痘苗病毒原核增强子样序列VV1的结构和功能的研究

增强子是基因转录调控的一个重要而必需的元件,其最.初发现于SV40早期基因的表达过程中[1,2].自此以后,相继发现这一远端基因调控序列广泛存在于真核细胞、原核细胞和病毒基因组中[3-7].本文选取活性较高的痘苗病毒原核增强子样序列VV1为目的片段,利用缺失和随机突变的方法对VV1功能区进行分析,阐明其结构和功能的关系,进一步丰富原核增强子的作用机理和基因转录调控方面的研究.     

病毒编码的启动子和增强子研究进展

本文介绍病毒编码的启动子和增强子的结构和功能特点。综述人类免疫缺陷病毒,人单纯疱疹病毒,巨细胞病毒,人乳头瘤病毒,Ｅｐｓｔｅｉｎ－Ｂａｒｒ病毒和乙型肝炎病毒启动子和增强子研究的主要进展,阐述这些启动子,增强子在病毒转录及调控中的作用及其机制和目前研究中有待解决的问题。     

增强子与真核基因转录起始

许多真核基因的转录起始,除启动子外,还需要增强子。增强子是真核基因组中通过增强转录起始而参与基因表达调控的一类序列,近年不断发现于动物病毒和真核细胞中。对SV40增强子及SV40早区转录起始已经有比较深入的研究。本文综合近年研完进展,对增强子作用特点及结构特点等作概括介绍,并对其作用机理进行了讨论。     

增强子与基因表达的调控

增强子(Enhanoer)又称活化子(Activator)、增强因子(Enhancerelement),是存在于许多真核基因组中的调控序列,它起着活化启动子从而增强转录起始的作用。增强子不只一种序列,而是一类序列,其长度和组成不同。例如,在SV40中,它位于基因上游区-113——257bp之间,是72bp的重复序列;而在多瘤病毒中则是一个244bp的序列。增强子不仅是许多真核基因有效转录不可缺少,而且在一些病毒的感染中也起着重要作用。增强子于1981年首先在猿猴病毒SV40     

肝癌细胞HepG2中增强子的识别及生物信息学分析

目的:整合增强子特征识别肝癌细胞HepG2增强子,并对其保守性、GC含量、转录因子调控、靶基因功能等进行分析,以期解析肝癌细胞增强子参与的调控网络。方法:通过整合H3K27ac、H3K4me1和H3K4me3组蛋白修饰及DNaseⅠ高敏位点的Chip-seq数据预测HepG2中的增强子,计算每个增强子的平均Phast Cons分数和GC含量,评估整体增强子的保守性与GC含量,整合ENCODE转录因子结合位点数据寻找转录因子-增强子调控,使用GREAT和DAVID分别对增强子和增强子的靶基因进行GO与KEGG通路功能富集分析。结果:共识别2254个肝细胞癌增强子,1432个增强子靶基因,135个转录因子的9983个增强子结合位点;比较随机位点靶基因,发现增强子显著正调控靶基因的表达;保守性与GC含量分析表明增强子具有显著高的保守性与GC含量,并存在C-T/C-T/C-T-G模式的motif;增强子功能分析显示增强子显著富集于蛋白结合、酶结合、转录因子结合、RNA聚合酶Ⅱ结合等已知增强子功能,增强子GO与KEGG通路功能富集分析表明增强子靶基因显著参与细胞增殖、细胞凋亡、细胞周期调控和细胞迁移等肿瘤相关的生物进程与信号通路。结论:识别的肝细胞癌增强子具有显著高的保守性与GC含量,受多种转录因子调控,对其靶基因起正调控作用并且显著富集于肿瘤相关生物学进程与信号通路中。     

昆虫杆状病毒的增强子(Enhancer)

人们早已发现,许多真核细胞DNA、动物病毒DNA和RNA肿瘤病毒基因组具有一种基因调控序列,能增加它所连接基因的转录效率,这种核苷酸序列称之为增强子或激活子(Enhancer或Activator)。最近,美国科学家Guarino和Summers等人首次发现昆虫杆状病毒苜蓿尺蠖丫纹夜蛾核多角体病毒(Autographa californica Nuclear Polyhedrosis Virus,AcNPV)基因组中有散在分布的增强子序列。它们是一种特殊方式的核苷酸重复序列,可大大增加病毒延迟早期基因(Delayed-Early Gene)的转录效     

