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Evidence for novel epigenetic marks within plants. 植物中新表观遗传标记的证据。
Pub Date : 2019-12-24 eCollection Date: 2019-01-01 DOI: 10.3934/genet.2019.4.70
Asaad M Mahmood, Jim M Dunwell

Variation in patterns of gene expression can result from modifications in the genome that occur without a change in the sequence of the DNA; such modifications include methylation of cytosine to generate 5-methylcytosine (5mC) resulting in the generation of heritable epimutation and novel epialleles. This type of non-sequence variation is called epigenetics. The enzymes responsible for generation of such DNA modifications in mammals are named DNA methyltransferases (DNMT) including DNMT1, DNMT2 and DNMT3. The later stages of oxidations to these modifications are catalyzed by Ten Eleven Translocation (TET) proteins, which contain catalytic domains belonging to the 2-oxoglutarate dependent dioxygenase family. In various mammalian cells/tissues including embryonic stem cells, cancer cells and brain tissues, it has been confirmed that these proteins are able to induce the stepwise oxidization of 5-methyl cytosine to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and finally 5-carboxylcytosine (5caC). Each stage from initial methylation until the end of the DNA demethylation process is considered as a specific epigenetic mark that may regulate gene expression. This review discusses controversial evidence for the presence of such oxidative products, particularly 5hmC, in various plant species. Whereas some reports suggest no evidence for enzymatic DNA demethylation, other reports suggest that the presence of oxidative products is followed by the active demethylation and indicate the contribution of possible TET-like proteins in the regulation of gene expression in plants. The review also summarizes the results obtained by expressing the human TET conserved catalytic domain in transgenic plants.

基因表达模式的变化可以由基因组的修饰引起,而基因组的修饰不会改变DNA的序列;这些修饰包括胞嘧啶甲基化生成5-甲基胞嘧啶(5mC),从而产生可遗传的外胚轴和新的外胚轴。这种非序列变异被称为表观遗传学。在哺乳动物中负责产生这种DNA修饰的酶被命名为DNA甲基转移酶(DNMT),包括DNMT1、DNMT2和DNMT3。这些修饰的氧化的后期阶段是由Ten - 11易位(TET)蛋白催化的,该蛋白含有属于2-氧葡萄糖酸盐依赖的双加氧酶家族的催化结构域。在包括胚胎干细胞、癌细胞和脑组织在内的各种哺乳动物细胞/组织中,已经证实这些蛋白能够诱导5-甲基胞嘧啶逐步氧化为5-羟甲基胞嘧啶(5hmC)、5-甲酰胞嘧啶(5fC)和最后的5-羧基胞嘧啶(5caC)。从初始甲基化到DNA去甲基化过程结束的每个阶段都被认为是可能调节基因表达的特定表观遗传标记。这篇综述讨论了在各种植物物种中存在这种氧化产物,特别是5hmC的有争议的证据。尽管一些报道认为没有证据表明酶促DNA去甲基化,但其他报道表明氧化产物的存在之后是活跃的去甲基化,并表明可能的tet样蛋白在植物基因表达调控中的作用。综述了在转基因植物中表达人TET保守催化结构域所取得的成果。
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引用次数: 11
The roles of genes in the bitter taste. 基因在苦味中的作用。
Pub Date : 2019-12-24 eCollection Date: 2019-01-01 DOI: 10.3934/genet.2019.4.88
Harem Othman Smail

The aims of this review were to understand the roles of bitter taste genes in humans. Some of the peoples have the capacity to taste some chemical substance such as phenylthiocarbamide (PTC) while others cant not based on the dietary hazards and food preferences. There are two alleles responsible to express these phenotypes which are homozygous recessive. In human TAS2R38 genes located on the chromosome number 7 and consist of different nucleotide polymorphism that related to detection of the phenotype of different chemical compounds such as 6-n-propylthiouracil (PROP) and phenylthiocarbamide bitterness and this Gene is the member of the TAS2R genes which are eleven pseudogenes and twenty that has roles in many biological processes. There are many factors that affect the bitter taste such as food, age, sex, and different diseases. The mechanism of food bitter taste and genotype of TAS2R38 until know not well understood due to that the proof of relation between bitter taste sensitivity and food is harmful. there are many different diseases can impact the influence of taste such as neoplasm and lifestyle such as consumption of alcohol along with the use of medication, head trauma, upper tract infections. On the other hand, A relation between TAS2R38 genotype and meal preferences has been observed among children, however, no associations have been mentioned among older adults. Some previous research proved some vital points that show an association between type 1 of diabetes and phenylthiocarbamide (PTC) but other studies cannot demonstrate that. However, of other disease such as obesity is controversial but other studies reported to the relationship between them.

