33种鱼类微型反向重复转座元件鉴定

微型反向重复转座元件(MITEs)是一类短的非自主DNA转座子,其分布的位置会对宿主产生影响。文章使用生物信息学的方法对无颌类、软骨鱼纲、肉鳍鱼纲和辐鳍鱼纲鱼类基因组进行了MITEs预测,最终在33种鱼类基因组中鉴定出2433个MITEs家族。文章发现鱼类基因组中MITEs含量存在较大差异(0.11%—21.18%),并且MITEs含量与鱼类基因组大小呈正相关关系。根据末端重复序列(TIRs)和靶位点重复序列(TSDs)的特征将MITEs分为10个超家族,其中TC1-Mariner超家族的含量最高。MITEs在鱼类基因组中的插入事件主要发生在4百万年前至今,大多数物种的MITEs在2百万—0.5百万年前发生了爆发式扩增。鱼类基因组中的MITEs多数插入到基因内部或附近,这些转座子可能在基因的表达调控方面存在重要作用。     

原生动物基因组转座元件的研究进展

转座元件是一类广泛分布于真核生物的可移动的遗传因子, 可以引起基因重组和变异, 在物种进化及遗传改良中起着重要作用。针对近年来原生动物全基因组序列中大量发现的转座元件, 文章着重比较了转座元件在锥虫、利什曼虫、微孢子虫、变形虫和滴虫基因组序列中的存在种类、分布特征及其功能意义。原生动物转座元件以LINE 和SINE为主, 其次是DNA转座元件和LTR反转座元件, 部分转座元件在高A+T含量区富集, 预示着转座元件与基因组序列A+T含量有着紧密联系。根据不同种微孢子虫基因组之间转座元件的差异, 推测在微孢子虫基因组进化过程中, 至少经历了一次转座元件的丢失事件。最后对转座元件在原生动物寄生虫的进一步研究和应用作了展望。     

毛竹微型颠倒重复序列的鉴定及分子标记开发

MITEs(miniature inverted-repeat transposable elements)又称颠倒重复序列,是缺少转座酶序列的非自主型转座子,在真核生物基因组含量丰富,是基因组多态性形成的重要驱动力之一.该研究利用MITE Tracker软件,在毛竹(Phyllostachys edulis)新版基因...     

CRISPR相关转座元件的研究及应用进展

CRISPR-Cas的基因编辑能力引发了人们对该系统的研究热潮。除了实现基因的敲除和插入,CRISPR-Cas系统还可以被应用于基因簇重组、单碱基编辑和基因转录调控,推动了生物工程领域的发展。然而,有限的同源重组效率使CRISPR-Cas系统的应用受到了一定的限制。与CRISPR-Cas系统相比,移动遗传元件(mobile genetic elements,MGE)在转座酶的调控下,不需要依赖同源重组即可将指定DNA片段定向插入到细胞染色体中。近几年,人们发现了具有转座机制的CRISPR相关的转座元件,它可以介导DNA靶向整合,同时其出色的重编程能力为该领域的研究带来了新的发展。本文主要介绍近年来CRISPR-Cas系统相关转座元件的研究方向和应用进展,以及人工融合的dCas9-transposase系统的应用策略。文中还提出了CRISPR相关转座元件未来的应用前景和潜在挑战,为基因编辑工具的发展方向提供了参考意见。     

可转座基因与植物基因组多样性

高等植物基因组含有大量各式各样的串联重复序列和出现频率很高的散布重复序列,如转座子、反转座子、短散布核元件和一些新发现的小型转座子等,它们当中的大多数是具有移动能力的可转座基因.这些可转座基因在漫长的进化过程中对基因和基因组多样性的形成所起的作用,成为近年来分子生物学领域中的重要研究内容.     

植物中活性MITEs转座子研究进展

MITEs(Miniature inverted-repeat transposable elements)转座子是一种特殊的转座子,其既有DNA转座子的转座特性——"剪切-粘贴"转座方式,又有RNA转座子的高拷贝特性。目前已被报道的MITEs种类和数量虽然很多,但是关于有转座活性的MITEs的报道却甚少。本文总结了近几年来有关活性MITEs的相关报道,发现具有转座活性的MITEs种类大都分布在Tourist家族,分别是m Ping、m Ging、Ph Tourist1、Tmi1和Ph Tst-3,另外还有Stowaway-like家族的d Tstu1和MITE-39以及Mutator家族的Ah MITE1。文中还分析了这些活性MITEs的结构(TIR和TSD)、拷贝数、进化模式以及转座特性等,为鉴定其他活性MITEs以及MITEs转座和扩增机制的研究奠定了基础。     

