EPIGENETICS 发表经过同行评审的原创研究和评论文章，提供了一个前所未有的论坛，可以揭示、共享和讨论表观遗传机制及其在不同生物过程中的作用。表观遗传学研究研究由除 DNA 序列修饰以外的机制引起的基因表达的可遗传变化。因此，表观遗传学在各种生物系统、疾病和学科中发挥着关键作用。感兴趣的主题包括（但不限于）：DNA甲基化核小体定位和修饰基因沉默印记核重编程染色质重塑非编码RNA非组蛋白染色体元件剂量补偿核组织表观遗传治疗和诊断营养和环境表观遗传学癌症表观遗传学神经表观遗传学

The journal "Epigenetics" publishes peer-reviewed original research and review articles, providing an unprecedented forum to reveal, share, and discuss epigenetic mechanisms and their roles in various biological processes. Epigenetic research focuses on heritable changes in gene expression caused by mechanisms other than DNA sequence modifications. Therefore, epigenetics plays a crucial role in various biological systems, diseases, and disciplines. Topics of interest include (but are not limited to): DNA methylation, nucleosome positioning and modification, gene silencing, imprinting, nuclear reprogramming, chromatin remodeling, non-coding RNA, non-histone chromosomal elements, dosage compensation, nuclear organization, epigenetic therapy and diagnostics, nutritional and environmental epigenetics, cancer epigenetics, and neuroepigenetics.

《Epigenetics》期刊发表经过同行评审的原创研究和评论文章，提供了一个前所未有的论坛，以揭示、共享和讨论表观遗传机制及其在不同生物过程中的作用。表观遗传学研究关注的是由除DNA序列修饰以外的机制引起的基因表达的可遗传变化。因此，表观遗传学在各种生物系统、疾病和学科中发挥着关键作用。感兴趣的主题包括（但不限于）：DNA甲基化、核小体定位和修饰、基因沉默、印记、核重编程、染色质重塑、非编码RNA、非组蛋白、染色体元件、剂量补偿、核组织、表观遗传治疗和诊断、营养和环境表观遗传学、癌症表观遗传学、神经表观遗传学。

Epigenetics

Obsessive-compulsive disorder (OCD) has recently been linked to increased methylation levels in the oxytocin receptor (OXTR) gene, and OXTR hypermethylation has predicted a worse treatment response to cognitive-behavioural therapy (CBT). Furthermore, OCD is associated with childhood trauma and stressful life events, which have both been shown to affect OXTR methylation. Here, we aimed to replicate findings of increased OXTR methylation as a predictor of disease and worse treatment response in an independent sample that received treatment within the public health care system. In addition, we aimed to extend previous findings by examining associations between OXTR hypermethylation, environmental stressors, OCD diagnosis, and treatment response. Methylation levels at two CpGs within OXTR exon III were compared between n = 181 OCD patients and n = 199 healthy controls using linear regression analysis. In a subsample of OCD patients (n = 98) with documented treatment data, we examined associations between methylation and treatment response to CBT. Childhood adversity and stressful life events were assessed using Childhood Trauma Questionnaire and Life Experience Survey, respectively. OCD patients exhibited significant hypermethylation at CpG site cg04523291 compared to controls, and increased methylation was associated with impaired treatment response. Moreover, hypermethylation at cg04523291 was associated with stressful life events in OCD patients, and with childhood adversity in controls. Yet, there were no significant mediation effects. In conclusion, we replicated the association between OXTR hypermethylation and OCD in the largest sample, so far. Furthermore, our findings support the role of OXTR methylation as a promising biomarker for treatment response in OCD.