这篇综述的目的是了解苦味基因在人类中的作用。一些人有能力尝出某些化学物质,如苯硫胺(PTC),而另一些人则不能,这是基于饮食危害和食物偏好。有两个等位基因负责表达这些表型,它们是纯合隐性的。TAS2R38基因位于人类第7号染色体上,由不同的核苷酸多态性组成,与6-n-丙基硫脲嘧啶(PROP)和苯硫脲苦味等不同化合物的表型检测有关,该基因是TAS2R基因中的11个假基因和20个在许多生物过程中起作用的基因。影响苦味的因素有很多,比如食物、年龄、性别和不同的疾病。由于苦味敏感性与食物之间的关系是有害的,TAS2R38基因型与食物苦味产生的机制尚不清楚。有许多不同的疾病会影响味觉的影响,比如肿瘤和生活方式,比如酒精和药物的使用,头部创伤,上呼吸道感染。另一方面,TAS2R38基因型与饮食偏好之间的关系已经在儿童中观察到,但是在老年人中没有提到关联。先前的一些研究证明了一些关键的观点,表明1型糖尿病和苯硫代氨基脲(PTC)之间存在关联,但其他研究无法证明这一点。然而,其他疾病,如肥胖,是有争议的,但其他研究报告了它们之间的关系。
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引用次数: 9
A robust circular RNA-based prognostic signature for postoperative recurrence in stage II/III colon cancer. 基于环状rna的II/III期结肠癌术后复发的可靠预后特征
Pub Date : 2019-09-30 eCollection Date: 2019-01-01 DOI: 10.3934/genet.2019.4.67
Ji Ruan
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引用次数: 3
Re-engineering anti-CTLA-4 antibodies for enhancing cancer immunotherapy efficacy and safety 重组抗ctla -4抗体,提高肿瘤免疫治疗的有效性和安全性
Pub Date : 2019-09-18 DOI: 10.3934/genet.2019.3.64
Sharvesh Raj Seeruttun
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引用次数: 0
PDE4B gene polymorphism in Russian patients with panic disorder 俄罗斯惊恐障碍患者PDE4B基因多态性研究
Pub Date : 2019-08-20 DOI: 10.3934/genet.2019.3.55
A. Malakhova, O. Rudko, V. Sobolev, A. Tretiakov, Elena A Naumova, Z. Kokaeva, J. Azimova, E. Klimov
Abstract Background Panic disorder is a complex disease of unclear etiology but with an apparent genetic component. PDE4B gene product is involved in many cell processes owing to its function-regulation of the level of a second messenger cAMP. PDE4B gene polymorphism has been shown to be associated with some mental disorders including panic disorder. Aims The goal of our study was to evaluate the role of 3 SNPs in the PDE4B gene in the development of panic disorder. Methods 94 patients diagnosed with panic disorder according to the DSM-IV criteria were enrolled in the study. The population control group included 192 subjects. Genotyping was carried out by real-time PCR with TaqMan probes. Results The investigated substitutions are not associated with panic disorder in general and in female/male cohorts (p > 0.05). The analysis of complex genotypes demonstrated two protective complex genotypes (rs1040716:A, T + rs10454453:A + rs502958:A and rs1040716:A, T + rs502958:A) associated with panic disorder in general regardless of the patient's gender (p < 0.05). These genotypes did not correlate with the patient's sex. Conclusions We found two complex protective genotypes associated with panic disorder. This can be due to the fact that predisposition to the disease are associated with other genes, while PDE4B gene polymorphism reduces their effect.
