Genome-wide profiling of histone H3 lysine 27 trimethylation and its modification in response to chilling stress in grapevine leaves

Histone H3 lysine 27 trimethylation(H3K27me3) is a histone modification associated with transcriptional repression. However, insights into the genome-wide pattern of H3K27me3 in grapevines are limited. Here, anti-H3K27 chromatin immunoprecipitation(ChIP), high-throughput sequencing, and transcriptome analysis were performed using leaves of Vitis amurensis. The leaves were treated at 4°C for 2 h and 24 h and used to investigate changes in H3K27me3 under chilling treatment. The results show that H3K27me3 is well-distributed both in gene regions(-50%) and in the intergenic region(-50%) in the grapevine genome(Vitis vinifera ‘Pinot Noir PN40024'). H3K27me3 was found to be localized in8 368 annotated gene regions in all detected samples(leaves at normal temperature and under chilling treatments) and mainly enriched in gene bodies with the adjacent promoter and downstream areas. The short-term chilling treatments(4°C for 2 h) induced 2 793 gains and 305losses in H3K27me3 modification. Subsequently, 97.3% of the alterations were restored to original levels after 24 h treatment. The ChIP-qPCR for five differential peaks showed similar results to the data for ChIP-seq, indicating that the chilling-induced H3K27me3 modification is reliable.Integrative analysis of transcriptome and ChIP-seq results showed that the expression of H3K27me3 target genes was significantly lower than those of non-target genes, indicating transcriptional repression of H3K27me3 in grapevine leaves. Furthermore, histone methylation alterations were detected in 82 genes and were related to either repression or activation of their expression during chilling stress. The findings provide the genome-wide H3K27me3 patterns in grapevines and shed light on uncovering its regulation in chilling stress responses.

Unraveling the relationship between histone methylation and nonalcoholic fatty liver disease

Non-alcoholic fatty liver disease(NAFLD)poses a significant health challenge in modern societies due to shifts in lifestyle and dietary habits.Its complexity stems from genetic predisposition,environmental influences,and metabolic factors.Epigenetic processes govern various cellular functions such as transcription,chromatin structure,and cell division.In NAFLD,these epigenetic tendencies,especially the process of histone methylation,are intricately intertwined with fat accumulation in the liver.Histone methylation is regulated by different enzymes like methyltransferases and demethylases and influences the expression of genes related to adipogenesis.While early-stage NAFLD is reversible,its progression to severe stages becomes almost irreversible.Therefore,early detection and intervention in NAFLD are crucial,and understanding the precise role of histone methylation in the early stages of NAFLD could be vital in halting or potentially reversing the progression of this disease.

“Identification Card”: Sites on Histone Modification of Cancer Cell

Formation of malignant tumor originating from normal healthy cell is a multistep process including genetic and epigenetic lesions. Previous studies of cell line model systems displayed that early important epigenetic events happened in stepwise fashion prior to cell immortalization. Once these epigenetic alterations are integrated into chromatin, they will perform vertical propagation through cell subculture. Hence, status of epigenetics is dramatically important in maintaining of cell identity. Histone modification is another factor of epigenetic alterations during human oncogenesis. Histones, one of main components of chromatin, can be modified post-translationally. Histone tail modifications are regulated by corresponding modification enzymes. This review focuses on the description of relationship between the main sites of histone modification and oncogenesis.

Histone modifications and alcohol-induced liver disease:Are altered nutrients the missing link?

Alcoholism is a major health problem in the United States and worldwide,and alcohol remains the single most significant cause of liver-related diseases and deaths.Alcohol is known to influence nutritional status at many levels including nutrient intake,absorption,utilization,and excretion,and can lead to many nutritional disturbances and deficiencies.Nutrients can dramatically affect gene expression and alcohol-induced nutrient imbalance may be a major contributor to pathogenic gene expression in alcohol-induced liver disease(ALD).There is growing interest regarding epigenetic changes,including histone modifications that regulate gene expression during disease pathogenesis.Notably,modifications of core histones in the nucleosome regulate chromatin structure and DNA methylation,and control gene transcription.This review highlights the role of nutrient disturbances brought about during alcohol metabolism and their impact on epigenetic histone modifications that may contribute to ALD.The review is focused on four critical metabolites,namely,acetate,S-adenosylmethionine,nicotinamide adenine dinucleotide and zinc that are particularly relevant to alcohol metabolism and ALD.

