Epigenomics最新文献_第3页

Dynamic visualization of DNA methylation in cell cycle genes during iPSC cardiac differentiation. iPSC 心脏分化过程中细胞周期基因 DNA 甲基化的动态可视化。

IF 3 4区医学

Epigenomics Pub Date : 2024-12-01 Epub Date: 2024-11-27 DOI: 10.1080/17501911.2024.2430171

Ning Li, Ba Thong Nguyen, Edward A Stitt, Zhenhe Zhang, W Robb MacLellan, Yiqiang Zhang

引用次数: 0

Circular RNAs as multifaceted molecular regulators of vital activity and potential biomarkers of aging. 环状 RNA 是生命活动的多方面分子调节剂和衰老的潜在生物标志物。

IF 3 4区医学

Epigenomics Pub Date : 2024-12-01 Epub Date: 2024-11-26 DOI: 10.1080/17501911.2024.2430165

Anna-Maria D Zharova, Alexey D Perenkov, Maria V Vedunova

{"title":"Circular RNAs as multifaceted molecular regulators of vital activity and potential biomarkers of aging.","authors":"Anna-Maria D Zharova, Alexey D Perenkov, Maria V Vedunova","doi":"10.1080/17501911.2024.2430165","DOIUrl":"10.1080/17501911.2024.2430165","url":null,"abstract":"Aging presents a significant challenge to health and social care systems due to the increasing proportion of the elderly population. The identification of reliable biomarkers to assess the progression of aging remains an unresolved question. Circular RNAs (circRNAs) are single-stranded covalently closed RNAs. They have been found to regulate various biological processes. CircRNAs are present in human biological fluids, are relatively stable, and accumulate with age, making them promising as biomarkers of aging. Current information on the expression of circRNAs in aging was analyzed using scientific databases. In this review, we have identified key stages in the study of circRNAs during aging and summarized the current understanding of their biogenesis. By focusing on the role of circRNAs in processes that contribute to aging - such as genomic stability, metabolism, cell death, and signaling pathways - we hypothesize that circRNAs may drive the aging process through their age-related accumulation and resultant deregulation. Examples of age-related differential expression of circRNAs in various species, including humans, are provided. This review highlights the importance of finding novel epigenetic biomarkers of aging, beyond the already identified molecules (circFOXO3, circRNA100783, circPVT1), and highlights circRNAs as a potential therapeutic target for the treatment of age-associated diseases.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1465-1475"},"PeriodicalIF":3.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142727417","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

SNHG12 in cancer-associated fibroblast-derived extracellular vesicle induces macrophage-myofibroblast transition. 癌症相关成纤维细胞源性细胞外囊泡中的 SNHG12 可诱导巨噬细胞-成纤维细胞转化。

IF 3 4区医学

Epigenomics Pub Date : 2024-12-01 Epub Date: 2024-11-20 DOI: 10.1080/17501911.2024.2430166

Tao Wu, Li Zeng, Chao Peng, Zheng Zhao, Weihao Mu, Song Wang, Deli Tan

引用次数: 0

Prenatal chemical exposures and the methylome: current evidence and opportunities for environmental epigenetics. 产前化学暴露和甲基组：环境表观遗传学的现有证据和机遇。

IF 3 4区医学

Epigenomics Pub Date : 2024-12-01 Epub Date: 2024-11-14 DOI: 10.1080/17501911.2024.2426441

Anne K Bozack, Leonardo Trasande

引用次数: 0

Role of long non-coding RNAs in neurofibromatosis and Schwannomatosis: pathogenesis and therapeutic potential. 长非编码 RNA 在神经纤维瘤病和许旺瘤病中的作用：发病机制和治疗潜力。

IF 3 4区医学

Epigenomics Pub Date : 2024-12-01 Epub Date: 2024-11-27 DOI: 10.1080/17501911.2024.2430170

Md Sadique Hussain, Somya Sharma, Alka Kumari, Almaz Kamran, Gurusha Bahl, Ajay Singh Bisht, Ayesha Sultana, Sumel Ashique, Prasanna Srinivasan Ramalingam, Sivakumar Arumugam

