BACKGROUND & AIMS: :Analysis of circulating nucleic acids in bodily fluids, referred to as "liquid biopsies", is rapidly gaining prominence. Studies have shown that cell-free DNA (cfDNA) has great potential in characterizing tumor status and heterogeneity, as well as the response to therapy and tumor recurrence. DNA methylation is an epigenetic modification that plays an important role in a broad range of biological processes and diseases. It is well known that aberrant DNA methylation is generalizable across various samples and occurs early during the pathogenesis of cancer. Methylation patterns of cfDNA are also consistent with their originated cells or tissues. Systemic analysis of cfDNA methylation profiles has emerged as a promising approach for cancer detection and origin determination. In this review, we will summarize the technologies for DNA methylation analysis and discuss their feasibility for liquid biopsy applications. We will also provide a brief overview of the bioinformatic approaches for analysis of DNA methylation sequencing data. Overall, this review provides informative guidance for the selection of experimental and computational methods in cfDNA methylation-based studies.

背景与目标： : 体液中循环核酸的分析，被称为 “液体活检”，正在迅速得到重视。研究表明，无细胞DNA (cfDNA) 在表征肿瘤状态和异质性以及对治疗和肿瘤复发的反应方面具有巨大潜力。DNA甲基化是一种表观遗传修饰，在广泛的生物学过程和疾病中起着重要作用。众所周知，异常的DNA甲基化可在各种样品中推广，并且在癌症发病机理的早期发生。cfDNA的甲基化模式也与其起源的细胞或组织一致。cfDNA甲基化谱的系统分析已成为癌症检测和起源确定的有前途的方法。在这篇综述中，我们将总结用于DNA甲基化分析的技术，并讨论其在液体活检应用中的可行性。我们还将简要概述用于分析DNA甲基化测序数据的生物信息学方法。总体而言，这篇综述为基于cfDNA甲基化的研究中实验和计算方法的选择提供了有益的指导。

BACKGROUND & AIMS: :Triple-negative breast cancer (TNBC) has poor clinical prognosis. Lack of TNBC-specific biomarkers prevents active clinical intervention. We reasoned that TNBC must have its specific signature due to the lack of three key receptors to distinguish TNBC from other types of breast cancer. We also reasoned that coupling methylation and gene expression as a single unit may increase the specificity for the detected TNBC signatures. We further reasoned that choosing the proper controls may be critical to increasing the sensitivity to identify TNBC-specific signatures. Furthermore, we also considered that specific drugs could target the detected TNBC-specific signatures. We developed a system to identify potential TNBC signatures. It consisted of (1) coupling methylation and expression changes in TNBC to identify the methylation-regulated signature genes for TNBC; (2) using TPBC (triple-positive breast cancer) as the control to detect TNBC-specific signature genes; (3) searching in the drug database to identify those targeting TNBC signature genes. Using this system, we identified 114 genes with both altered methylation and expression, and 356 existing drugs targeting 10 of the 114 genes. Through docking and molecular dynamics simulation, we determined the structural basis between sapropterin, a drug used in the treatment of tetrahydrobiopterin deficiency, and PTGS2, a TNBC signature gene involved in the conversion of arachidonic acid to prostaglandins. Our study reveals the existence of rich TNBC-specific signatures, and many can be drug target and biomarker candidates for clinical applications.

背景与目标： : 三阴性乳腺癌 (TNBC) 临床预后较差。TNBC特异性生物标志物的缺乏阻碍了积极的临床干预。我们认为，由于缺乏三种关键受体来区分TNBC与其他类型的乳腺癌，TNBC必须具有其特定的特征。我们还认为，将甲基化和基因表达作为单个单元偶联可能会增加检测到的TNBC签名的特异性。我们进一步认为，选择适当的控件对于提高识别TNBC特定签名的敏感性可能至关重要。此外，我们还认为特定药物可以针对检测到的TNBC特异性特征。我们开发了一个识别潜在TNBC签名的系统。它由 (1) 结合甲基化和TNBC中的表达变化来鉴定TNBC的甲基化调节签名基因; (2) 以TPBC (三阳性乳腺癌) 为对照来检测TNBC特异性签名基因; (3) 在药物数据库中搜索以识别那些靶向TNBC签名基因。使用该系统，我们鉴定了114个具有改变的甲基化和表达的基因，并356了靶向10个114基因的现有药物。通过对接和分子动力学模拟，我们确定了用于治疗四氢生物蝶呤缺乏症的药物沙丙蝶呤与参与花生四烯酸向前列腺素转化的TNBC签名基因PTGS2之间的结构基础。我们的研究揭示了存在丰富的TNBC特异性签名，并且许多可能是临床应用的药物靶标和生物标志物候选者。

