基因绝缘子——一类新发现的基因调节元件

最近几年,一类称为“绝缘子”的新的基因元件被众多的实验室发现和证实,大大丰富了我们对基因在染色质环境中如何形成拓扑学上独立的调节单元的认识。这个刚刚被找到的又一个基因“黑匣子”,尽管我们对其仍是一知半解,但让人们意外和兴奋的是：这类基因元件能给我们在转基因动物和基因治疗方面的研究和应用提供新的工具。     

染色质调节元件与不同启动子的相互作用对基因表达调控的影响

为探究DNA序列元件对不同启动子调节转基因稳定表达的影响,利用遍在染色质开放元件 (Ubiquitous chromatin opening elements,UCOE) 和基质黏附序列 (Scaffold/matrix-attachment regions,MAR) 分别与含增强子的oct4基因启动子、含CpG岛的sox2基因启动子和不含调控元件的nanog基因启动子以及同时包含增强子和CpG岛的CMV启动子组合构建pOCT4-MAR、pOCT4-UCOE、pSOX2-MAR、pSOX2-UCOE、pNANOG-MAR、pNANOG-UCOE、pCMV-UCOE、pCMV-MAR等质粒,分析这些质粒稳定转染后的表达量和嵌合表达差异。结果发现,UCOE与含增强子元件的oct4启动子组合能较稳定高效表达,而MAR与含CpG岛的sox2启动子组合能较稳定高效表达。利用排除位置效应原因的嵌合表达对染色质高级结构调控基因表达的稳定性分析表明：(1) 通常情况下UCOE比MAR调节的表达载体的表达更高效和更稳定;UCOE连接含CpG岛的启动子形成开放染色质调节的高表达更稳定;(2) MAR与启动子上TATA盒或增强子可能通过染色质环产生高表达,但相对不稳定。结论：染色质调节元件UCOE和MAR与启动子调控元件之间能通过染色质开放状态或染色质环调控基因稳定表达。     

组织因子基因的顺式调节元件

人组织因子基因位于１ｐ２１－２２,启动子区有２个ＡＰ－１位点、１个ｋＢ样位点,５个Ｓｐ１位点及３个Ｅｇｒ－１位点。其中ＴＥ的基础表达与５个Ｓｐ１位点均有关;血清反应元件与近端３个Ｓｐ１位点和３个Ｅｇｒ－１位点有关;     

多个顺式作用元件调节血管紧张素原基因表达

血管紧张素原是最强的血管活性物质——血管紧张素Ⅱ的唯一前体,在不同的生理和病理条件下,其水平各异．为了研究血管紧张素原基因表达的调控,将人血管紧张素原基因５′端侧翼序列１．２ｋｂ同氯霉素乙酰转移酶（ＣＡＴ）基因编码序列连接,构成表达载体,并且在此基础上构建５′端系列缺失的突变表达载体,用这些表达载体转染ＨｅｐＧ２和ＣＯＳ－７,确定了正负调控元件;同时应用ＤＮＡ－蛋白质凝胶泳动检测技术,发现核蛋白质与该顺式元件的结合,从而证明多个顺式作用元件调节血管紧张素原基因的表达．     

固醇调节元件结合蛋白1及其靶基因网络

固醇调节元件结合蛋白1(Sterol regulatory element-binding protein 1, SREBP-1)是重要的核转录因子之一, 能调控内源性胆固醇、脂肪酸、甘油三酯和磷脂合成所需酶的表达, 以维持血脂动态平衡。研究表明, SREBP-1及其靶基因网络的异常可引起胰岛素抵抗、Ⅱ型糖尿病、心功能紊乱、血管并发症和肝脂肪变等一系列代谢性疾病。近年高通量组学技术的发展极大扩展了对SREBP-1靶基因及其转录调控模式的了解。文章对SREBP-1蛋白结构、活化过程、DNA结合位点及其调控的靶基因等方面的研究进展进行了综述, 并着重介绍了基于组学数据的转录调控网络的构建, 这将有助于更好的认识SREBP-1在脂类代谢中的作用, 为深入探讨脂质代谢性疾病的治疗提供新线索。     

