How selfish retrotransposons are silenced in Drosophila germline and somatic cells

Transposable elements (TEs) are DNA elements found in the genomes of various organisms. TEs have been highly conserved during evolution, suggesting that they confer advantageous effects to their hosts. However, due to their ability to transpose into virtually any locus, TEs have the ability to generate deleterious mutations in the host genome. In response, a variety of different mechanisms have evolved to mitigate their activities. A main defense mechanism is RNA silencing, which is a gene silencing mechanism triggered by small RNAs. In this review, we address RNA silencing mechanisms that silence retrotransposons, a subset of TEs, and discuss how germline and somatic cells are equipped with different retrotransposon silencing mechanisms.     

小RNAs在沉默转座因子中的作用

在很多生物基因组中都存在DNA成分的转座序列,它们能够转座到基因组的很多位点,对基因组造成很大的危害,如破坏编码基因、改变基因表达的调节网络、使染色体断裂或造成大范围基因重排等。真核生物已经进化出了多种机制来控制这些寄生核酸序列造成的损伤,以维持基因组完整性。虽然这些机制在不同生物中有些差异,但其中一种主要的机制是通过小RNAs介导的,这些小RNAs包括小干扰RNAs、piwi相互作用的小RNAs、微小RNAs、扫描RNAs和21U-RNAs等。这些小RNAs可以通过DNA水平剪切转座序列,或在转录和(或)转录后水平沉默转座成分。该文就这些小RNAs沉默转座成分的机制和功能做一论述。     

Mutator超家族转座子研究进展

转座子是一类可以在基因组中不同遗传位点间移动的DNA序列,在其转移过程中有时会伴随自身拷贝数的增加。作为基因组的重要组成部分,转座子可以通过多种方式影响宿主基因及基因组的结构与功能,进而在宿主的演化过程中扮演重要角色。目前依据转座过程中间体类型的不同可以将其分为I类转座子和II类转座子。Mutator超家族转座子是20世纪70年代在玉米(Zea may L.)中发现的一类特殊的转座子,其属于II类转座子,广泛存在于真核生物基因组中,包含遗传特征明晰可分的众多转座子家族。此外,该超家族转座子转座频率高,倾向于插入基因富含区及低拷贝序列区,可快速产生大量新的突变体,目前已被广泛应用于正向及反向遗传学研究。本文结合近年来相关研究结果,围绕Mutator超家族转座子的分类组成、结构特征、转座机制、插入偏好、靶位点重复序列以及玉米自主性MULEs元件展开综述,并对转座子研究面临的问题及未来研究方向进行了探讨,旨在与研究领域内的同行探讨相关研究的可能突破点、未来发展方向及可能产生的重大影响。     

The use of a non-LTR element to date the formation of the Sdic gene cluster

Transposable elements comprise a considerable part of eukaryotic genomes, and there is increasing evidence for their role in the evolution of genomes. The number of active transposable elements present in the host genome at any given time is probably small relative to the number of elements that no longer transpose. The elements that have lost the ability to transpose tend to evolve neutrally. For example, non-LTR retrotransposons often become 5′ truncated due to their own transposition mechanism and hence lose their ability to transpose. The resulting transposons can be characterized as “dead-on-arrival” (DOA) elements. Because they are abundant and ubiquitous, and evolve neutrally in the location where they were inserted, these DOA non-LTR elements make a useful tool to date molecular events. There are four copies of a “dead-on-arrival” RT1C element on the recently formed Sdic gene cluster of Drosophila melanogaster, that are not present in the equivalent region of the other species of the melanogaster subgroup. The life history of the RT1C elements in the genome of D. melanogaster was used to determine the insertion chronology of the elements in the cluster and to date the duplication events that originated this cluster.     

Structural organization of the genes encoding the small nuclear RNAs U1 to U6 of Tetrahymena thermophila is very similar to that of plant small nuclear RNA genes.

We report the sequences of the genes encoding the small nuclear RNAs (snRNAs) U1 to U6 of the ciliate Tetrahymena thermophila. The genes of the individual snRNAs exist in two to six slightly different copies per haploid genome. Sequence analyses of the gene-flanking regions indicate that there are two classes of snRNA genes. Both classes are characterized by several conserved sequence elements, some of which are unique to each class and some of which are found in both classes. Comparison of the promoter structure of the snRNA genes of T. thermophila with the promoter structures of snRNA genes of other organisms revealed several similarities to plant snRNA genes. These similarities include the overall promoter architecture as well as specific sequence elements. The structural organization of the 3' flanking region of some of the T. thermophila snRNA genes is not observed in other organisms. This finding is discussed in relation to a possible role in snRNA 3'-end formation.     

The bacteriophage Mu transposase protein can form high-affinity protein-DNA complexes with the ends of transposable elements of the Tn 3 family

The 37 kb transposable bacteriophage Mu genome encodes a transposase protein which can recognize and bind to a consensus sequence repeated three times at each extremity of its genome. A subset of this consensus sequence (5'-PuCGAAA(A)-3') is found in the ends of many class II prokaryotic transposable elements. These elements, like phage Mu, cause 5 bp duplications at the site of element insertion, and transpose by a cointegrate mechanism. Using the band retardation assay, we have found that crude protein extracts containing overexpressed Mu transposase can form high-affinity protein-DNA complexes with Mu att R and the ends of the class II elements Tn 3 (right) and IS101. No significant protein-DNA complex formation was observed with DNA fragments containing the right end of the element IS102, or a non-specific pBR322 fragment of similar size. These results suggest that the Mu transposase protein can specifically recognize the ends of other class II transposable elements and that these elements may be evolutionarily related.     