BACKGROUND & AIMS: :Bullying among children is ubiquitous and associated with pervasive mental health problems. However, little is known about the biological pathways that change after exposure to bullying. Epigenome-wide changes in DNA methylation in peripheral blood were studied from pre- to post measurement of bullying exposure, in a longitudinal study of the population-based Generation R Study and Avon Longitudinal Study of Parents and Children (combined n = 1,352). Linear mixed-model results were meta-analysed to estimate how DNA methylation changed as a function of exposure to bullying. Sensitivity analyses including co-occurring child characteristics and risks were performed, as well as a Gene Ontology analysis. A candidate follow-up was employed for CpG (cytosine-phosphate-guanine) sites annotated to 5-HTT and NR3C1. One site, cg17312179, showed small changes in DNA methylation associated to bullying exposure (b = -2.67e-03, SE = 4.97e-04, p = 7.17e-08). This site is annotated to RAB14, an oncogene related to Golgi apparatus functioning, and its methylation levels decreased for exposed but increased for non-exposed. This result was consistent across sensitivity analyses. Enriched Gene Ontology pathways for differentially methylated sites included cardiac function and neurodevelopmental processes. Top CpG sites tended to have overall low levels of DNA methylation, decreasing in exposed, increasing in non-exposed individuals. There were no gene-wide corrected findings for 5-HTT and NR3C1. This is the first study to identify changes in DNA methylation associated with bullying exposure at the epigenome-wide significance level. Consistent with other population-based studies, we do not find evidence for strong associations between bullying exposure and DNA methylation.

背景与目标： : 儿童欺凌无处不在，并与普遍存在的精神卫生问题相关。然而，人们对暴露于欺凌之后发生变化的生物途径知之甚少。在基于人群的R世代研究和父母和儿童的Avon纵向研究的纵向研究中，从欺凌暴露的测量前后研究了外周血中DNA甲基化的表观基因组范围变化 (合并n = 1,352)。对线性混合模型结果进行了荟萃分析，以估计DNA甲基化如何随暴露于欺凌行为而变化。进行了敏感性分析，包括共同发生的儿童特征和风险，以及基因本体论分析。对5-HTT和NR3C1注释的CpG (胞嘧啶-磷酸-鸟嘌呤) 位点进行了候选随访。一个位点cg17312179显示出与欺凌暴露相关的DNA甲基化的微小变化 (b = -2.67e-03，SE = 4.97e-04，p = 7.17e-08)。该位点与RAB14注释，RAB14是一种与高尔基体功能有关的癌基因，其甲基化水平在暴露时降低，而在未暴露时升高。该结果在敏感性分析中是一致的。差异甲基化位点的丰富基因本体论途径包括心脏功能和神经发育过程。顶级CpG位点的DNA甲基化水平总体较低，暴露时降低，未暴露个体中增加。5-HTT和NR3C1没有全基因校正的发现。这是第一项在表观基因组范围的显着性水平上确定与欺凌暴露相关的DNA甲基化变化的研究。与其他基于人群的研究一致，我们没有发现欺凌暴露与DNA甲基化之间强烈关联的证据。