Application of histone modification in the risk prediction of the biochemical recurrence after radical prostatectomy

The role of histone modifications in the development and progression of cancer remains unclear. Here,we gave an investigation of the relationship between the various histone modifications and the risk prediction of the biochemical recurrence after radical prostatectomy （RP）. Histone 3 lysine 4 dimethylation （H3K4diMe）,trimethylation （H3K4triMe）,lysine 36 trimethylation （H3K36triMe）,histone 4 lysine 20 trimethylation （H4K20triMe）and acetylation of histome 3 lysine 9 （H3K9Ac） were evaluated using immnuohistochemistry coupled with the tissue microarray technique in 169 primary prostatectomy tissue samples. Recursive partitioning analysis （RPA） was used to analyze the data. Through global histone modification analysis in patients who underwent radical prostatectomy,we found that H3K4triMe can predict the risk of the biochemical recurrence for the low grade prostate cancer （Gleason score≤6） after RP. In the case of high grade prostate cancer （Gleason score≥7）,H4K20triMe and H3K9Ac accompanying with the pre-operation prostate-specific antigen （PSA） level could also predict the risk of the biochemical recurrence after RP. In combination with the Gieason score and pre-operation PSA level,the acetylation and methylation of histones H3 and H4 can predict the biochemical recurrence of the prostate cancer following RP.

Bivalent histone modifications during tooth development

Histone methylation is one of the most widely studied post-transcriptional modifications. It is thought to be an important epigenetic event that is closely associated with cell fate determination and differentiation. To explore the spatiotemporal expression of histone H3 lysine 4trimethylation（H3K4me3） and histone H3 lysine 27 trimethylation（H3K27me3） epigenetic marks and methylation or demethylation transferases in tooth organ development, we measured the expression of SET7, EZH2, KDM5 B and JMJD3 via immunohistochemistry and quantitative polymerase chain reaction（qP CR） analysis in the first molar of BALB/c mice embryos at E13.5, E15.5, E17.5, P0 and P3, respectively. We also measured the expression of H3K4me3 and H3K27me3 with immunofluorescence staining. During murine tooth germ development, methylation or demethylation transferases were expressed in a spatial–temporal manner. The bivalent modification characterized by H3K4me3 and H3K27me3 can be found during the tooth germ development, as shown by immunofluorescence. The expression of SET7, EZH2 as methylation transferases and KDM5 B and JMJD3 as demethylation transferases indicated accordingly with the expression of H3K4me3 and H3K27me3 respectively to some extent. The bivalent histone may play a critical role in tooth organ development via the regulation of cell differentiation.

Role of the histone methyltransferases Ezh2 and Suv4-20h1/Suv4-20h2 in neurogenesis

Mechanisms regulating neurogenesis involve broad and complex processes that represent intriguing therapeutic targets in the field of regenerative medicine.One influential factor guiding neural stem cell proliferation and cellular differentiation during neurogenesis are epigenetic mechanisms.We present an overview of epigenetic mechanisms including chromatin structure and histone modifications;and discuss novel roles of two histone modifiers,Ezh2 and Suv4-20h1/Suv4-20h2(collectively referred to as Suv4-20h),in neurodevelopment and neurogenesis.This review will focus on broadly reviewing epigenetic regulatory components,the roles of epigenetic components during neurogenesis,and potential applications in regenerative medicine.

Epigenetic modifications and metabolic memory in diabetic retinopathy:beyond the surface

Epigenetics focuses on DNA methylation,histone modification,chromatin remodeling,noncoding RNAs,and other gene regulation mechanisms beyond the DNA sequence.In the past decade,epigenetic modifications have drawn more attention as they participate in the development and progression of diabetic retinopathy despite tight control of glucose levels.The underlying mechanisms of epigenetic modifications in diabetic retinopathy still urgently need to be elucidated.The diabetic condition facilitates epigenetic changes and influences target gene expression.In this review,we summarize the involvement of epigenetic modifications and metabolic memory in the development and progression of diabetic retinopathy and propose novel insights into the treatment of diabetic retinopathy.

Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels

In addition to DNA sequence information, site-specific histone modifications are another important determinant of gene expression in a eukaryotic organism. We selected four modification sites in common histones that are known to significantly impact chromatin function and generated monoclonal or polyclonal antibodies that recognize each of those site-specific modifications. We used these antibodies to demonstrate that the site-specific histone modification levels remain relatively constant in different organs of the same organism. We also compared the levels of selected histone modifications among several representative organisms and found that site-specific modifications are highly variable among different organisms, providing new insight into the evolutionary divergence of specific histone modifications.

Histone modification as a drug resistance driver in brain tumors

Patients with brain tumors,specifically,malignant forms such as glioblastoma,medulloblastoma and ependymoma,exhibit dismal survival rates despite advances in treatment strategies.Chemotherapeutics,the primary adjuvant treatment for human brain tumors following surgery,commonly lack efficacy due to either intrinsic or acquired drug resistance.New treatments targeting epigenetic factors are being explored.Post-translational histone modification provides a critical regulatory platform for processes such as chromosome condensation and segregation,apoptosis,gene transcription,and DNA replication and repair.This work reviews how aberrant histone modifications and alterations in histone-modifying enzymes can drive the acquisition of drug resistance in brain tumors.Elucidating these mechanisms should lead to new treatments for overcoming drug resistance.

组蛋白乳酸化修饰在恶性肿瘤中的研究进展

组蛋白赖氨酸乳酸化修饰是2019年新发现的一种酰化修饰,在基因表达、细胞代谢以及疾病治疗等生物过程中发挥着重要作用。近年来,乳酸化修饰生化相关研究取得突破性进展,尤其是在乳酸化修饰的生理功能以及与疾病相关性等领域逐渐受到关注。本文简要介绍乳酸化修饰的鉴定、生物学功能及其在恶性肿瘤中的作用,这将为进一步探索乳酸化修饰的功能和机制提供理论基础。

表观遗传修饰对ABO基因表达影响的研究进展

ABO血型的精准鉴定对临床安全输血至关重要。血清学和基因分型技术的应用使疑难血型鉴定问题得到一定程度的解决,但临床仍有表型与基因型不匹配的问题存在,影响血型鉴定和有效输血。表观遗传修饰是调控基因表达的重要方式,包括DNA甲基化、组蛋白修饰和非编码RNA调控。ABO基因的表达受到表观遗传机制的调控,因此表观遗传修饰对ABO基因表达的影响可能是这部分血型难以鉴定的分子机制之一。DNA甲基化水平对ABO基因表达影响的研究较多,但有关其他表观遗传修饰机制的研究较少,尤其是多种类型的非编码RNA被发现,它们对ABO基因表达的调控机制需要更多的研究进行探讨。

软骨肉瘤的表观遗传学研究进展

软骨肉瘤是第二常见的原发性恶性骨肿瘤,其治疗效果差,易复发和转移,对放化疗均不敏感,治疗方式在过去30~40年间停滞不前,还是以手术切除为主。对于软骨肉瘤的发生发展机制研究仍未完全明确,亦无特效药物。因此,探寻软骨肉瘤新的发生发展机制,从而寻找新的治疗方法和药物靶点,对临床治疗具有重大意义。有研究发现表观遗传学在软骨肉瘤发生发展中有重要作用。表观遗传学是指DNA序列未发生变化,但生物体的表型发生了可遗传性的改变,其机制主要包括DNA甲基化、非编码RNA调控、组蛋白修饰、染色质重塑等。该文就目前表观遗传学在软骨肉瘤中的研究进展做一综述,为进一步深入软骨肉瘤的研究,寻找新的治疗靶点提供方向。

