Discovery of transposable element activity among progeny of tissue culture--derived maize plants

Tissue culture-derived plants of many species have often been observed to possess both genetic and cytogenetic abnormalities. A high frequency of structurally altered chromosomes in maize (Zea mays L.) plants regenerated from tissue culture led to the prediction that newly activated transposable elements could be detected in regenerated plants. Testcrosses of 1200 progeny from 301 regenerated maize plants confirmed that ten regenerated plants from two independent embryo cell lines contained an active Actransposable element. No active Ac elements were present in the explant sources. Recovery of transposable element activity in regenerated plants indicates that some tissue culture-derived genetic variability may be the result of insertion or excision of transposable elements, or both.     

Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila

To study adaptation, it is essential to identify multiple adaptive mutations and to characterize their molecular, phenotypic, selective, and ecological consequences. Here we describe a genomic screen for adaptive insertions of transposable elements in Drosophila. Using a pilot application of this screen, we have identified an adaptive transposable element insertion, which truncates a gene and apparently generates a functional protein in the process. The insertion of this transposable element confers increased resistance to an organophosphate pesticide and has spread in D. melanogaster recently.     

The origins of gene instability in yeast

Two unstable mutations at the his4 locus of yeast are due to the insertion of the transposable elements Ty912 and Ty917 into the his4 regulatory region. The two transposons are related, one being derived from the other by a substitution of 4000 base pairs of DNA. Element Ty912 includes identical terminal repeats, whereas the terminal repeats of Ty917 are not identical. Transposition of Ty912 or Ty917 generates 5-base-pair duplications of the target DNA at either end of the element. Expression and reversion of a his4 gene containing Ty912 or Ty917 is controlled by three unlinked regulatory genes. The properties of these regulatory genes are similar to those described for the controlling elements in maize.     

A single genetic unit specifies two transposition functions in the maize element activator

The self-mobile maize transposable element Ac (Activator) displays two trans-acting genetic functions: it induces transposition of the element Ds (Dissociation) but, as its dosage is increased, it also inhibits transposition. Previous work has shown that the 4563 base pair (bp)-long Ac element contains three open reading frames (ORF's) and that a deletion in ORF 1 in wx-m9(Ds), a Ds derivative from Ac isolated at the wx (waxy) locus, results in loss of transposition. The Ds element in the bronze allele bz-m2(DI) is shown to have arisen from Ac by a 1312-bp deletion that is located almost entirely within ORF 2 and does not affect ORF 1. The Ds elements in wx-m9(Ds) and bzm2(DI), defective in ORF 1 and ORF 2, respectively, do not complement genetically to restore the transposition function of Ac; therefore, this function must be specified jointly by ORF's 1 and 2. Furthermore, since bz-m2(DI) does not contribute to Ac's inhibitory dosage effect, both Ac properties result from the expression of the same genetic functional unit.     

Heritable somatic excision of a Drosophila transposon

A mutation in the white gene of Drosophila mauritiana that results from insertion of the transposable element mariner is genetically unstable in both germ cells and somatic cells. Somatic instability is indicated by the occurrence of animals having mosaic eyes with patches of pigmented cells on a peach-colored background. Normally uncommon, the frequency of mosaicism is so greatly enhanced in a particular mutant strain that virtually every animal in the strain is an eye-color mosaic. The molecular basis of the mosaicism is the excision of the mariner element from its location in the DNA of the white gene in somatic cells. The phenomenon results from a single dominant genetic factor located in chromosome 3. Genetic control over the excision of transposable elements may play a role in determining the persistence of transposable elements in the genome.     