BACKGROUND & AIMS: :The DNA damage response is mediated by both DNA repair proteins and epigenetic markers. Here, we observe that N6-methyladenosine (m6A), a mark of the epitranscriptome, was common in RNAs accumulated at UV-damaged chromatin; however, inhibitors of RNA polymerases I and II did not affect the m6A RNA level at the irradiated genomic regions. After genome injury, m6A RNAs either diffused to the damaged chromatin or appeared at the lesions enzymatically. DNA damage did not change the levels of METTL3 and METTL14 methyltransferases. In a subset of irradiated cells, only the METTL16 enzyme, responsible for m6A in non-coding RNAs as well as for splicing regulation, was recruited to microirradiated sites. Importantly, the levels of the studied splicing factors were not changed by UVA light. Overall, if the appearance of m6A RNAs at DNA lesions is regulated enzymatically, this process must be mediated via the coregulatory function of METTL-like enzymes. This event is additionally accompanied by radiation-induced depletion of 2,2,7-methylguanosine (m3G/TMG) in RNA. Moreover, UV-irradiation also decreases the global cellular level of N1-methyladenosine (m1A) in RNAs. Based on these results, we prefer a model in which m6A RNAs rapidly respond to radiation-induced stress and diffuse to the damaged sites. The level of both (m1A) RNAs and m3G/TMG in RNAs is reduced as a consequence of DNA damage, recognized by the nucleotide excision repair mechanism.

背景与目标： : DNA损伤反应是由DNA修复蛋白和表观遗传标记介导的。在这里，我们观察到N6-methyladenosine (m6A) 是表位组的标志，在紫外线受损的染色质处积累的RNA中很常见; 然而，RNA聚合酶I和II的抑制剂不影响辐照基因组区域的m6A RNA水平。基因组损伤后，m6A rna扩散到受损的染色质中或以酶促的方式出现在病变处。DNA损伤不会改变METTL3和METTL14甲基转移酶的水平。在受照射的细胞的子集中，只有负责非编码rna中的m6A以及剪接调节的METTL16酶被募集到微照射位点。重要的是，所研究的拼接因子的水平不会因UVA光而改变。总体而言，如果通过酶调节DNA损伤处m6A rna的出现，则该过程必须通过METTL样酶的共调节功能来介导。该事件还伴随着辐射诱导的RNA中2,2，7-甲基鸟苷 (m3G/TMG) 的耗尽。此外，紫外线照射还降低了rna中N1-methyladenosine (m1A) 的整体细胞水平。基于这些结果，我们更喜欢m6A rna快速响应辐射诱导的压力并扩散到受损部位的模型。由于DNA损伤，rna中 (m1A) rna和m3G/TMG的水平均降低，这被核苷酸切除修复机制所识别。

BACKGROUND & AIMS: -2

背景与目标： -2

BACKGROUND & AIMS: :Krüppel-like factor 4 (KLF4) has a tumor suppressor role in the progression of gastric cancer (GC), and inhibition or loss of KLF4 expression was identified in GC. The aim of this study was to explore the new molecular mechanism of KLF4 inactivation in gastric cancer. Herein, we report that Helicobacter pylori infection or Cag pathogenicity island protein A (CagA) gene transduction resulted in KLF4 expression downregulation and promoted gastric epithelial cell and gastric cancel cell proliferation, migration, and colony formation. Mechanistically, we found that CagA gene transduction led to DNA methylation of the KLF4 promoter, an effect that was relevant to the significant downregulation of TET1 expression. Causally, knockdown of TET1 expression decreased KLF4 expression, whereas overexpression of TET1 had the opposite effect. Clinically, we found that KLF4 expression and the 5-hmC levels were lower in GC cells with H pylori infection than in GC cells without H pylori infection. Thus, our study not only sheds new light on how H pylori infection promotes the progression of GC but also elucidates a novel mechanism of KLF4 inactivation in GC pathogenesis. During pathogenesis, an alteration in the H pylori/CagA-TET1-KLF4 signaling pathway plays a critical role, suggesting that this pathway may be a prospective target for gastric carcinoma intervention and therapy.