摘要背景惊恐障碍是一种病因不明但具有明显遗传成分的复杂疾病。PDE4B基因产物通过调控第二信使cAMP的水平参与了许多细胞过程。PDE4B基因多态性已被证明与包括恐慌症在内的一些精神障碍有关。目的探讨PDE4B基因中3个snp在惊恐障碍发生中的作用。方法选取94例符合DSM-IV标准的惊恐障碍患者作为研究对象。人口对照组包括192名受试者。采用TaqMan探针进行实时PCR分型。结果所调查的替代与惊恐障碍在总体和男女队列中均无相关性(p < 0.05)。复杂基因型分析显示,无论患者性别如何,两种保护性复杂基因型(rs1040716:A, T + rs10454453:A + rs502958:A和rs1040716:A, T + rs502958:A)与恐慌障碍普遍相关(p < 0.05)。这些基因型与患者的性别无关。结论:我们发现两种复杂的保护性基因型与惊恐障碍相关。这可能是由于这种疾病的易感性与其他基因有关,而PDE4B基因多态性降低了它们的影响。
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引用次数: 4
Molecular characterization of the netrin-1 UNC-5 receptor in Lucilia sericata larvae 丝光绿蝇幼虫netrin-1 UNC-5受体的分子特征
Pub Date : 2019-08-02 DOI: 10.3934/genet.2019.3.46
Tahereh Karamzadeh, H. Alipour, Marziae Shahriari-Namadi, A. Raz, K. Azizi, M. Bagheri, M. Moemenbellah-Fard
Abstract Larval therapy with Lucilia sericata is a promising strategy in wound healing. Axon guidance molecules play vital roles during the development of the nervous system and also regulate the capacity of neuronal restoration in wound healing. Netrin-1, one of the proteins that larvae secrete, plays a useful role in cell migration and nerve tissue regeneration. The UNC-5 receptor combines with a netrin-1 signal and transmits the signal from one side of the membrane to the other side, initiating a change in cell activity. In the current study, we identified the full length of the UNC-5 receptor mRNA in L. sericata using different sets of primers, including exon junction and specific region primers. The coding sequence (CDS) of the UNC-5 receptor was sequenced and identified to include 633 base-pair nucleic acids, and BLAST analysis on its nucleotide sequence revealed 96% identity with the Lucilia cuprina netrin-1 UNC-5 receptor. The protein residue included 210 amino acids (aa) and coded for a protein with 24 kD weight. This gene lacked the signal peptide. Furthermore, the UPA domain is conserved in UNC-5. It lied at the interval of 26–131 aa. We identified the CDS of netrin-1 UNC-5 receptor in L. sericata. It could be applied to research activities implementing a new essential component design in wound healing.
摘要蚕丝绿蝇幼虫治疗是一种很有前途的创面愈合方法。轴突引导分子在神经系统发育过程中起着重要的作用,并在伤口愈合过程中调节神经元的修复能力。Netrin-1是幼虫分泌的一种蛋白质,在细胞迁移和神经组织再生中起着有益的作用。UNC-5受体与netrin-1信号结合,并将信号从膜的一侧传递到另一侧,从而引发细胞活性的变化。在本研究中,我们使用不同的引物,包括外显子连接和特定区域引物,鉴定了丝蚕UNC-5受体mRNA的全长。对UNC-5受体的编码序列(CDS)进行测序和鉴定,包括633个碱基对的核酸,BLAST分析显示其核苷酸序列与Lucilia cuprina netrin-1 UNC-5受体的同源性为96%。该蛋白残基包含210个氨基酸(aa),编码一个分子量为24 kD的蛋白。这个基因缺少信号肽。此外,UPA域在UNC-5中是保守的。在26 ~ 131aa之间。我们鉴定了丝蚕netrin-1 UNC-5受体的CDS。它可以应用于在伤口愈合中实施一种新的基本组件设计的研究活动。
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引用次数: 6
The epigenetics of diabetes, obesity, overweight and cardiovascular disease. 糖尿病、肥胖症、超重和心血管疾病的表观遗传学。
Pub Date : 2019-08-01 eCollection Date: 2019-01-01 DOI: 10.3934/genet.2019.3.36
Harem Othman Smail

The objectives of this review were once to understand the roles of the epigenetics mechanism in different types of diabetes, obesity, overweight, and cardiovascular disease. Epigenetics represents a phenomenon of change heritable phenotypic expression of genetic records taking place except changes in DNA sequence. Epigenetic modifications can have an impact on a whole of metabolic disease with the aid of specific alteration of candidate genes based totally on the change of the target genes. In this review, I summarized the new findings in DNA methylation, histone modifications in each type of diabetes (type 1 and type 2), obesity, overweight, and cardiovascular disease. The involvement of histone alterations and DNA methylation in the development of metabolic diseases is now widely accepted recently many novel genes have been demonstrated that has roles in diabetes pathway and it can be used for detection prediabetic; however Over the modern-day years, mass spectrometry-based proteomics techniques positioned and mapped one-of a kind range of histone modifications linking obesity and metabolic diseases. The main point of these changes is rapidly growing; however, their points and roles in obesity are no longer properly understood in obesity. Furthermore, epigenetic seen in cardiovascular treatment revealed a massive quantity of modifications affecting the improvement and development of cardiovascular disease. In addition, epigenetics are moreover involved in cardiovascular risk factors such as smoking. The aberrant epigenetic mechanisms that make a contribution to cardiovascular disease.