绝缘子调控基因的表达

绝缘子在调控真核基因时空特异表达的过程中起着至关重要的作用.它的主要功能是增强子阻断和异染色质屏障.已经有竞争、阻断和成环等模型描述其增强子阻断功能;而它的异染色质屏障功能主要是通过影响染色质组蛋白的翻译后修饰来实现.已经确定的绝缘子包括果蝇基因组中的染色质特化结构(specialized chromatin structures, scs)和scs、gypsy、鸡珠蛋白β基因座上游的DNaseⅠ高敏感位点cHS4以及小鼠或人Igf2/H19基因座上的印记控制区(imprinting control region, ICR)和DNA甲基化区域(DNA methylated regions, DMR)元件等.许多转录因子参与绝缘子的基因调控作用,例如脊椎动物中的CCCTC结合因子(CCCTC binding factor,CTCF).利用基因组学和生物信息学等方法,还可以在基因组中发现新的绝缘子元件.     

生物钟基因3及其表达的调节机制

众所周知 ,生物体的新陈代谢过程 ,细胞和细胞器官的生理功能 ,以及心理行为等生命活动往往随着昼夜循环而发生规律性的变化。就是在实验室恒定的条件下 ,消除一切环境因子的影响 ,生命活动仍表现出昼夜节律性的变化。这说明昼夜节律受体内的测时系统——生物钟的控制。从 5 0年代至今 ,人们对生物的昼夜节律及其调控机制进行了深入地研究 ,特别是应用生物化学和分子生物学的方法 ,使人们逐步了解了生物节律的特点 ,生物钟基因及其表达的调控机制。1　生物钟基因存在于不同生物体中的昼夜节律时钟都表现出 3个共同的特点 :1 )在恒定的环境条…     

绝缘子—一种新的真核生物基因表达调控元件

绝缘子——一种新的真核生物基因表达调控元件陈朝霞明镇寰（杭州大学生命科学学院,杭州３１００１２）关键词绝缘子边界元件基因调控近十几年来,真核生物基因表达调控研究取得了令人瞩目的成果,但同时也留给人们许多难解的谜。如增强子调控功能的无方向性、可以在离基...     

真核生物基因表达的调控元件——绝缘子

在真核生物基因组中,绝缘子（ｉｎｓｕｌａｔｏｒ）既是一种边界元件,又是一种控制基因表达的调控元件。目前在果蝇和鸡等的基因组中已发现多个绝缘子,它们是通过阻断邻近的调控元件与其所界定的启动子之间的相互作用而产生调控效应。绝缘子的调控是一个由许多蛋白质因子参与的复杂过程,对绝缘子功能的进一步研究,将为解开真核生物基因表达的调控之谜提供有力的证据。１　绝缘子及染色质边界元件真核生物染色体是由一系列各自独立的高度有序的染色质结构域组成,这些结构域在功能和结构上都是独立的,它们是由边界元件所界定。迄今为止…     

LCRG1基因启动子关键顺式调节元件的鉴定

LCRG1基因(laryngeal carcinoma related genel,LCRG1)是一个新的喉癌候选抑瘤基因,其转录调控机制一直未被阐明.通过限制性内切酶酶切介导对LCRG1基因(-169～+127)区域进行剪切体分析,将LCRG1基因最小启动子定位于-169～-57.应用连接体扫描突变体分析,将关键顺式作用元件确定在-137～-122.生物信息学提示该区存在SP1、E2F1/DP1、EKLF和ZF9转录因子结合位点.利用已知反式作用因子与报告基因质粒进行共转染,提示Sp1为有效的反式作用因子,且能上调LCRG1基因的表达.凝胶迁移阻滞实验确定LCRG1基因关键的顺式作用元件区域具有Sp1结合位点.LCRG1基因启动子-137～-122片段在该基因表达过程中可能起重要作用,为LCRG1基因功能研究提供了新的证据.     