{"title":"Role of long non-coding RNAs in neurofibromatosis and Schwannomatosis: pathogenesis and therapeutic potential.","authors":"Md Sadique Hussain, Somya Sharma, Alka Kumari, Almaz Kamran, Gurusha Bahl, Ajay Singh Bisht, Ayesha Sultana, Sumel Ashique, Prasanna Srinivasan Ramalingam, Sivakumar Arumugam","doi":"10.1080/17501911.2024.2430170","DOIUrl":"10.1080/17501911.2024.2430170","url":null,"abstract":"Neurofibromatosis (NF) is identified as genetic disorder characterized by multiple tumors on nerve tissues. NF1 is the most prevalent form, identified by neurofibromas and skin changes. NF1 is the most prevalent neurofibromatosis disorder, distinct from the rarer NF2 and schwannomatosis (SWN) conditions. NF2, including NF2-related SWN (NF2-SWN), predominantly involves schwannoma formation and differs from NF1 in its genetic basis and clinical presentation. Despite the established genetic basis of NF, effective treatments remain scarce. Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression, impacting pathways vital to tumor biology. This review explores the lncRNAs role in NF pathogenesis along with their potential as therapeutic targets. LncRNAs such as ANRIL and H19 show dysregulated expression in NF, influencing signaling pathways like Ras/MAPK and JAK/STAT, thereby contributing to tumor development. Understanding these interactions sheds light on the molecular mechanisms underlying NF and highlights lncRNAs as potential biomarkers of diagnosis and prognosis of NF. Additionally, therapeutic strategies targeting lncRNAs with antisense oligonucleotides (ASOs) or CRISPR-Cas9 offer promising treatment options. The present review emphasizes crucial role of lncRNAs in NF pathogenesis and their promise to create innovative treatments, aiming to improve patient outcomes and meet the urgent need for effective NF therapies.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1453-1464"},"PeriodicalIF":3.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142727424","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

tRNA-derived RNAs in human milk extracellular vesicles and associations with breastfeeding variables and maternal diet. 人乳细胞外囊泡中的 tRNA 衍生 RNA 及其与母乳喂养变量和母体饮食的关系。

IF 3 4区医学

Epigenomics Pub Date : 2024-12-01 Epub Date: 2024-11-24 DOI: 10.1080/17501911.2024.2430943

Abigail Gaylord, Elizabeth A Holzhausen, Bridget Chalifour, William B Patterson, Pei Wen Tung, Andrea A Baccarelli, Michael I Goran, Tanya L Alderete, Allison Kupsco

{"title":"tRNA-derived RNAs in human milk extracellular vesicles and associations with breastfeeding variables and maternal diet.","authors":"Abigail Gaylord, Elizabeth A Holzhausen, Bridget Chalifour, William B Patterson, Pei Wen Tung, Andrea A Baccarelli, Michael I Goran, Tanya L Alderete, Allison Kupsco","doi":"10.1080/17501911.2024.2430943","DOIUrl":"10.1080/17501911.2024.2430943","url":null,"abstract":"Aims: To describe tDRs in human milk EVs and their associations with maternal body mass index, age, dietary indices, breastfeeding frequency, season and time of milk collection in a Latina population.Materials & methods: We sequenced small RNAs from EVs from 109 mature human milk samples collected at 1 month after delivery in the Southern California Mother's Milk Study. We grouped tDRs using hierarchical clustering and clusters were compared across tDR characteristics. We analyzed associations of tDRs with intrinsic maternal variables (body mass index, age), maternal nutrition (caloric intake, Healthy Eating Index, Dietary Inflammatory Index), and variables related to feeding and milk collection (breastfeeding frequency, season and time of milk collection) using negative binomial models.Results: We identified 338 tDRs expressed in 90% or more of milk EV samples, of which 113 were identified in all samples. tDR-1:26-Gly-CCC-1-M4 accounted for most reads (79%). Pathway analysis revealed a wide array of biological processes and disease mechanisms across the four tDR clusters. tDRs were associated with season of collection, time of collection, breastfeeding frequency, and the dietary inflammatory index.Conclusions: tDRs are abundant in milk EVs and may be sensitive to maternal diet, seasonality, time of day, and breastfeeding frequency.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1429-1441"},"PeriodicalIF":3.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142709354","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

CXXC5 stabilizes DNA methylation patterns in mouse embryonic stem cells. CXXC5 可稳定小鼠胚胎干细胞的 DNA 甲基化模式。

IF 3 4区医学

Epigenomics Pub Date : 2024-11-01 Epub Date: 2024-11-25 DOI: 10.1080/17501911.2024.2426450

Seung-Gi Jin, Jennifer Johnson, Zhijun Huang, Wei Cui, Thomas Dunwell, Gerd P Pfeifer