转座元件mariner

自mariner转座元件在Drosophila mauritiana中首次发现至今已经在包括人类在内的多种生物体中证实了mariner及类mariner元件（MLEs）的存在。MLEs属于mariner/Tc1超家族-II型转座元件中分布最广、种类最多的超家族之一。MLEs的转座酶都具有“D,D(34)D”的结构,并能催化MLEs通过“剪切和粘贴”机制进行转座。它们的宿主广泛和多样,能够进行种系传递,这都表明MLEs的转座不需要宿主特异元件的参与。 MLEs对多种生物尤其对脊椎动物的成功转化更支持了它们的不依赖宿主的转座机制,而且让人们看到了它们作为转基因载体的巨大潜能。 Abstract: Mariner and mariner-like elements (MLEs) have been found in a wide range of organisms including human since its discovery in Drosophila mauritiana. MLEs belong to the mariner/Tc1 superfamily, one of the most diverse and widespread Class II transposable elements. MLEs have a conserved “D,D(34)D” motif in their transposases and they transpose by cut-and-paste mechanisms. Their extraordinarily wide host range and horizontal transmission in distantly related species indicate that they do not need additional host-specific factors for transposition. The evidence that MLEs could transform a wide variety of organisms especially the vertebrates supported the host-independent mechanism and suggested the availability as a kind of potential transforming vector.     

反向重复结构在抗植物病毒上的研究进展

双链RNA(dsRNA)的形成是启动RNA沉默的关键因子,而插入了反向重复结构的表达载体能有效地转录产生hpRNA,从而能高效启动RNA沉默。分析了反向重复结构构建的特点,综述了近些年利用该结构启动RNA沉默后在抗植物病毒上的研究进展。     

基因重复研究进展

基因复制是基因通过不等交换,反转录转座或由全基因组复制等途径产生一个与原基因相似的基因或碱基序列,它与生物体基因组大小的进化、新基因的起源、物种的分化以及基因抗突变的能力大小等都密切相关。本文综述了复制基因的产生和保留机制、选择作用、分化的途径以及复制基因进化速率等方面的相关研究,揭示了基因复制对于生物进化的重要性,以引起大家对该领域的了解与关注。关键词：基因复制;复制基因;不等交换;反转录转座;全基因组复制     

基于蓝藻全基因组原始数据的转座元件挖掘及组成分析

二代测序技术及全基因组多样性比较是现代生物学及信息科学研究的热点,对基因组中转座元件(Transposable element)的分析已成为基因组比较分析的重要组成部分。目前对于转座元件的种类、数量和组成的挖掘和分析一般是基于完全拼接后的全基因组序列,对在此之前的海量短片段序列后期处理及拼接仍是目前基因组研究的盲点,以转座元件为主的重复序列在拼接过程中也存在着不可避免的拼接误差或丢失,给转座元件系统的分析带来不确定。文章旨在建立一套分析流程,对铜绿微囊藻NIES 843全基因组构建的罗氏(Roche)公司454测序随机模拟原始数据集的转座元件(主要类型为插入序列:Insert sequence,IS)组成进行分析,结果表明,采用对核酸探针扫描后备选序列分成3组,并分设氨基酸检测阈值的方案分析得到的结果较为可靠,结果显示铜绿微囊藻NIES843的蓝藻转座元件占基因组比例的10.38%,归属于14个IS家族,66个IS亚家族。与之前基于完整拼接基因组数据的两套不同分析流程得到的结果相比,在丰度及家族/亚家族组成上无显著差异,在转座元件序列水平上也显示了高比例的相似性序列重叠,证实了本研究流程在基于高通量测序原始数据的转座元件分析方面具可靠性及实用性。     

Glider and Vision: Two New Families of Miniature Inverted-Repeat Transposable Elements in Xenopus Laevis Genome

We have characterised from Xenopus laevis two new short interspersed repetitive elements, we have named Glider and Vision, that belong to the family of miniature inverted-repeat transposable elements (MITEs). Glider was first characterised in an intronic region of the α-tropomyosin (α-TM) gene and database search has revealed the presence of this element in 10 other Xenopus laevis genes. Glider elements are about 150 bp long and for some of them, their terminal inverted repeats are flanked by potential target-site duplications. Evidence for the mobility of Glider element has been provided by the presence/absence of one element at corresponding location in duplicated α-TM genes. Vision element has been identified in the promoter region of the cyclin dependant kinase 2 gene (cdk2) where it is boxed in a Glider element. Vision is 284 bp long and is framed by 14-bp terminal inverted repeats that are flanked by 7-bp direct repeats. We have estimated that there are about 20,000 and 300 copies of Glider and Vision respectively scattered throughout the laevis genome. Every MITEs elements but two described in our study are found either in 5′ or in 3′ regulatory regions of genes suggesting a potential role in gene regulation. This revised version was published online in August 2006 with corrections to the Cover Date.     