Poly(ADP-ribose) Polymerase-1 (PARP-1) Contributes to the Barrier Function of a Vertebrate Chromatin Insulator

The prototypic chromatin insulator cHS4 has proven effective in reducing silencing chromosomal position effects in a variety of settings. Most of this barrier insulator activity has been mapped to a 250-bp core region, as well as to several proteins that bind this region. However, recent studies from our laboratory demonstrated that an extended 400-bp core region of the cHS4 element is necessary to achieve full barrier insulator activity when used as a single copy in the context of recombinant gammaretroviral and lentiviral vectors. In this study, electrophoretic gel mobility shift assays revealed specific DNA-protein binding activities associated with the distal portion of this extended core region. Affinity purification and tandem mass spectrometry studies led to the identification of one of these proteins as poly(ADP-ribose) polymerase-1 (PARP-1). The identity of this binding activity as PARP-1 was subsequently verified by a variety of biochemical studies in vitro and by chromatin immunoprecipitation studies in vivo. Functional studies with gammaretroviral reporter vectors in cell lines and primary mouse bone marrow progenitor cultures showed that cHS4 barrier activity was abrogated upon mutation of the putative PARP-1-binding site or upon treatment with a PARP inhibitor, respectively. The barrier activity of the cHS4 element was also found to be abrogated in studies using bone marrow from Parp1-null mice. Taken together, this study demonstrates that binding of PARP-1 plays a key functional role in the barrier activity of the extended cHS4 insulator core element.     

Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective

The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference-making causes of phenotypes is re-examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. This review argues that it is appropriate to treat genes as specific actual difference-makers for the molecular regulation of gene expression. However, they are often neither stable, proportional, nor specific as causes of the overall dynamic behavior of regulatory networks. Dynamical models, properly formulated and validated, provide the tools to probe cause-and-effect relationships in complex biological systems, allowing to go beyond the limitations of genetic reductionism to gain an integrative understanding of the causal processes underlying complex phenotypes.     

起始密码子区域相关序列多态性的开发及在苜蓿遗传多样性上的应用

目前广泛使用的基于PCR基础的分子标记多为扩增非编码区域,或是随机基因组中扩增,在QTL定位中得到的位点一般与目标性状基因距离较远,我们开发了一个新的基于启动子序列目的基因型分子标记技术——启动子区域相关序列多态性（SCRP）,试图使标记能够更为准确的反映不同品种的遗传基础。它利用启动子位置保守一致序列 （“Kozak”序列） 作为其上游引物,利用内含子富含“AATT”的特性,作为核心序列设计下游引物,上下游引物均为18bp,引物间通过组合配对的方式作为扩增引物对。设计了14条上游引物和10条下游引物,共140对引物组合,对34个苜蓿品种进行扩增,研究了34个苜蓿的遗传多样性。每个PCR反应产生3~16个50~2000bp的条带,结果表明该标记简单、可靠、具有较高多态性,并且扩增区域为一种目的基因型分子标记,在种质资源研究中具有重要价值。     

Dynamic Light Regulation of Photosynthesis (A Review)

Regulatory reactions providing the photosynthetic apparatus with the ability to respond to variations of irradiance by changes in activities of the light and the dark stages of photosynthesis within a time range of seconds and minutes are considered in the review. At the light stage, such reactions are related to the changes in both distribution of light energy between two photosystems and probability of nonphotochemical dissipation of absorbed quanta in PSI and PSII. These regulatory reactions operate in a negative feedback mode, thus avoiding overreduction of electron transport chain and minimizing the probability of generation of reactive oxygen species. The crucial role in preventing the generation of reactive oxygen species belongs to dynamic regulation of electron transport activity despite the presence of complex system of their detoxification in chloroplasts. In dark reactions of Calvin cycle, the regulatory responses involve a positive feedback principle being related to redox regulation of activities of several enzymes, which is sensitive to the reduction status of PSI acceptor side. The complex of regulatory reactions based on negative and positive feedback principles provides prolonged functioning of a chloroplast and high stability of photosynthetic activity under various light conditions.     