Transposition of a bacterial insertion sequence in chloroplasts

Bacterial transposable elements (IS elements, transposons) represent an important determinant of genome structure and dynamics, and are a major force driving genome evolution. Here, we have tested whether bacterial insertion sequences (IS elements) can transpose in a prokaryotic compartment of the plant cell, the plastid (chloroplast). Using plastid transformation, we have integrated different versions of the Escherichia coli IS element IS 150 into the plastid genome of tobacco ( Nicotiana tabacum ) plants. We show that IS 150 is faithfully mobilized inside the chloroplast, and that enormous quantities of transposition intermediates accumulate. As synthesis of the IS 150 transposase is dependent upon programmed ribosomal frame shifting, our data indicate that this process also occurs in chloroplasts. Interestingly, all insertion events detected affect a single site in the plastid genome, suggesting that the integration of IS 150 is highly sequence dependent. In contrast, the initiation of the transposition process was found to be independent of the sequence context. Finally, our data also demonstrate that plastids lack the capacity to repair double-strand breaks in their genomes by non-homologous end joining, a finding that has important implications for genome stability, and which may explain the peculiar immunity of the plastid to invading promiscuous DNA sequences of nuclear and mitochondrial origin.     

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.     

Repetitive elements in genomes of parasitic protozoa.

Repetitive DNA elements have been a part of the genomic fauna of eukaryotes perhaps since their very beginnings. Millions of years of coevolution have given repeats central roles in chromosome maintenance and genetic modulation. Here we review the genomes of parasitic protozoa in the context of the current understanding of repetitive elements. Particular reference is made to repeats in five medically important species with ongoing or completed genome sequencing projects: Plasmodium falciparum, Leishmania major, Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia. These organisms are used to illustrate five thematic classes of repeats with different structures and genomic locations. We discuss how these repeat classes may interact with parasitic life-style and also how they can be used as experimental tools. The story which emerges is one of opportunism and upheaval which have been employed to add genetic diversity and genomic flexibility.     

Fungal transposable elements and genome evolution

The transposable elements (TEs) identified in fungal genomes reflect the whole spectrum of eukaryotic transposable elements. Most of our knowledge comes from species representing different ecological situations: plant pathogens, industrial, and field strains, most of them lacking the sexual stage. A number of changes in gene structure and function has been shown to be TE-mediated: inactivation of gene expression upon insertion within or adjacent to a gene, DNA sequence variation through excision and probably extensive chromosomal rearrangements due to recombination between members of a particular family. Moreover, TEs may have other roles in evolution related to their ability to be horizontally transferred and to capture and transpose chromosomal host sequences, thus providing a mechanism for dispersing sequences to new sites. However, the activity of transposable elements and consequently their proliferation within a host genome can be affected, in some fungal species which undergo meiosis, by silencing processes. Our understanding of the biological effects of TEs on the fungal genome has increased dramatically in the past few years but elucidation of the extent to which transposons contribute to genetic variation in nature, providing the flexibility for populations to adapt successfully to environmental changes is an important area for future research. This revised version was published online in August 2006 with corrections to the Cover Date.     

Progress in Plant CACTA Elements

Transposable elements are DNA fragments that can insert new chromosomal locations. On the basis of the mechanism of transposition, transposable elements were divided into two classes. Class 1 elements were retroelements that used reverse transposase to transpose by an RNA intermediate. Class 2 elements or DNA transposons transposed directly from DNA to DNA. Of the Class 2 elements, CACTA superfamily, so far identified exclusively in plants and previously regarded as low-copy-transposon for the conserved mechanism of propagation, recently received considerable interest because of their increasing evidence reiterating their high copies in some plant genomes. This article aimed at outlining CACTA elements with regard to their structure, transposition, and utilization.     

植物CACTA转座子的研究进展

转座子是染色体上可移动的DNA序列,根据转座机制可将其分为：通过RNA中间体进行转座的逆转录座子（Retrotransposon）和通过DNA中间体进行转座的转座子（Transposon）。En／Spm家族转座子是后者中的一类,它的末端反向重复序列（Terminal inverted repeats,TIRs）具有保守的5个碱基CACTA,所以通常又称为CACTA转座子。除此之外,其靶位点一般为3bp的同向重复（Target site duplication,TSD）;亚末端区域分布着若干正向或反向的重复序列（Subterminal repeat,STR）。迄今为止,CACTA转座子仅发现于植物基因组。过去一直认为由于其相对保守的转座机制而拷贝较少,但最近研究发现,该因子多拷贝存在于某些禾本科植物基因组中。由于该家族在基因组中分布的广泛性,具有用作分子指纹的应用前景。本文就其结构、转座机制和应用前景等做一综述。     

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。