胃癌组蛋白H3第4位赖氨酸的三甲基化修饰相关长链非编码RNA预后模型的构建与验证

目的 探索胃癌组蛋白H3第4位赖氨酸的三甲基化(trimethylation of lysine 4 on histone H3,H3K4me3)修饰相关长链非编码RNA(long non-coding RNA,LncRNA)特征,构建相关预后模型并预测胃癌免疫治疗疗效。方法 从癌症基因组图谱数据库下载胃癌相关转录组测序数据和对应的患者临床资料,通过构建H3K4me3相关调节因子基因与LncRNA的共表达网络识别H3K4me3修饰相关LncRNA,并将癌症基因组图谱数据库中370例符合筛选标准的胃癌患者样本(整体组)按1:1随机抽样划分为训练组(n=185)和验证组(n=185)。随后基于单因素Cox回归、Lasoo回归分析构建H3K4me3相关LncRNA预后风险评分模型并进行内部验证。Kaplan-Meier生存分析和受试者操作特征曲线(receiver operating characteristic curve,ROC曲线)被用于验证模型的预测性能。通过单因素和多因素Cox回归分析评估风险评分等临床指标的预后预测价值。结合风险评分、年龄和肿瘤TNM分期构建预测胃癌患者总生存率的列线图模型,ROC曲线与校准图被用于评估列线图的预测准确性。借助共识聚类识别异质性聚类亚群并进行免疫治疗疗效预测。结果 基于共表达网络关系识别了14个具有预后价值的H3K4me3相关LncRNA并构建了相关风险模型及评价体系。根据训练组预后风险评分模型获得的中位风险评分将训练组、验证组和整体组胃癌患者划分为高、低风险,Kaplan-Meier生存曲线显示低风险患者的总体生存情况要优于高风险患者(P<0.05)。此外,该模型在训练组中预测胃癌患者1、3、5年总生存率的曲线下面积(area under curve,AUC)分别为0.708、0.730、0.770,在验证组中分别为0.690、0.648、0.713,而在整体组中分别为0.697、0.670、0.724。多因素Cox回归分析显示基于H3K4me3相关LncRNA构建的风险评分模型是预测胃癌患者预后的独立因素(P<0.001)。构建的列线图预测胃癌患者1、2、3年总生存率的AUC分别为0.727、0.780、0.717,且其校准曲线与理想曲线相接近。基于共识聚类算法进一步识别了2种具有异质性免疫特征的H3K4me3-LncRNA亚群,其中亚组Ⅱ具有更高的免疫细胞浸润水平和更强的免疫应答潜力,并对5-氟尿嘧啶、奥沙利铂等显示出更高的药物敏感性,而亚组Ⅰ则可能对磷脂酰肌醇3-激酶特异性抑制剂具有更高的敏感性。结论 本研究构建了一个H3K4me3-LncRNA风险评分模型以预测胃癌患者的预后,并揭示了其异质性微观特征及在预测免疫治疗疗效方面的潜在价值。

高原动物低氧适应的表观遗传学机制研究

高原低氧环境是生物在高海拔地区所面临的主要生存挑战。动物高原适应性遗传基础复杂,相关研究主要聚焦在比较基因组、群体基因组和进化基因组,正选择基因集中体现在低氧诱导因子(HIF)调控通路。目前,动物高原适应的表观遗传学机制越来越受到关注。表观遗传学可以调节基因表达的可塑性和稳定性,影响细胞功能和生物体适应环境变化的能力。研究表明,高原生物经历了长期的低氧适应,表现出了与表观遗传学相关的适应性调节。DNA甲基化和组蛋白修饰是表观遗传学的重要修饰方式,与高原适应密切相关,通过调控基因表达水平影响细胞功能。HIF作为低氧环境中的关键转录因子复合物,其稳定性和活性受到表观遗传学的调控。DNA甲基化和组蛋白修饰直接影响HIF信号通路的功能,而非编码RNA和细胞色素P450(CYP450)酶等表观遗传机制同样也参与了HIF信号通路的调控。深入理解高原低氧环境适应与表观遗传学之间的关系以及HIF信号通路的表观遗传学作用机制,对于揭示适应性进化和相关疾病的发生机制具有重要意义。笔者总结了高原低氧环境适应与表观遗传学的关系,并重点探讨了HIF信号通路在表观遗传学调控中的作用机制。