背景与目标： : kr ü ppel样因子4 (KLF4) 在胃癌 (GC) 的进展中具有抑癌作用，并且在GC中鉴定出KLF4表达的抑制或丧失。本研究旨在探讨KLF4在胃癌中失活的分子机制。本文报道幽门螺杆菌感染或Cag致病性岛蛋白A (CagA) 基因转导导致KLF4表达下调，促进胃上皮细胞和胃取消细胞增殖、迁移和集落形成。从机制上讲，我们发现CagA基因转导导致KLF4启动子的DNA甲基化，这与TET1表达的显着下调有关。原因是，敲除TET1表达会降低KLF4表达，而TET1的过表达则具有相反的作用。临床上，我们发现幽门螺杆菌感染的GC细胞中KLF4表达和5-hmC水平低于不幽门螺杆菌感染的GC细胞。因此，我们的研究不仅为幽门螺杆菌感染如何促进GC的进展提供了新的思路，而且还阐明了GC发病机理中KLF4失活的新机制。在发病过程中，幽门螺杆菌/CagA-TET1-KLF4信号通路的改变起着至关重要的作用，表明该通路可能是胃癌干预和治疗的前瞻性靶标。

BACKGROUND & AIMS: :DNA methylation is an ancient process found in all domains of life. Although the enzymes that mediate methylation have remained highly conserved, DNA methylation has been adapted for a variety of uses throughout evolution, including defense against transposable elements and control of gene expression. Defects in DNA methylation are linked to human diseases, including cancer. Methylation has been lost several times in the course of animal and fungal evolution, thus limiting the opportunity for study in common model organisms. In the past decade, plants have emerged as a premier model system for genetic dissection of DNA methylation. A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more.

背景与目标： : DNA甲基化是一个古老的过程，存在于生命的所有领域。尽管介导甲基化的酶保持高度保守，但DNA甲基化已适用于整个进化过程中的多种用途，包括防御转座因子和控制基因表达。DNA甲基化缺陷与人类疾病有关，包括癌症。在动物和真菌进化过程中，甲基化已多次丢失，从而限制了在常见模式生物中进行研究的机会。在过去的十年中，植物已成为DNA甲基化基因解剖的主要模型系统。最近将植物遗传学与强大的基因组方法相结合，导致了许多令人兴奋的发现，并有望实现更多。

BACKGROUND & AIMS: BACKGROUND:Coeliac disease (CD) is a autoimmune disease characterised by mucosal inflammation in the small intestine in response to dietary gluten. Genetic factors play a key role with CD individuals carrying either the HLA-DQ2 or HLA-DQ8 haplotype, however these haplotypes are present in half the general population making them necessary but insufficient to cause CD. Epigenetic modifications, including DNA methylation that can change in response to environmental exposure could help to explain how interactions between genes and environmental factors combine to trigger disease development. Identifying changes in DNA methylation profiles in individuals with CD could help discover novel genomic regions involved in the onset and development of CD. METHODS:The Illumina InfiniumMethylation450 Beadchip array (HM450) was used to compare DNA methylation profiles in saliva, in CD and non-CD affected individuals. CD individuals who had been diagnosed at least 2 years previously; were on a GFD; and who were currently asymptomatic; were compared to age and sex-matched non-CD affected healthy controls. Bisulphite pyrosequencing was used to validate regions found to be differentially methylated. These regions were also validated in a second larger cohort of CD and non-CD affected individuals. RESULTS:Methylation differences within the HLA region at HLA-DQB1 were identified on HM450 but could not be confirmed with pyrosequencing. Significant methylation differences near the SLC17A3 gene were confirmed on pyrosequencing in the initial pilot cohort. Interestingly pyrosequencing sequencing of these same sites within a second cohort of CD and non-CD affected controls produced significant methylation differences in the opposite direction. CONCLUSION:Altered DNA methylation profiles appear to be present in saliva in CD individuals. Further work to confirm whether these differences are truly associated with CD is needed.