Katharina Bey

Rafael Campos-Martin

Julia Klawohn

Benedikt Reuter

Rosa Grützmann

Anja Riesel

Michael Wagner

Alfredo Ramirez

Norbert Kathmann

Hypermethylation of the oxytocin receptor gene (OXTR) in obsessive-compulsive disorder: further evidence for a biomarker of disease and treatment response

DNA methyltransferase 1 (DNMT1) is essential for DNA methylation, gene regulation and chromatin stability. We previously discovered DNMT1 mutations cause hereditary sensory and autonomic neuropathy type 1 with dementia and hearing loss (HSAN1E; OMIM 614116). HSAN1E is the first adult-onset neurodegenerative disorder caused by a defect in a methyltransferase gene. HSAN1E patients appear clinically normal until young adulthood, then begin developing the characteristic symptoms involving central and peripheral nervous systems. Some HSAN1E patients also develop narcolepsy and it has recently been suggested that HSAN1E is allelic to autosomal dominant cerebellar ataxia, deafness, with narcolepsy (ADCA-DN; OMIM 604121), which is also caused by mutations in DNMT1. A hotspot mutation Y495C within the targeting sequence domain of DNMT1 has been identified among HSAN1E patients. The mutant DNMT1 protein shows premature degradation and reduced DNA methyltransferase activity. Herein, we investigate genome-wide DNA methylation at single-base resolution through whole-genome bisulfite sequencing of germline DNA in 3 pairs of HSAN1E patients and their gender- and age-matched siblings. Over 1 billion 75-bp single-end reads were generated for each sample. In the 3 affected siblings, overall methylation loss was consistently found in all chromosomes with X and 18 being most affected. Paired sample analysis identified 564,218 differentially methylated CpG sites (DMCs; P < 0.05), of which 300 134 were intergenic and 264 084 genic CpGs. Hypomethylation was predominant in both genic and intergenic regions, including promoters, exons, most CpG islands, L1, L2, Alu, and satellite repeats and simple repeat sequences. In some CpG islands, hypermethylated CpGs outnumbered hypomethylated CpGs. In 201 imprinted genes, there were more DMCs than in non-imprinted genes and most were hypomethylated. Differentially methylated region (DMR) analysis identified 5649 hypomethylated and 1872 hypermethylated regions. Importantly, pathway analysis revealed 1693 genes associated with the identified DMRs were highly associated in diverse neurological disorders and NAD+/NADH metabolism pathways is implicated in the pathogenesis. Our results provide novel insights into the epigenetic mechanism of neurodegeneration arising from a hotspot DNMT1 mutation and reveal pathways potentially important in a broad category of neurological and psychological disorders.

Zhifu Sun

Yanhong Wu

Tamas Ordog

Saurabh Baheti

Jinfu Nie

Xiaohui Duan

Kaori Hojo

Jean-Pierre Kocher

Peter J Dyck

Christopher J Klein

Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E

Posttranslational histone modifications define chromatin structure and function. In recent years, a number of studies have characterized many of the enzymatic activities and diverse regulatory components required for monomethylation of histone H3 lysine 4 (H3K4me1) and the expression of specific genes. The challenge now is to understand how this specific chemical modification is written and the Set7 methyltransferase has emerged as a key regulatory enzyme mediating methylation of lysine residues of histone and non-histone proteins. In this review, we comprehensively explore the regulatory proteins modified by Set7 and highlight mechanisms of specific co-recruitment of the enzyme to activating promoters. With a focus on signaling and transcriptional control in disease we discuss recent experimental data emphasizing specific components of diverse regulatory complexes that mediate chromatin modification and reinterpretation of Set7-mediated gene expression.

Samuel Keating

Assam El-Osta

Transcriptional regulation by the Set7 lysine methyltransferase

Set7赖氨酸甲基转移酶的转录调控

Epigenetic machinery contributes to gene regulation in eukaryotic species. However, the machinery including more than 600 epigenetic regulator (ER) genes responsible for reading, writing, and erasing histone modifications and DNA modifications remains largely uncharacterized across species. We compile a comprehensive list of ERs based on an evolutionary analysis across 23 species, which is the most comprehensive ER list in various species until recently. We further perform comparative transcriptomic analyses across different tissues in humans, mice, as well as other amniote species. We observe a consistent tissue-of-origin expression specificity pattern of duplicated ER genes across species and suggest links between expression specificity and ER gene evolution as well as ER function. Additional analyses further suggest that ER duplication can generate tissue-specific ER genes with the same epigenetic substrates, which may be closely related to their regulatory specificity in tissue development. Our work can serve as a foundation to better comprehend the tissue-specific expression patterns of ER genes from an evolutionary perspective and also the functional implications of ERs in tissue-specific epigenetic regulation.