鼻咽癌细胞中ezrin基因增强子区的定位分析

本研究采用嵌套缺失和荧光素酶检测技术对鼻咽癌CNE2细胞ezrin基因增强子区进行定位分析。实验结果显示,CNE2细胞中,ezrin基因-1541/-706具有转录激活和转录增强作用,存在转录正调控区和负调控区。对5个潜在转录调控区的进一步研究发现,ezrin基因-1297/-1186对ezrin启动子和SV40启动子具有显著的转录增强作用;其它4个区域对启动子不表现转录调控作用,或表现弱的转录增强作用。结果表明,ezrin基因-1297/-1186是具有增强子作用的关键转录调控区,它有可能与其它潜在转录调控区以共同或协同的方式调控ezrin基因转录。     

增强子作用机制研究进展

增强子是能够增强启动子转录活性的ＤＮＡ顺式作用序列。增强子的结构与启动子相似,也是由多个元件组成,每个元件可以与一种或多种转录调控因子结合。增强子可以在启动子区的上游或下游起增强转录作用且与其距转录起点的远近无关。如Ｔ细胞受体α链基因的增强子位于启动...     

增强子RNA的功能特性及其在人类疾病中的重要调控作用

增强子是基因组上一段可以被转录调控蛋白识别并结合的区域,作为顺式调控元件和启动子共同参与基因转录过程。增强子在激活状态下,打开局部染色质并暴露DNA基序以吸引转录因子,从而进一步招募RNA聚合酶产生一类非编码RNA,即增强子RNA(enhancer RNA,eRNA)。eRNA可促进增强子与启动子特异性染色质远程互作参与基因转录调节,或与转录因子等调控蛋白结合促进基因转录,具有多样的功能和调控机制,从而在细胞的发育和分化、疾病发生发展等众多生物过程中起重要作用。该文就e RNA特性、功能、鉴定、数据库资源,以及eRNA在人类神经系统疾病、癌症、免疫代谢类疾病、心血管疾病等中的功能作用研究进展作一系统综述,探讨eRNA的未来研究方向,及在疾病中作为潜在治疗靶点的可能及目前存在的挑战。     

增强子调控癌症发生发展的机制研究

增强子是一段具有转录调控功能的DNA序列,主要通过顺式调控方式发挥作用。由于增强子及其调控基因在位置和距离上的不确定性,大大增加了研究增强子作用机制的复杂性和困难性。越来越多的证据表明,增强子与癌症等疾病的发生发展密切相关,因此开展癌症相关增强子的研究,将有助于全面解析癌症发病机制,并推动抗肿瘤药物的高效研发,具有重要的社会意义和经济价值。目前对于增强子的鉴定不充分,增强子在癌症和其他疾病中的发生发展调控机制尚未得到完整的解析。本文主要对增强子和超级增强子及其特性进行介绍,并在全基因组水平上对增强子的预测和鉴定进行了描述,最后总结了近年来增强子在癌症等疾病发生过程中所发挥的调控作用,从而为未来解析增强子调控机制以及癌症的诊断和治疗提供参考。     

Primary soluble plasmic degradation product of human cross-linked fibrin. Isolation and stoichiometry of the (DD)E complex.

The formation of the (DD)E complex and fragments DD and E upon proteolysis of human cross-linked fibrin was studied by timed digestions using varying amounts of plasmin. The (DD)E complex was the primary soluble degradation product released form cross-linked fibrin. This complex contained fragments DD and E1. Upon further digestion (DD)E1 complex was cleaved to (DD)E2 complex whereby only the fragment E moiety was affected. However, when fragment E2 was digested to fragment E3, dissociation of the complex occurred. Thus, fragments DD and E3 are the terminal plasmic digestion products of cross-linked fibrin. This pattern was consistent regardless of the plasmin to fibrin ratio; however, the rate of production of the terminal degradation products was directly dependent upon enzyme concentration. Digestion conditions were modified so that either the (DD)E complex or fragment DD was the predominant degradation product, allowing for the purification of these species by one-step gel filtration. The molar ratio of fragment DD to fragment E in the (DD)E complex was investigated by dissociation of the complex and by reassociation of the purified components. The (DD)E complex contains one molecule of fragment DD and one molecule of fragment E.     

Interaction between complementary polymerization sites in the structural D and E domains of human fibrin.

Plasmic degradation products of human fibrin, fragments DD, D, and E, bind to fibrin. It has been inferred from this observation that the binding occurs by attraction of complementary sites located in the NH2- and COOH-terminal domains of the fibrin molecule. The interaction between fragments D1 and E1 has been investigated in this work since it represents the first step in the process of fibrin clot formation. Fragment D1, that was initially as active as fragment DD, lost most of its anticoagulant activity after purification by cation-exchange chromatography. The lability of fragment D1 function explained the previous unsuccessful attempts to form a complex between fragments D1 and E1. The loss of fragment D1 anticoagulant activity was not associated with the cleavage of the gamma 63-85 chain segment, since fragments D1A and D1 identically inhibited the fibrin monomer polymerization rate. In order to demonstrate the formation of a complex between fragments D1 and E1, three lines of experiments were advanced. First, the anticoagulant activity of fragment D1 was neutralized by fragment E1 in a dose-dependent manner, demonstrating that the association between these fragments involved polymerization sites. Second, two products, D1.E1 and D1.E1.D1, were stabilized in a reaction with bifunctional cross-linking reagents, proving the formation of D.E complexes in aqueous solution. Third, immobilized fragment D1 bound fragments E1 and E2, but not fragment E3, showing that fragments E1 and E2 attached via a polymerization site to the complementary one in fragment D1, since this association was disrupted by fibrin polymerization inhibitory peptide GPRP. These results provided direct evidence for specific binding between the structural D and E domains of fibrin mediated through complementary polymerization sites. Thus, the initial formation of fibrin clot fibers appears to be driven by specific association of these sites.     