122份栽培桃品种（系）黄白肉性状的分子标记辅助鉴定

【目的】 类胡萝卜素裂解双脱氧酶基因（Carotenoid Cleavage Dioxygenases 4,CCD4）控制桃果肉颜色（白/黄）,CCD4存在3种等位基因。本研究利用Indel、SSR荧光标记毛细管电泳及SNP鉴定等基因分型技术分析我国主要桃黄白肉品种（系）中CCD4等位基因的差异,为主要黄/白肉品种（系）的基因型鉴定、亲本选配和选择相应的分子标记对不同来源子代的果肉颜色进行鉴定奠定基础。【方法】利用已经报道的桃不同果肉颜色中CCD4等位基因3种突变类型,合成不同引物进行PCR扩增,LTR反转录转座子插入突变经1%的琼脂糖凝胶电泳检测,CT单元重复的PCR产物在ABI3730XL测序仪上进行SSR荧光标记毛细管电泳检测,SNP标记经Sanger测序后利用ContigExpress软件分析CCD4等位基因的碱基替换（A→T）。综合以上结果,统计每份材料中CCD4等位基因的突变类型与果肉颜色的一致性。【结果】通过对不同来源的122份桃品种（系）材料进行基因型分析,发现CCD4发生LTR反转录转座子插入突变材料的基因型共有31份,占总材料的25.4%,其中纯合插入突变材料的片段扩增长度为729 bp,共有8份,占总突变的25.8%;CCD4发生微卫星重复序列突变材料存在2 bp的插入,扩增片段长度为179 bp,该类型共有68份,占总材料的55.7%,其中纯合插入材料25份,占总突变的36.8%;CCD4发生A→T碱基替换突变的材料较少,仅有1份,占总材料的0.82%,实际应用中可以不考虑该种类型。CT和LTR插入的两种突变类型的黄肉品种（系）有7份,占总材料的5.7%。研究结果表明,LTR反转录转座子插入突变和微卫星序列重复突变是黄肉桃中CCD4等位基因的主要突变类型。其中CCD4发生一种纯合突变或两种杂合突变桃品种（系）为黄肉类型,分子标记鉴定结果与调查的122份桃品种（系）黄白肉表型性状完全一致,准确率为100%。【结论】采用分子标记明确了122个桃品种（系）黄/白肉性状的基因型,为不同亲本组合子代表型鉴定的标记类型选择提供了技术支撑,为建立桃种质材料黄/白性状的分子辅助育种体系和黄肉桃的选育奠定了基础。     

Temperature effects on the rate of ty transposition

An assay has been developed to measure the rate of transposition of the transposable element Ty in Saccharomyces cerevisiae. The assay is based on the altered expression of the glucose-repressible alcohol dehydrogenase gene of yeast upon insertion of a Ty in front of this gene. By this assay the transposition rate of Ty elements was found to increase approximately 100-fold at temperatures lower than 30 degrees C, the optimum growth temperature for Saccharomyces cerevisiae.     

Isolating the Mutator Transposable Element Insertional Mutant Gene mio16 of Maize Using Double Selected Amplification of Insertion Flanking Fragments (DSAIFF)

Mutator transposable element (Mu) has been used as an effective tool to clone maize (Zea mays L.) genes. One opaque endosperm mutant (mio16) was identified in a pool of Mu inserted mutants. A modified method, termed the double selected amplification of insertion flanking fragments (DSAIFF), was employed to isolate the Mu flanking fragments (MFFs) of mio16. The target site duplications (TSDs) isolated from the Msp I and Mse I digested MFFs had a same 9-bp sequence and were confirmed to be the flanking sequence of one identically inserted gene. Co-segregation analysis suggested that the MFFs were associated with the mutant opaque endosperm, and mio16 was mapped in silico onto the physical position ranged from 229 965 021 to 229 965 409 bp of the maize chromosome 4.09 bin. The full-length cDNA of the wild-type gene was obtained by an RT-PCR primer-scanning technique, and Mio16 was found to putatively encode a homolog of the Arabidopsis MAP3K delta-1 protein kinase. RT-PCR result the mRNA expression of mio16 region anchored by primers Mu20 and af276 was not interrupted by Mu insertion. Further researches will be done to elucidate how the expression of mio16 is alternated by Mu insertion.     

Insertional mutagenesis of the Drosophila genome with single P elements

A versatile genetic method for identifying and cloning Drosophila melanogaster genes affecting any recognizable phenotype is described. Strains are constructed in which the insertion of a single P transposable element has caused a new mutation, greatly simplifying the genetic and molecular analysis of the affected gene. Mutagenesis is initiated by crossing two strains, each of which contains a specially designed P element. One element (jumpstarter), encoding P element transposase, efficiently mobilizes the second nonautonomous transposon (mutator), whose structure facilitates selection and cloning of new insertion mutations. Random mutator transpositions are captured in individual stocks that no longer contain jumpstarter, where they remain stable. This method was used to construct 1300 single P element insertion stocks which were then screened for recessive mutations. A library of single-element insertion strains will allow the structure and function of Drosophila genes to be readily correlated, and should have many other applications in Drosophila molecular genetics.     