背景与目标：

BACKGROUND & AIMS: :Major depressive disorder (MDD) is the leading cause of disability worldwide and is associated with high rates of suicide and medical comorbidities. Current antidepressant medications are suboptimal, as most MDD patients fail to achieve complete remission from symptoms. At present, clinicians are unable to predict which antidepressant is most effective for a particular patient, exposing patients to multiple medication trials and side effects. Since MDD's etiology includes interactions between genes and environment, the epigenome is of interest for predictive utility and treatment monitoring. Epigenetic mechanisms of antidepressant medications are incompletely understood. Differences in epigenetic profiles may impact treatment response. A systematic literature search yielded 24 studies reporting the interaction between antidepressants and eight genes (BDNF, MAOA, SLC6A2, SLC6A4, HTR1A, HTR1B, IL6, IL11) and whole genome methylation. Methylation of certain sites within BDNF, SLC6A4, HTR1A, HTR1B, IL11, and the whole genome was predictive of antidepressant response. Comparing DNA methylation in patients during depressive episodes, during treatment, in remission, and after antidepressant cessation would help clarify the influence of antidepressant medications on DNA methylation. Individuals' unique methylation profiles may be used clinically for personalization of antidepressant choice in the future.

背景与目标： : 重度抑郁症 (MDD) 是全球残疾的主要原因，与自杀和医疗合并症的高发生率有关。当前的抗抑郁药物是次优的，因为大多数MDD患者无法完全缓解症状。目前，临床医生无法预测哪种抗抑郁药对特定患者最有效，使患者暴露于多种药物试验和副作用。由于MDD的病因包括基因与环境之间的相互作用，因此表观基因组对于预测效用和治疗监测很有意义。抗抑郁药物的表观遗传机制尚不完全清楚。表观遗传谱的差异可能会影响治疗反应。系统的文献搜索产生了24项研究，报告了抗抑郁药与八个基因 (BDNF，MAOA，SLC6A2，SLC6A4，HTR1A，HTR1B，IL6，IL11) 和全基因组甲基化之间的相互作用。BDNF，SLC6A4，HTR1A，HTR1B，IL11和全基因组中某些位点的甲基化可预测抗抑郁反应。在抑郁发作期间，治疗期间，缓解期间以及抗抑郁药停止后比较患者的DNA甲基化将有助于阐明抗抑郁药物对DNA甲基化的影响。个人独特的甲基化谱可以在临床上用于抗抑郁药的个性化选择。

BACKGROUND & AIMS: :The aim of the current study was to investigate the role of BRCA1 gene aberrations in sporadic triple-negative breast cancer (TNBC) and its impact on anthracycline-based therapy. BRCA1 promoter methylation was analyzed in 70 TNBC and compared with the clinical and pathologic characteristics. As a control group, we used 70 patients with non-TNBC. BRCA1 promoter methylation was observed in 65.2 % of patients and was similar in both groups. BRCA1 promoter methylation was associated with decreased intensity of BRCA1 protein expression (P = 0.002) and significant increase of median disease-free survival (DFS) of TNBC patients receiving adjuvant anthracycline-based chemotherapy (P = 0.001). Multivariate analysis revealed that BRCA1 promoter methylation remains a favorable factor in regard to DFS (HR 0.224; 95 % CI 0.092-0.546, P = 0.001) in TNBC after adjustment for other prognostic factors. In contrast, in non-TNBC, BRCA1 promoter methylation was not associated with any clinical and pathologic parameters. BRCA1 promoter methylation is a common mechanism of BRCA1 gene aberration in sporadic breast cancer and is predictive for better response to anthracycline-based therapies.

背景与目标： : 本研究的目的是研究BRCA1基因畸变在散发性三阴性乳腺癌 (TNBC) 中的作用及其对蒽环类药物治疗的影响。在70个TNBC中分析了BRCA1启动子甲基化，并与临床和病理特征进行了比较。作为对照组，我们使用了70例非TNBC患者。在65.2% 患者中观察到BRCA1启动子甲基化，两组相似。BRCA1启动子甲基化与接受基于蒽环类药物的辅助化疗的TNBC患者BRCA1蛋白表达强度降低 (P = 0.002) 和中位无病生存期 (DFS) 显著增加 (P = 0.001) 相关。多变量分析显示，在调整其他预后因素后，BRCA1启动子甲基化仍然是TNBC中DFS (HR 0.224; 95% CI 0.092-0.546，P = 0.001) 的有利因素。相反，在非TNBC中，BRCA1启动子甲基化与任何临床和病理参数无关。BRCA1启动子甲基化是散发性乳腺癌中BRCA1基因畸变的常见机制，并且可以预测对基于蒽环类药物的治疗有更好的反应。