Jilu Wang

Aiai Shi

Jie Lyu

A comprehensive atlas of epigenetic regulators reveals tissue-specific epigenetic regulation patterns

To distinguish DNA methylation (DNAm) from cell proportion changes in whole placental villous tissue research, we developed a robust cell type-specific DNAm reference to estimate cell composition. We collated new and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (

Kyle A. Campbell

Justin A. Colacino

John Dou

Dana C. Dolinoy

Sung Kyun Park

Rita Loch-Caruso

Vasantha Padmanabhan

Kelly M. Bakulski

Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies

胎盘和免疫细胞DNA甲基化参考面板用于流行病学研究中bulk组织细胞成分估计

Loneliness is a complex human trait that is highly polygenic and found to affect gene expression related to inflammatory and immunological functioning. To date, no epigenome-wide association studies of loneliness have tested whether differentially methylated sites are annotated to genes associated with inflammatory and immunological processes. Using 281 individual adult twins' DNA methylation data from the Louisville Twin Study, we performed an epigenome-wide analysis of loneliness to address this gap in the literature. In the discovery analysis, 169 twins were used to prioritize probes and test associations with DNA methylation age acceleration, and 56 independent monozygotic (MZ) twin pairs (112 individuals) were used in a within-family replication analysis. Among the 837,274 sites analyzed, no probe sites were statistically significant at the genome-wide level (p < 5.97 × 10−8), but 25 suggestive sites (p < 5 × 10−5) were annotated to genes related to various biological processes, including inflammatory response and protein-binding functions that extend prior findings. The nominal associations at these suggestive probe sites were highly correlated (r = .72) between the discovery sample and the MZ pair replication sample. Finally, loneliness significantly correlated with the DunedinPACE DNA methylation measure, suggesting that higher levels of loneliness were associated with accelerated epigenetic age as quantified by a measure that indexes longitudinal changes across multiple organ systems.

Christopher R. Beam

Ebrahim Zandi

Eric Turkheimer

Morgan Lynch

Alaina I. Gold

Thalida Em Arpawong

Sophie A. Bell

Alyssa C. Kam

Jonathan Becker

Deborah Winders Davis

Epigenome-wide association study of loneliness in a sample of U.S. middle-aged twins

美国中年双胞胎样本中孤独感的表观基因组关联研究

Male infertility has been a primary cause of global infertility, affecting 8–12% of couples worldwide. Previous studies have shown that semen quality decreases with advanced aging with an increased presence of inflammatory cells. In this study, we examined changes in the epigenome across a diverse cohort that includes both fertile and infertile men. We also compare the age-associated changes in semen to those observed in buccal swabs in order to characterize differences in epigenetic aging across diverse tissues. We found that variations in the semen methylome associated with aging are linked to inflammatory genes. Many age-associated sites are demethylated with advanced aging and are associated with the activation of inflammatory pathways. By contrast, we do not observe age-associated changes in inflammatory genes in buccal swab methylomes, which instead are characterized by changes to bivalent promoters. Our findings highlight the potential of epigenetic markers as indicators of male reproductive health.