{"title":"CXXC5 stabilizes DNA methylation patterns in mouse embryonic stem cells.","authors":"Seung-Gi Jin, Jennifer Johnson, Zhijun Huang, Wei Cui, Thomas Dunwell, Gerd P Pfeifer","doi":"10.1080/17501911.2024.2426450","DOIUrl":"10.1080/17501911.2024.2426450","url":null,"abstract":"Aims: Mammalian genomes encode 12 proteins that contain a CXXC zinc finger domain. Most members of this family are large multi-domain proteins that function in the control of DNA methylation and histone methylation patterns. CXXC5 is a smaller member of the family, along with its closest homologue CXXC4. These two proteins lack known catalytic domains. Here, we have characterized CXXC5 in mouse embryonic stem (ES) cells.Materials & methods: We used gene knockouts, RNA sequencing, and DNA methylation analysis by whole-genome bisulfite sequencing.Results & conclusions: We show that CXXC5 is a nuclear protein that interacts with 5-methylcytosine oxidases (TET proteins). Removal of CXXC5 from ES cells leads to very few changes in gene expression. CXXC5 extensively colocalizes with TET1 and TET2 at CpG islands. CXXC5 inactivation leads to a substantial reduction of DNA methylation levels that affects all genomic compartments including genic and intergenic regions and CpG island shores. We propose a model in which CXXC5 serves as an anchor for TET proteins at CpG islands. In the absence of CXXC5, the 5-methylcytosine oxidases become dislodged from CpG islands and are enabled to induce genome-scale DNA demethylation. Thus, CXXC5 serves as a stabilizer of DNA methylation patterns.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1351-1363"},"PeriodicalIF":3.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142709433","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

DNA methylation analysis of multiple genes in thymic epithelial tumors. 胸腺上皮肿瘤多个基因的DNA甲基化分析

IF 3 4区医学

Epigenomics Pub Date : 2024-11-01 Epub Date: 2024-11-08 DOI: 10.1080/17501911.2024.2419362

Vanessa Nicolì, Marianna Giangreco, Eleonora Pardini, Iacopo Petrini, Diana Bacchin, Vittorio Aprile, Franca Melfi, Marco Lucchi, Melania Guida, Roberta Ricciardi, Michelangelo Maestri, Martina Lari, Lucia Migliore, Andrea Stoccoro, Fabio Coppedè

引用次数: 0

The Two Faces of HDAC3: Neuroinflammation in Disease and Neuroprotection in Recovery. HDAC3 的两面性：疾病中的神经炎症和康复中的神经保护。

IF 3 4区医学

Epigenomics Pub Date : 2024-11-01 Epub Date: 2024-11-08 DOI: 10.1080/17501911.2024.2419357

Cal Rosete, Annie Vogel Ciernia

{"title":"The Two Faces of HDAC3: Neuroinflammation in Disease and Neuroprotection in Recovery.","authors":"Cal Rosete, Annie Vogel Ciernia","doi":"10.1080/17501911.2024.2419357","DOIUrl":"10.1080/17501911.2024.2419357","url":null,"abstract":"Histone deacetylase 3 (HDAC3) is a critical regulator of gene expression, influencing a variety of cellular processes in the central nervous system. As such, dysfunction of this enzyme may serve as a key driver in the pathophysiology of various neuropsychiatric disorders and neurodegenerative diseases. HDAC3 plays a crucial role in regulating neuroinflammation, and is now widely recognized as a major contributor to neurological conditions, as well as in promoting neuroprotective recovery following brain injury, hemorrhage and stroke. Emerging evidence suggests that pharmacological inhibition of HDAC3 can mitigate behavioral and neuroimmune deficits in various brain diseases and disorders, offering a promising therapeutic strategy. Understanding HDAC3 in the healthy brain lays the necessary foundation to define and resolve its dysfunction in a disease state. This review explores the mechanisms of HDAC3 in various cell types and its involvement in disease pathology, emphasizing the potential of HDAC3 inhibition to address neuroimmune, gene expression and behavioral deficits in a range of neurodegenerative and neuropsychiatric conditions.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1373-1388"},"PeriodicalIF":3.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11728336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603219","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

The mystique of epigenetic regulation: the remarkable case of a human noncoding RNA, nc886. 表观遗传调控的神秘性：人类非编码 RNA nc886 的非凡案例。

IF 3 4区医学

Epigenomics Pub Date : 2024-11-01 Epub Date: 2024-10-28 DOI: 10.1080/17501911.2024.2415278

Yeon-Su Lee, Yong Sun Lee

引用次数: 0