU protein interacts with histone H3.<b>Conclusion: </b> <i>Lacticaseibacillus</i> can epigenetically alter specific genetic pathways in human intestinal cells.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1081-1096"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141787568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Epigenetics of cerebrovascular diseases: an update review of clinical studies. 脑血管疾病的表观遗传学：临床研究的最新回顾。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-07-29 DOI: 10.1080/17501911.2024.2377947
Anna Maria Ciaccio, Antonino Tuttolomondo
{"title":"Epigenetics of cerebrovascular diseases: an update review of clinical studies.","authors":"Anna Maria Ciaccio, Antonino Tuttolomondo","doi":"10.1080/17501911.2024.2377947","DOIUrl":"10.1080/17501911.2024.2377947","url":null,"abstract":"<p><p>Cerebrovascular diseases, especially stroke, are critical and heterogenous clinical conditions associated with high mortality and chronic disability. Genome-wide association studies reveal substantial stroke heritability, though specific genetic variants account for a minor fraction of stroke risk, suggesting an essential role for the epigenome. Epigenome-wide association studies and candidate gene approaches show that DNA methylation patterns significantly influence stroke susceptibility. Additionally, chromatin remodelers and non-coding RNA regulate gene expression in response to ischemic conditions. In this updated review, we summarized the progress of knowledge on epigenetics in the field of ischemic stroke underlying opportunities and challenges.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1043-1055"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141787569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gut microbiota defined epigenomes of Alzheimer's and Parkinson's diseases reveal novel targets for therapy. 确定了阿尔茨海默氏症和帕金森氏症表观基因组的肠道微生物群揭示了新的治疗靶点。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2023-12-13 DOI: 10.2217/epi-2023-0342
Shabnam Nohesara, Hamid Mostafavi Abdolmaleky, Sam Thiagalingam, Jin-Rong Zhou
{"title":"Gut microbiota defined epigenomes of Alzheimer's and Parkinson's diseases reveal novel targets for therapy.","authors":"Shabnam Nohesara, Hamid Mostafavi Abdolmaleky, Sam Thiagalingam, Jin-Rong Zhou","doi":"10.2217/epi-2023-0342","DOIUrl":"10.2217/epi-2023-0342","url":null,"abstract":"<p><p>The origins of Alzheimer's disease (AD) and Parkinson's disease (PD) involve genetic mutations, epigenetic changes, neurotoxin exposure and gut microbiota dysregulation. The gut microbiota's dynamic composition and its metabolites influence intestinal and blood-brain barrier integrity, contributing to AD and PD development. This review explores protein misfolding, aggregation and epigenetic links in AD and PD pathogenesis. It also highlights the role of a leaky gut and the microbiota-gut-brain axis in promoting these diseases through inflammation-induced epigenetic alterations. In addition, we investigate the potential of diet, probiotics and microbiota transplantation for preventing and treating AD and PD via epigenetic modifications, along with a discussion related to current challenges and future considerations. These approaches offer promise for translating research findings into practical clinical applications.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"57-77"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138799264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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