Monoclonal antibodies against laminin A chain fragment E3 and their effects on binding to cells and proteoglycan and on kidney development.

Rat monoclonal antibodies were raised against fragment E3 of the mouse Engelbreth-Holm-Swarm (EHS) tumor laminin and selected according to their exclusive reaction with laminin A chain by immunoblotting and staining pattern in embryonic kidneys by immunofluorescence. Immunochemical studies of nine purified antibodies showed a comparable reaction with unfragmented laminin and fragment E3 but no cross-reaction with several other, unrelated laminin fragments including the major cell-binding fragment E8. Reduction or pepsin digestion of fragment E3 reduced or abolished antibody binding indicating that most of the epitopes involved are conformation dependent and do not include carbohydrates. They are, however, not identical as shown by different reactivities after proteolytic or chemical cleavage of E3. Four of the antibodies were highly active in inhibiting cell adhesion of the teratocarcinoma cell line F9 and the Schwannoma cell line RN22 on fragment E3 (IC50 approximately 1 microgram/ml), while the others were distinctly less active. No inhibition was observed for cell adhesion on unfragmented laminin, consistent with previous findings that this is largely mediated by binding of fragment E8 to alpha 6 beta 1 integrin. A distinct correlation was observed between cell adhesion inhibition and the inhibition of heparansulfate proteoglycan and heparin binding to fragment E3. Since heparin is not very efficient in inhibiting cell adhesion, it indicates that heparin- and cell-binding sites on fragment E3 are in close proximity but not identical. Two of the antibodies also showed partial inhibition of kidney tubule formation in organ culture of embryonic kidney mesenchyme while the other antibodies were inactive. It suggests some but probably minor involvement of the fragment E3 structure of laminin in this developmental process.     

Purification of a small receptor-binding peptide from the central region of the colicin E1 molecule

An Mr = 16,000 receptor-binding fragment of colicin E1 has been obtained by cyanogen bromide digestion of colicin E1. The purified 16-kDa fragment shows binding properties similar to those of an Mr = 38,000 colicin E1 receptor-binding fragment generated by thermolysin treatment. Treatment of the 38-kDa fragment with cyanogen bromide also yields the 16-kDa fragment. By comparing the NH2-terminal amino acid sequence of the 16-kDa fragment with the known colicin E1 sequence, the receptor-binding fragment can be shown to occupy the central region of the colicin molecule, extending from residue 231 to 370. It is inferred that the 16-kDa fragment binds efficiently to the colicin receptor because it is able to protect sensitive cells against the lethal effects of colicins E1 and E2 and, when pre-adsorbed to the cell, to physically displace colicin E1. Unlike the 38-kDa receptor-binding fragment, the 16-kDa fragment was found to be devoid of channel-forming ability previously shown to be associated with the COOH-terminal region of the colicin E1 polypeptide.     

Differences in laminin fragment interactions of normal and transformed endothelial cells

Bovine aortic and microvascular endothelial cells showed good adhesion with spreading on fibronectin or collagen IV and to a lower extent on laminin. Recognition of native laminin was due to its long arm fragment E8 and was mediated by alpha 6 integrins as demonstrated by antibody inhibition. A considerably stronger, RGD-dependent interaction was observed with the isolated laminin short arm fragment P1 previously shown to represent a cryptic cell-binding site. No adhesion was observed with the heparin-binding fragment E3. In contrast, murine microvascular endothelial cells transformed by the polyoma middle T oncogene showed preferential adherence and spreading on laminin via its E8 cell-binding site and also showed adhesion to fragment E3. Attachment to laminin fragment P1 and to collagen IV was low or negative and was never followed by spreading. These data show that the transformation of microvascular endothelial cells, which give them the property to form hemangiomas, also leads to changes in cell adhesion to extracellular matrix proteins, particularly to laminin fragments.     