Neuroendocrine disruption without direct endocrine mode of action: Polychloro-biphenyls (PCBs) and bisphenol A (BPA) as case studies

Endocrine disruption is commonly thought to be restricted to a direct endocrine mode of action i.e. the perturbation of the activation of a given type of hormonal receptor by its natural ligand. Consistent with the WHO definition of an endocrine disrupter, a key issue is the “altered function(s) of the endocrine system”. Such altered functions can result from different chemical interactions, beyond agonistic or antagonistic effect at a given receptor. Based on neuroendocrine disruption by polychlorinated biphenyls and bisphenol A, this paper proposes different mechanistic paradigms that can result in adverse health effects. They are a consequence of altered endocrine function(s) secondary to chemical interaction with different steps in the physiological regulatory processes, thus accounting for a possibly indirect endocrine mode of action.     

A Brief Review on the Human Encyclopedia of DNA Elements (ENCODE) Project

The ENCyclopedia Of DNA Elements (ENCODE) project is an international research consortium that aims to identify all functional elements in the human genome sequence. The second phase of the project comprised 1640 datasets from 147 different cell types, yielding a set of 30 publications across several journals. These data revealed that 80.4% of the human genome displays some functionality in at least one cell type. Many of these regulatory elements are physically associated with one another and further form a network or three-dimensional conformation to affect gene expression. These elements are also related to sequence variants associated with diseases or traits. All these findings provide us new insights into the organization and regulation of genes and genome, and serve as an expansive resource for understanding human health and disease.     

Genetic control of colour /pattern polymorphism in British populations of the spittlebug Philaenus sputnarius (L.) (Homoptera: Aphrophoridae)

The results of breeding experiments designed to determine the genetic control of the colour/pattern polymorphism in Philaenus spumarius in certain British populations are described and contrasted to previously published results for material taken from populations in southern Finland. The 11 principal phenotypes are controlled by seven alleles at a single autosomal locus, with complex patterns of dominance and co-dominance. In Finland, and most of the rest of the species' extensive range, the eight melanic morphs are wholly or substantially limited to the females, in which they are dominant to the typical form. Previously, this sex limitation has been explained in terms of reduced penetrance of melanic alleles in males and/or dominance reversal between the sexes, such that the eight melanic phenotypes (controlled by five alleles which are adjacent in the dominance heirarchy) are dominant to typical in the females but recessive in the males. Published data on morph frequencies in S Finland and on breeding experiments using material collected from these populations are re-examined and it is shown that neither theory accounts adequately for all the evidence. By contrast, in most British populations there is greatly increased penetrance in males of the melanic morphs which are strictly female-limited elsewhere. Breeding experiments, using P. spumarius taken from selected British populations, provide clear evidence that melanics are dominant to typical in both sexes. This difference in genetic control is entirely consistent with the balance of morph frequencies between the sexes in the populations from which the breeding material for the two separate studies was taken. Experimental material for this study was taken from populations in the Cynon Valley in south Wales, which have the highest melanic frequencies in the species' range and show particularly clear expression of melanic phenotypes in males. Both of these features are strongly correlated with severe aerial pollution from a local smokeless fuel factory. Selection for melanism in these populations is clearly strong, which probably accounts for the high level of penetrance and the dominance of melanics to typical in both sexes. Although further experiments are needed, it is suggested that regulatory loci, controlling the penetrance and expression of melanic alleles in males, could account for the observed differences in genetic control between populations in Britain and Finland.     

Early senescence induced by 2-3H-benzoxazolinone (BOA) in Arabidopsis thaliana

Measurements of chlorophyll a fluorescence, nutrient and trace elements, total protein content and malonyldialdehyde in leaves of Arabidopsis thaliana between 1 and 192 h after treatment with 0, 1 or 3 mM 2-3H-benzoxazolinone (BOA), together with imaging of chlorophyll a fluorescence and of the distributions of hydrogen peroxide and superoxide anion, suggested that the primary phytotoxic action of BOA is the induction of premature senescence, and that oxidative stress is a secondary effect that sets in a day or two later.