这篇综述的目的曾经是了解表观遗传学机制在不同类型的糖尿病、肥胖、超重和心血管疾病中的作用。表观遗传学是指除DNA序列变化外,遗传记录的可遗传表型表达发生变化的现象。表观遗传学修饰可以在完全基于靶基因变化的候选基因的特定改变的帮助下对整个代谢性疾病产生影响。在这篇综述中,我总结了DNA甲基化、组蛋白修饰在每种类型的糖尿病(1型和2型)、肥胖、超重和心血管疾病中的新发现。组蛋白改变和DNA甲基化参与代谢性疾病的发展现已被广泛接受。最近,许多新基因已被证明在糖尿病途径中发挥作用,并可用于检测糖尿病前期;然而,近年来,基于质谱的蛋白质组学技术定位并绘制了一系列将肥胖和代谢性疾病联系起来的组蛋白修饰之一。这些变化的要点是迅速增长;然而,他们在肥胖中的观点和作用在肥胖中不再被正确理解。此外,在心血管治疗中观察到的表观遗传学揭示了大量影响心血管疾病改善和发展的修饰。此外,表观遗传学还与吸烟等心血管风险因素有关。导致心血管疾病的异常表观遗传学机制。
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引用次数: 0
Histone glycation: Linking metabolic perturbation with epigenetic misregulation in cancer 组蛋白糖化:癌症中代谢扰动与表观遗传失调的联系
Pub Date : 2019-05-31 DOI: 10.3934/genet.2019.2.14
Xiayao Diao
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引用次数: 6
Physiological responses and transcriptome analysis of the Kochia prostrata (L.) Schrad. to seedling drought stress 匍匐木的生理反应和转录组分析。对幼苗干旱胁迫
Pub Date : 2019-05-31 DOI: 10.3934/genet.2019.2.17
Xiaojuan Wang, Jianghong Wu, Zhongren Yang, Fenglan Zhang, Hailian Sun, Xiao Qiu, Fengyan Yi, Ding Yang, Fengling Shi
Abstract Kochia prostrata is a good forage plant, which has important economic and ecological value in arid and semi-arid regions of China. Drought is one of the main factors affecting its productivity. At present, there are few studies on the mechanism of drought resistance. In order to reveal the changes of physiological and biochemical indexes, stomatal structure and gene expression profiles of Kochia prostrata under drought treatment, the classical determination method and high-throughput Illumina Hiseq sequencing platform were applied to the control group (CK) and drought treatment group of Kochia prostrata. The results showed that under the condition of moderate to mild drought stress, the SOD activity reached the maximum value of 350.68 U/g min on the 5th day of stress, and under the condition of severe drought stress, the SOD activity reached the maximum on the 2nd day of stress. The accumulation of Proline remained at a high level on the 5th day of stress, and there was at least one epidermal cell interval between the two adult stomatal of the leaf epidermis, so that the evaporation shell of each stomatal did not overlap, it ensures the efficient gas exchange of the stomatal, indicating that the Kochia prostrata has strong drought resistance. A total of 1,177.46 M reads were obtained by sequencing, with a total of 352.25 Gbp data and Q30 of 85%. In the differential gene annotation to the biological process (BP), a total of 261 GO terms were enriched in the up-regulated genes, and a total of 231 GO terms were enriched in the down-regulated genes. The differentially expressed genes (DEGs) were obtained in 27 KEGG metabolic pathways, which laid a foundation for revealing the molecular mechanism of drought tolerance.
摘要蜈蚣草是一种良好的饲料植物,在中国干旱半干旱区具有重要的经济和生态价值。干旱是影响其生产力的主要因素之一。目前,对抗旱机理的研究较少。为了揭示干旱处理下头草生理生化指标、气孔结构和基因表达谱的变化,采用经典测定方法和高通量Illumina Hiseq测序平台对对照组(CK)和干旱处理组头草进行检测。结果表明,在中~轻度干旱胁迫条件下,SOD活性在胁迫第5天达到最大值350.68 U/g min,在重度干旱胁迫条件下,SOD活性在胁迫第2天达到最大值。脯氨酸积累在胁迫第5天仍保持较高水平,且叶表皮的两个成体气孔之间至少存在一个表皮细胞间隔,使得每个气孔的蒸发壳不重叠,保证了气孔的高效气体交换,说明prochia具有较强的抗旱性。测序共获得1177.46 M reads,共352.25 Gbp数据,Q30为85%。在生物过程的差异基因注释(BP)中,上调基因中共富集了261个GO项,下调基因中共富集了231个GO项。在27条KEGG代谢途径中获得了差异表达基因(DEGs),为揭示干旱耐受性的分子机制奠定了基础。
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引用次数: 3
Linking metabolic and epigenetic regulation in the development of lung cancer driven by TGFβ signaling TGFβ信号驱动肺癌发展的代谢和表观遗传调控
Pub Date : 2019-05-31 DOI: 10.3934/genet.2019.2.11
Liyi Zhang
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引用次数: 1
期刊
AIMS Genetics
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