BACKGROUND & AIMS: :Arginine methylation is a common posttranslational modification that modulates protein function. SCY1-like pseudokinase 1 (SCYL1) is crucial for neuronal functions and interacts with γ2-COP to form coat protein complex I (COPI) vesicles that regulate Golgi morphology. However, the molecular mechanism by which SCYL1 is regulated remains unclear. Here, we report that the γ2-COP-binding site of SCYL1 is arginine-methylated by protein arginine methyltransferase 1 (PRMT1) and that SCYL1 arginine methylation is important for the interaction of SCYL1 with γ2-COP. PRMT1 was colocalized with SCYL1 in the Golgi fraction. Inhibition of PRMT1 suppressed axon outgrowth and dendrite complexity via abnormal Golgi morphology. Knockdown of SCYL1 by small interfering RNA (siRNA) inhibited axon outgrowth, and the inhibitory effect was rescued by siRNA-resistant SCYL1, but not SCYL1 mutant, in which the arginine methylation site was replaced. Thus, PRMT1 regulates Golgi morphogenesis via SCYL1 arginine methylation. We propose that SCYL1 arginine methylation by PRMT1 contributes to axon and dendrite morphogenesis in neurons.

背景与目标： : 精氨酸甲基化是一种常见的翻译后修饰，调节蛋白质功能。SCY1-like假激酶1 (SCYL1) 对于神经元功能至关重要，并与 γ2-COP相互作用以形成调节高尔基体形态的外壳蛋白复合物I (coci) 囊泡。然而，调节SCYL1的分子机制仍不清楚。在这里，我们报告了SCYL1的 γ2-COP结合位点被蛋白精氨酸甲基转移酶1 (PRMT1) 甲基化，并且SCYL1精氨酸甲基化对于SCYL1与 γ2-COP的相互作用很重要。PRMT1与高尔基体中的SCYL1共定位。抑制PRMT1通过异常的高尔基体形态抑制了轴突生长和树突复杂性。小干扰RNA (siRNA) 敲除SCYL1可抑制轴突的生长，并且抑制作用被抗siRNA的SCYL1所挽救，但不能被SCYL1突变体所挽救，其中精氨酸甲基化位点被取代。因此，PRMT1通过SCYL1精氨酸甲基化调节高尔基形态发生。我们建议PRMT1的scyl精氨酸甲基化有助于神经元的轴突和树突形态发生。

BACKGROUND & AIMS: :Aberrant CpG methylation of tumor suppressor gene regulatory elements is associated with transcriptional silencing and contributes to malignant transformation of different tissues. It is presumed that methylated DNA sequences recruit repressor machinery to actively shutdown gene expression. The Kaiso protein is a transcriptional repressor expressed in human and murine colorectal tumors that can bind to methylated clusters of CpG dinucleotides. We show here that Kaiso represses methylated tumor suppressor genes and can bind in a methylation-dependent manner to the CDKN2A in human colon cancer cell lines. The contribution of Kaiso to epigenetic silencing was underlined by the fact that Kaiso depletion induced tumor suppressor gene expression without affecting DNA methylation levels. As a consequence, colon cancer cells became susceptible to cell cycle arrest and cell death mediated by chemotherapy. The data suggest that Kaiso is a methylation-dependent "opportunistic" oncogene that silences tumor suppressor genes when they become hypermethylated. Because Kaiso inactivation sensitized colon cancer cell lines to chemotherapy, it is possible that therapeutic targeting of Kaiso could improve the efficacy of current treatment regimens.