Junxi Feng

Liudmilla Rubbi

Reza Kianian

Jesse Nelson Mills

Vadim Osadchiy

John Tucker Sigalos

Sriram Venkata Eleswarapu

Matteo Pellegrini

Epigenetic aging of semen is associated with inflammation

精液表观遗传衰老与炎症相关

Atherosclerosis is a chronic inflammatory disease characterized by fatty plaque deposits on artery walls. Elevated plasma homocysteine (Hcy) levels are an independent risk factor for atherosclerosis. Research on the mechanism by which Hcy promotes atherosclerosis has gradually turned to epigenetic inheritance, but the correlation between Hcy and m6A (N6-methyladenosine) modification has not been reported. In this study, MeRIP-seq was performed on macrophages and Hcy-treated macrophages. GO and KEGG analyses were used to perform functional analysis of differentially methylated genes. qRT-PCR and western blot were taken to determine the expression of CD209, CD163L1, proinflammatory, and anti-inflammatory factors. Flow cytometry was used to detect the proportion of M2 macrophages. The results showed that after Hcy treatment, the overall m6A methylation of macrophages was down-regulated, and 856 differential methylation peaks were annotated to 781 genes. These included CD209 and CD163L1, whose m6A methylation was inhibited after treatment with Hcy. In addition, mRNA and protein expressions of CD209 and CD163L1 were also inhibited after Hcy treatment. Overexpression of CD209 or CD163L1 prevents the Hcy-induced decrease in the proportion of M2 macrophages. This article identified changes in the modification level of m6A in macrophages by Hcy and revealed the possible mechanism by which Hcy induces macrophage polarization.

Yu Liang

Yongbo Wang

Jia Tan

Jingxuan Shu

Ya Xu

Mingyuan Wang

Shengjun Yang

Linna Ma

Homocysteine affects macrophage polarization by altering m6A methylation of scavenger receptors CD209 and CD163L1

同型半胱氨酸通过改变清道夫受体CD209和CD163L1的m6A甲基化影响巨噬细胞极化

Idiopathic pulmonary fibrosis (IPF) is a progressive and life-threatening respiratory disease characterized by worsening lung function due to excessive scarring. The objective of this study was to investigate the role of the long non-coding RNA ANRIL (antisense non-coding RNA in the INK4 locus) in the development of IPF. Our research revealed a significant increase in ANRIL expression in pulmonary fibrosis, consistent with prior studies indicating elevated ANRIL levels in fibrotic tissues. In vitro experiments demonstrated that elevated ANRIL expression promoted fibroblast activation, as evidenced by the upregulation of fibrosis-related markers. Mechanistically, we found that ANRIL interacts with let-7d-5p, a microRNA involved in gene regulation, acting as a sponge for let-7d-5p. Functional experiments confirmed a potential influence of let-7d-5p on fibroblast activation through direct interaction with ANRIL. Furthermore, our investigation identified TGFBR1 as a potential mediator of ANRIL's fibrogenic effects. Silence of TGFBR1 mitigated the fibrotic phenotype induced by ANRIL overexpression. Collectively, these results suggest that ANRIL promotes fibroblast activation and fibrosis development, possibly through the let-7d-5p/TGFBR1 axis, indicating that ANRIL could be a potential therapeutic target for pulmonary fibrosis.

Weidong Wu

Nanding Yu

Weiming Chen

Yong Zhu

ANRIL upregulates TGFBR1 to promote idiopathic pulmonary fibrosis in TGF-β1-treated lung fibroblasts via sequestering let-7d-5p

ANRIL 上调 TGFBR1 促进 TGF-β1 处理肺成纤维细胞中的特发性肺纤维化通过捕获 let-7d-5p

Abbreviation	Epigenetics.
Journal Impact	3.06
Quartiles(Global)	GENETICS & HEREDITY(Q2)

ISSN	1559-2294, 1559-2308
h-index	111

Publication Information	Publisher: Taylor and Francis Ltd.，Publishing cycle: Quarterly，Journal Type: journal，Open Access Journals: Yes
Basic data	Year of publication: 2006，Proportion of original research papers: 94.90%，Self Citation Rate:3.40%， Gold OA Rate: 64.21%
Journal Fees	$3300Details
Average review cycle	网友分享经验：一般,3-8周

Epigenetics

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Hypermethylation of the oxytocin receptor gene (OXTR) in obsessive-compulsive disorder: further evidence for a biomarker of disease and treatment response

Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E

Transcriptional regulation by the Set7 lysine methyltransferase

A comprehensive atlas of epigenetic regulators reveals tissue-specific epigenetic regulation patterns

Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies

Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies

Epigenome-wide association study of loneliness in a sample of U.S. middle-aged twins

Epigenetic aging of semen is associated with inflammation

Homocysteine affects macrophage polarization by altering m6A methylation of scavenger receptors CD209 and CD163L1

ANRIL upregulates TGFBR1 to promote idiopathic pulmonary fibrosis in TGF-β1-treated lung fibroblasts via sequestering let-7d-5p