Thrombin binding to the A alpha-, B beta-, and gamma-chains of fibrinogen and to their remnants contained in fragment E

In order to study thrombin interaction with fibrinogen, thrombin binding to fragments D and E (prepared by plasmin digestion of fibrinogen) and to intact S-carboxymethylated chains of fibrinogen (A alpha, B beta, and gamma) was analyzed by autoradiography, immunoblotting, and affinity chromatography. Complex formation was observed between late fragment E and thrombin but not with fragment D. The three reduced chain remnants of fragment E all formed complexes with thrombin. Also, thrombin bound to the intact, separated A alpha, B beta, and gamma chains of fibrinogen as well as to the alpha and beta chains of fibrin. In these experiments the extended substrate-binding site, but not the catalytic-binding site, was being examined because fragment E had as its amino-terminal amino acids Val20 in the alpha chain, Lys54 in the beta chain, and Tyr1 in the gamma chain. Also, thrombin inhibited in its active center by D-phenyl-alanyl-L-prolyl-L-arginine-chloromethyl ketone bound to fragment E and to the separated chains in the same manner as unmodified thrombin. A lysine residue to thrombin was essential for its binding to fibrinogen. Thrombin attached to CNBr-activated Sepharose through its amino groups did not bind to fragment E, but when thrombin was attached through its carboxyl groups, it bound fragment E.     

Binding of lys-plasminogen to E-fragment of fibrinogen

The interaction of Lys-plasminogen and its fragments with fibrinogen fragment E was studied by equilibrium affinity binding. A quantitative analysis of binding parameters revealed two types of binding sites responsible for Lys-plasminogen interaction with the immobilized fragment E, i.e., with a high (Kd = 1.5 x 10(-6) M) and low (Kd = 82 x 10(-6) M) affinity ones. Among plasminogen fragments, only miniplasminogen and KI-3 bound immobilized fragment E and were eluted by epsilon-aminocaproic acid. Hence, two lysine binding sites may be involved in the binding of Lys-plasminogen to fragment E; they are localized in the KI-3 and K5 kringle structures.     

Antibody to integrin alpha 6 subunit specifically inhibits cell-binding to laminin fragment 8

A large number of cell lines which attach and spread on laminin show a comparable binding either to both laminin fragments P1 and E8 or exclusively to E8. Adhesion to fragment E8 was with one exception completely inhibited by a monoclonal antibody to the alpha 6 integrin subunit, indicating that VLA-6 or a related structure is the major cellular receptor for laminin. It is not involved in fragment P1 adhesion. Synthetic peptides possessing RGD or YIGSR sequences were without inhibitory activity for alpha 6-mediated adhesion to fragment E8.     

Molecular mechanisms of avian neural crest cell migration on fibronectin and laminin

We have examined the molecular interactions of avian neural crest cells with fibronectin and laminin in vitro during their initial migration from the neural tube. A 105-kDa proteolytic fragment of fibronectin encompassing the defined cell-binding domain (65 kDa) promoted migration of neural crest cells to the same extent as the intact molecule. Neural crest cell migration on both intact fibronectin and the 105-kDa fragment was reversibly inhibited by RGD-containing peptides. The 11.5-kDa fragment containing the RGDS cell attachment site was also able to support migration, whereas a 50-kDa fragment corresponding to the adjacent N-terminal portion of the defined cell-binding domain was unfavorable for neural crest cell movement. In addition to the putative "cell-binding domain," neural crest cells were able to migrate on a 31-kDa fragment corresponding to the C-terminal heparin-binding (II) region of fibronectin, and were inhibited in their migration by exogenous heparin, but not by RGDS peptides. Heparin potentiated the inhibitory effect of RGDS peptides on intact fibronectin, but not on the 105-kDa fragment. On substrates of purified laminin, the extent of avian neural crest cell migration was maximal at relatively low substrate concentrations and was reduced at higher concentrations. The efficiency of laminin as a migratory substrate was enhanced when the glycoprotein occurred complexed with nidogen. Moreover, coupling of the laminin-nidogen complex to collagen type IV or the low density heparan sulfate proteoglycan further increased cell dispersion, whereas isolated nidogen or the proteoglycan alone were unable to stimulate migration and collagen type IV was a significantly less efficient migratory substrate than laminin-nidogen. Neural crest cell migration on laminin-nidogen was not affected by RGDS nor by YIGSR-containing peptides, but was reduced by 35% after addition of heparin. The predominant motility-promoting activity of laminin was localized to the E8 domain, possessing heparin-binding activity distinct from that of the N-terminal E3 domain. Migration on the E8 fragment was reduced by greater than 70% after addition of heparin. The E1' fragment supported a minimal degree of migration that was RGD-sensitive and heparin-insensitive, whereas the primary heparin-binding E3 fragment and the cell-adhesive P1 fragment were entirely nonpermissive for cell movement.(ABSTRACT TRUNCATED AT 400 WORDS)