背景与目标： : 抑癌基因调控元件的异常CpG甲基化与转录沉默有关，并有助于不同组织的恶性转化。推测甲基化的DNA序列会招募阻遏机制以主动关闭基因表达。Kaiso蛋白是在人和鼠结直肠肿瘤中表达的转录阻遏物，可以与CpG二核苷酸的甲基化簇结合。我们在这里显示Kaiso抑制甲基化的肿瘤抑制基因，并且可以以甲基化依赖性方式与人结肠癌细胞系中的CDKN2A结合。Kaiso耗竭诱导肿瘤抑制基因表达而不影响DNA甲基化水平这一事实强调了Kaiso对表观遗传沉默的贡献。结果，结肠癌细胞变得容易受到化学疗法介导的细胞周期停滞和细胞死亡的影响。数据表明，Kaiso是一种甲基化依赖性的 “机会性” 癌基因，当肿瘤抑制基因被高甲基化时，它们会沉默。由于Kaiso灭活使结肠癌细胞系对化疗敏感，因此Kaiso的靶向治疗可能会提高当前治疗方案的疗效。

BACKGROUND & AIMS: :Epilepsy is a frequent neurological disorder, although onset and progression of seizures remain difficult to predict in affected patients, irrespective of their epileptogenic condition. Previous studies in animal models as well as human epileptic brain tissue revealed a remarkably diverse pattern of gene expression implicating epigenetic changes to contribute to disease progression. Here we mapped for the first time global DNA methylation patterns in chronic epileptic rats and controls. Using methyl-CpG capture associated with massive parallel sequencing (Methyl-Seq) we report the genomic methylation signature of the chronic epileptic state. We observed a predominant increase, rather than loss of DNA methylation in chronic rat epilepsy. Aberrant methylation patterns were inversely correlated with gene expression changes using mRNA sequencing from same animals and tissue specimens. Administration of a ketogenic, high-fat, low-carbohydrate diet attenuated seizure progression and ameliorated DNA methylation mediated changes in gene expression. This is the first report of unsupervised clustering of an epigenetic mark being used in epilepsy research to separate epileptic from non-epileptic animals as well as from animals receiving anti-convulsive dietary treatment. We further discuss the potential impact of epigenetic changes as a pathogenic mechanism of epileptogenesis.

背景与目标： : 癫痫是一种常见的神经系统疾病，尽管无论发病情况如何，癫痫发作的发作和进展仍难以预测。先前在动物模型以及人类癫痫脑组织中的研究揭示了一种非常不同的基因表达模式，这些基因表达涉及表观遗传变化，从而导致疾病进展。在这里，我们首次绘制了慢性癫痫大鼠和对照组的全球DNA甲基化模式。使用与大规模平行测序 (methyl-Seq) 相关的甲基-CpG捕获，我们报告了慢性癫痫状态的基因组甲基化特征。我们观察到慢性大鼠癫痫的主要增加，而不是DNA甲基化的丧失。使用来自相同动物和组织标本的mRNA测序，异常甲基化模式与基因表达变化呈负相关。给予生酮，高脂，低碳水化合物饮食可减轻癫痫发作的进展，并改善DNA甲基化介导的基因表达变化。这是在癫痫研究中使用无监督的表观遗传标记聚类的第一份报告，该遗传标记用于将癫痫与非癫痫动物以及接受抗惊厥饮食治疗的动物分开。我们进一步讨论了表观遗传变化作为癫痫发生的致病机制的潜在影响。

BACKGROUND & AIMS: :In rodents, the display of reproductive behavior occurs during the proestrus-estrus transition of the estrus cycle. This behavior is regulated by estradiol and progesterone mainly via their intracellular receptors. Two isoforms of the progesterone receptor have been described (A and B), and they have different promoters for their regulation. It has been demonstrated that the mRNA for both isoforms changes during the proestrus-estrus transition. It has been recently established that DNA methylation can be transient and cyclical in gene promoters, however, these changes have only been reported in vitro but not in physiological models. The aim of this study was to analyze the pattern of DNA methylation in the PR (A and B) promoter regions during the proestrus-estrus transition in the rat hypothalamus and its correlation with the regulation of mRNA expression. The results demonstrated a differential mRNA expression of the progesterone receptor (A and B) isoforms. The expression of total PR did not change significantly during the proestrus day, while the expression of isoform B increased significantly at 17:00 h, followed by a significant decrease at 21:00 h of the proestrus day. Interestingly, we also found that the isoform A promoter was mainly unmethylated at all studied time points. In contrast, the isoform B promoter showed a transient methylation increase during the evening of proestrus. The overall results indicate that there is a switch of progesterone receptor isoforms expression during the evening of proestrus that is related to the differential gene methylation patterns of their promoter regions, mainly for the isoform B promoter.