精细胞中促进组蛋白-鱼精蛋白替换的分子机制研究进展

在精子形成过程中,圆形精子细胞核内染色质中的组蛋白逐渐被鱼精蛋白替代,使染色质凝聚得更为紧凑,奠定成熟精子头部特异形态的结构基础。若组蛋白-鱼精蛋白替换缺陷,将导致精子核凝聚失败,表现出精子形态异常和活力降低,受精困难。研究显示,组蛋白翻译后修饰、瞬时DNA链断裂、DNA链断裂修复和染色质重塑复合体识别等一系列变化都会促进组蛋白-鱼精蛋白的替换,本文从以上几个方面综述了目前对于促进组蛋白-鱼精蛋白替换分子机制的研究进展,以期为雄性不育症的诊断和治疗提供理论基础。

组蛋白乳酸化与疾病关系研究进展

组蛋白是染色质的主要蛋白组分,对生物遗传信息的调控有重要作用。乳酸作为细胞代谢的常见产物,可影响细胞遗传信息的表达。组蛋白在相关酶的作用下,会发生多种基团的化学修饰,其中乳酸化是重要的化学修饰之一。文章主要综述了组蛋白乳酸化的发生及其影响因素、组蛋白乳酸化与常见疾病的相互关系及治疗相关的研究进展。

Mechanism and application of feedback loops formed by mechanotransduction and histone modifications

Mechanical stimulation is the key physical factor in cell environment.Mechanotransduction acts as a fundamental regulator of cell behavior,regulating cell proliferation,differentiation,apoptosis,and exhibiting specific signature alterations during the pathological process.As research continues,the role of epigenetic science in mechanotransduction is attracting attention.However,the molecular mechanism of the synergistic effect between mechanotransduction and epigenetics in physiological and pathological processes has not been clarified.We focus on how histone modifications,as important components of epigenetics,are coordinated with multiple signaling pathways to control cell fate and disease progression.Specifically,we propose that histone modifications can form regulatory feedback loops with signaling pathways,that is,histone modifications can not only serve as downstream regulators of signaling pathways for target gene transcription but also provide feedback to regulate signaling pathways.Mechanotransduction and epigenetic changes could be potential markers and therapeutic targets in clinical practice.

改性HMS分子筛在多相催化反应中的应用

中孔HMS分子筛的扩散性能好、水热稳定性高,可作为载体或催化剂应用于多类有机化学反应,尤其是分子尺寸较大的有机化合物的反应。综述了改性HMS分子筛作为催化剂在环氧化、Baeyer-Villiger氧化、过氧化、高级氧化、烷基化、Friedel-Crafts酰基化、羰基化、羟基化、脱保护、歧化、酯化、Fischer-Tropsh合成、Diels-Alder加成、脱氢、加氢、加氢脱硫、异构化、光催化等18种反应中的应用进展。笔者认为改性HMS分子筛将在更多的化学反应中得到应用。

组蛋白乙酰化修饰对牙周炎发生发展影响的研究进展

牙周炎是由菌斑生物膜引起的慢性炎症性疾病,牙周微环境稳态对于牙周健康至关重要。表观遗传学探讨环境等非遗传因素如何在DNA核苷酸序列不发生改变的前提下调控基因的表达,从而影响疾病的发生发展。组蛋白乙酰化修饰是常见的表观遗传修饰之一,主要受组蛋白乙酰化酶和组蛋白去乙酰化酶的调节,调节失衡可引起基因调控紊乱,导致慢性炎症、自身免疫性疾病和癌症等疾病。组蛋白乙酰化修饰与牙周炎发生发展有明确的相关性。现分别从发生牙周炎时牙龈上皮细胞、免疫细胞和牙周膜干细胞中组蛋白乙酰化修饰的变化,阐明组蛋白乙酰化修饰在牙周炎发生发展过程中的作用及其分子机制,为牙周炎的表观治疗提供依据。