沉默抑制子CMV 2b基因的克隆及其反向重复植物表达载体的构建

从安徽亳州采集表现明显CMV症状的烟草样本,取ELISA检测阳性反应最强的样本提取总RNA。设计特异性引物扩增CMV RNA2部分片段,克隆并测序。其中包含的2b基因全长336个核苷酸,编码111个氨基酸。将来源于安徽烟草的CMV 2b基因与其它CMV 2b基因进行序列比对,结果表明,来源于安徽烟草的CMV 2b基因与来源于韩国的2b基因AF033667的核苷酸序列相似性最高,达98.8%。构建2b基因系统关系树,也表明来源于安徽烟草的CMV 2b基因与AF033667亲缘关系最近。以安徽CMV 2b为模板,分别扩增大小约为300 bp的正向片段CMV 2b（r）和反向片段CMV 2b（i）。先后将反向片段CMV 2b（i）和正向片段CMV 2b（r）分别插入载体pSK-In所含intron两侧,获得重组质粒pSK-2b（r）-In-2b（i）。再将含intron的正反向片段插入pBIN438,最终得到含CMV 2b部分序列反向重复的植物表达载体pBIN-2b（r）-In-2b（i）。     

果蝇P转座因子的研究进展

果蝇P因子是DNA转座子,在近几十年里受到很大关注。可用于确认有关基因,克隆基因以及安置基因回到基因组。P因子的高易动性及其保持和对内部序列强烈的修饰作用也是P因子的本质特征。P因子的另一重要用途是用于产生转基因果蝇。目的基因置于质粒内P因子中可在转座酶的作用下插入前胚盘胚。携带目的基因的P因子可从质粒转座到任意染色体上。据报道,在典型实验中,插入可育果蝇的10％～20％可产生转化体后裔。但是以这种可动DNA片段作为载体尚存在转移基因的不稳定性及与内源跳跃基因的相互影响。本文介绍了果蝇P转座因子的一些研究进展。这些因子的遗传可动性也使它们适用于建造载体产生转基因生物。若如此,载体导入外源基因组的遗传稳定性问题将是一个重要课题。 Abstract：P elements in D.melanogaster are DNA transposons and received greater attention within the last few decades.P elements are used for identifying genes of interest,for cloning them,and for placing them back into the genome.The high mobility of P elements and their retention of this mobility and drastic modiffications to their internal sequences are also essential features.Another most important use of P elements is that of making transgenic flies.Desired gene is placed between P-element ends,usually within a plasmid,and injected into preblastoderm embryos in the presence of transposase.This P element then transposes from the plasmid to a random chromosomal site.Reported in a typical experiment,10％～20％ of the fertile injected flies produce transformant progeny.But the instability of the transferred gene carried on a piece of mobile DNA as a vector and its interaction with endogenous jumping genes.This paper introduced the studies advances of P transposable element in Drosophila.The genetic mobility of these elements can also make them suitable for the construction of vectors to create transgenic organisms.If so,the genetic stability of the vectors introduced to a foreign genome should be a important subject.     

Insertion Preference of Maize and Rice Miniature Inverted Repeat Transposable Elements as Revealed by the Analysis of Nested Elements

A 128-bp insertion into the maize waxy-B2 allele led to the discovery of Tourist, a family of miniature inverted repeat transposable elements (MITEs). As a special category of nonautonomous elements, MITEs are distinguished by their high copy number, small size, and close association with plant genes. In maize, some Tourist elements (named Tourist-Zm) are present as adjacent or nested insertions. To determine whether the formation of multimers is a common feature of MITEs, we performed a more thorough survey, including an estimation of the proportion of multimers, with 30.2 Mb of publicly available rice genome sequence. Among the 6600 MITEs identified, >10% were present as multimers. The proportion of multimers differs for different MITE families. For some MITE families, a high frequency of self-insertions was found. The fact that all 340 multimers are unique indicates that the multimers are not capable of further amplification.     