背景与目标： : 在啮齿动物中，生殖行为的显示发生在发情周期的发情-发情过渡期间。雌二醇和孕酮主要通过其细胞内受体来调节这种行为。已经描述了孕激素受体的两种同工型 (A和B)，它们具有不同的启动子来调节它们。已经证明，两种同工型的mRNA在发情-发情过渡期间都会发生变化。最近已经确定，基因启动子中的DNA甲基化可以是短暂的和周期性的，但是，这些变化仅在体外报道，而在生理模型中没有报道。这项研究的目的是分析大鼠下丘脑发情-发情过渡期间PR (A和B) 启动子区域中DNA甲基化的模式及其与mRNA表达调控的相关性。结果表明孕激素受体 (a和B) 亚型的mRNA表达差异。总PR的表达在发情日没有显着变化，而同工型B的表达在发情日的17:00 h显着增加，随后在发情日的21:00 h显着降低。有趣的是，我们还发现同种型A启动子在所有研究的时间点主要未甲基化。相反，同工型B启动子在发情期晚上显示出短暂的甲基化增加。总体结果表明，在发情期晚上，孕激素受体同工型表达存在切换，这与其启动子区域的差异基因甲基化模式有关，主要是同工型B启动子。

BACKGROUND & AIMS: :Epigenome editing is a promising technology, potentially allowing the stable reprogramming of gene expression profiles without alteration of the DNA sequence. Targeted DNA methylation has been successfully documented by many groups for silencing selected genes, but recent publications have raised concerns regarding its specificity. In the current work, we developed new EpiEditors for programmable DNA methylation in cells with a high efficiency and improved specificity. First, we demonstrated that the catalytically deactivated Cas9 protein (dCas9)-SunTag scaffold, which has been used earlier for signal amplification, can be combined with the DNMT3A-DNMT3L single-chain effector domain, allowing for a strong methylation at the target genomic locus. We demonstrated that off-target activity of this system is mainly due to untargeted freely diffusing DNMT3A-DNMT3L subunits. Therefore, we generated several DNMT3A-DNMT3L variants containing mutations in the DNMT3A part, which reduced their endogenous DNA binding. We analyzed the genome-wide DNA methylation of selected variants and confirmed a striking reduction of untargeted methylation, most pronounced for the R887E mutant. For all potential applications of targeted DNA methylation, the efficiency and specificity of the treatment are the key factors. By developing highly active targeted methylation systems with strongly improved specificity, our work contributes to future applications of this approach.

背景与目标： : 表观基因组编辑是一项有前途的技术，可能允许基因表达谱的稳定重编程而不改变DNA序列。靶向DNA甲基化已被许多小组成功地记录为沉默选定的基因，但最近的出版物引起了人们对其特异性的关注。在当前的工作中，我们开发了用于细胞中可编程DNA甲基化的新型EpiEditors，具有高效率和改进的特异性。首先，我们证明了较早用于信号扩增的催化失活Cas9蛋白 (dCas9)-SunTag支架可以与DNMT3A-DNMT3L的单链效应结构域结合，从而在靶基因组基因座处实现强甲基化。我们证明了该系统的脱靶活动主要是由于未靶向的自由扩散DNMT3A-DNMT3L亚基。因此，我们在DNMT3A部分产生了几个包含突变的DNMT3A-DNMT3L变体，这降低了它们的内源性DNA结合。我们分析了所选变体的全基因组DNA甲基化，并证实了未靶向甲基化的显着降低，对于R887E突变体最为明显。对于靶向DNA甲基化的所有潜在应用，治疗的效率和特异性是关键因素。通过开发具有高度改善的特异性的高活性靶向甲基化系统，我们的工作为该方法的未来应用做出了贡献。