Plant MITEs: useful tools for plant genetics and genomics

MTTEs (Miniature inverted-repeat transposabie elements) are reminiscence ot non-autonomous DNA (class Ⅱ) elements, which are distinguished from other transposable elements by their small size, short terminal inverted repeats (TIRs), high copy numbers, genie preference, and DNA sequence identity among family members. Although MITEs were first discovered in plants and still actively reshaping genomes, they have been isolated from a wide range of eukaryotic organisms. MITEs can be divided into Tourist-like, Stowaway-like, and pogo-like groups, according to similarities of their TIRs and TSDs (target site duplications). In despite of several models to explain the origin and amplification of MITEs, their mechanisms of transposition and accumulation in eukaryotic genomes remain poorly understood owing to insufficient experimental data. The unique properties of MITEs have been exploited as useful genetic tools for plant genome analysis. Utilization of MITEs as effective and informative genomic markers and pot     

水稻转座子研究进展

转座子是植物基因组的重要组成部分,对于研究植物基因组进化等具有重要意义。随着水稻全基因组测序计划的开展和完成,水稻转座子研究取得了极大进展,目前已经在水稻基因组中发现了几乎所有类型的转座子,约占水稻基因组的35%。在正常情况下,大多数水稻转座子不具有转座活性,但是在特定的条件下（如组织培养或辐射等）,水稻基因组中沉默的转座子可以被激活,从而可能导致插入突变并影响基因的表达。在水稻中已鉴定出6个有活性的转座子,其中Tos17已被应用到水稻功能基因组研究中。转座子序列的新的分子标记转座子展示（transposon display,TD）现已被开发,并在水稻遗传作图和遗传分化研究中得到应用。     

高等植物helitron转座子的研究进展

作为重复序列的一种主要类型,转座子在高等植物基因组中具有相当丰富的DNA含量,在改变基因结构、调节基因表达、影响基因组进化,以及创造新基因的过程中扮演着重要的角色。Helitron转座子是DNA转座子的一种,在转座过程中经常捕获基因或基因片段,以及插入到基因附近或基因内部,因此在改变基因组构成、影响基因组的进化过程以及改变基因型和表型等方面起着重要作用。该文对国内外近年来有关植物基因组中helitron转座子的结构特征、鉴定和分类方法、基因组中的含量和在染色体上的分布,以及转座扩增和基因片段的捕获等方面的研究进展进行了综述,并对helitron转座子研究过程中存在的问题进行了讨论,对今后helitron相关的研究进行了展望。     

Transposable elements and the evolution of genome size in eukaryotes

It is generally accepted that the wide variation in genome size observed among eukaryotic species is more closely correlated with the amount of repetitive DNA than with the number of coding genes. Major types of repetitive DNA include transposable elements, satellite DNAs, simple sequences and tandem repeats, but reliable estimates of the relative contributions of these various types to total genome size have been hard to obtain. With the advent of genome sequencing, such information is starting to become available, but no firm conclusions can yet be made from the limited data currently available. Here, the ways in which transposable elements contribute both directly and indirectly to genome size variation are explored. Limited evidence is provided to support the existence of an approximately linear relationship between total transposable element DNA and genome size. Copy numbers per family are low and globally constrained in small genomes, but vary widely in large genomes. Thus, the partial release of transposable element copy number constraints appears to be a major characteristic of large genomes.     

Transposable Element Distribution in the Yeast Genome Reflects A Role in Repeated Genomic Rearrangement Events on an Evolutionary Time Scale

Statistical analysis of the distribution of transposable elements (TEs) and tRNA genes in the genome of yeast Saccharomyces cerevisiae indicated that, although tRNA genes and other genes transcribed by RNA polymerase III are targets for TE insertion, the distribution of TEs was significantly more clumped than that of tRNAs. Genomic blocks putatively duplicated as the result of an ancient polyploidization event contained fewer TEs than expected by their length, and nearly two thirds of duplicated blocks lacked TEs altogether. In addition, the edges of duplicated blocks tended to be located in TE-poor genomic regions. These results can be explained by the hypotheses: (1) that transposition events have occurred well after block duplication; (2) that TEs have frequently played a role in genomic rearrangement events in yeast. According to this model, duplicated blocks identifiable as such in the present-day yeast genome are found largely in regions with low TE density because in such regions the duplicated structure has not been obscured by TE-mediated rearrangements.