植物水平基因转移研究进展

水平基因转移,一般分为细胞内部或者跨越物种边界的遗传物质交流。跨界直接介导方式,包括共生、内共生、寄生、嫁接等。细胞内的基因转移,主要包括细胞核与细胞器基因组间的相互渗透;跨越物种边界的遗传物质交流,主要涉及寄生与寄主植物的基因横向转移,寄主与寄生植物mRNA也会发生大规模的水平转移。基于基因组学研究进展,本研究综述了植物水平基因转移的迁移序列类型、迁移方向及迁移机制:首先,植物细胞的线粒体基因组能够整合细胞核转座元件以及叶绿体起源的tRNA基因,线粒体和叶绿体基因组的功能基因及间区序列能够迁移到核基因组;其次,植物种间,通过寄生、嫁接等方式转移大量的DNA(如线粒体基因、叶绿体基因和转座元件)和RNA(如mRNA)序列;迁移机制涉及到DNA介导和RNA介导方式,迁移方向包括单向和双向转移。迁移序列的基因功能活性研究是重要的后续研究方向。     

Hybrid dysgenesis in D. melanogaster is not a general release mechanism for DNA transpositions

Many spontaneous mutations are caused by the insertion or excision of DNA elements. Since most mutations are deleterious, evolution should favor a mechanism for genetically controlling the rate of movement of transposable elements in most, if not all, organisms. In Drosophila melanogaster a syndrome of correlated genetic changes, including mutation, chromosome breakage, and sterility, is observed in the hybrid progeny of crosses between different strains. This syndrome, which is termed hybrid dysgenesis, results from the movement of P-DNA elements. What is not clear is whether the movement of other types of transposable elements is under the same coordinated control. In this study the ability of hybrid dysgenesis to increase the rate of excision of 12 DNA elements at 16 mutant alleles and to induce insertion-bearing mutations to change to other mutant states was tested. The data show that hybrid dysgenesis caused by P-element transpositions does not act as a general stimulus for the movement of other Drosophila transposable elements.     

麦克林托克转座因子理论建立的哲学思考

对麦克林托克发现及创立转座因子理论的过程进行了阐述和哲学分析。转座因子的创立是知识继承与创新相统一的结果,是收敛式思维和发散式思维相平衡的产物;对偶然现象的非逻辑思维是自然认知的突破点。     

牛亚科物种转座子与串联重复序列之间的进化关系

【目的】重复序列是真核生物基因组中重要组成部分,对物种进化、基因遗传变异、转录调控等具有重要作用。研究旨在揭示牛亚科物种重复序列特征,研究转座子和串联重复序列间的进化关系,为牛亚科物种重复序列的研究提供理论支撑。【方法】以普通牛、瘤牛、牦牛、水牛、野牛以及大额牛6个牛亚科物种的基因组序列为研究对象,利用TRF和RepeatMasker软件对6个牛亚科物种基因组中的串联重复序列（tandem repeats sequence,TRs）和转座子（transposable elements,TEs）进行鉴定,并通过本地BLAST比对,分析两类重复序列间的相似性,单位点（single-locus TRs, slTRs）和多位点串联重复序列（mutiple-locus TRs, mlTRs）以及转座子内部的串联重复特征。【结果】（1）6个牛亚科物种中,重复序列在普通牛中的比例最高,为49.13%,其次为水牛46.82%、大额牛46.66%、瘤牛42.70%、野牛42.36%、牦牛42.34%;其中转座子在基因组中的比例为40.57%—45.71%,高于串联重复序列的比例（1.50%—3.42%）。（2）串联重复序列中,mlTRs的比例（76%—99%）显著高于slTRs（1%—24%）,表明mlTRs为6个牛亚科物种中串联重复序列的主要组成。（3）TE-derieved的串联重复序列分析表明,TRs中43%—84%的序列来源于转座子,其中多位点串联重复序列可高达94%。（4）TRs-related 转座子及其活性分析表明,与TRs具有相似性的转座子主要来自非长末端重复序列（non-Long Terminal Repeats, non-LTR）,包括SINE（Short Interspersed Nuclear Element, SINE）和长末端重复序列（Long Interspersed Nuclear Element, LINE）,其中SINE/Core-RTE（主要为BOV-A2）的数量（14 423—24 193）和相对丰度（4.06%—6.77%）最高,被认为是牛亚科物种中最年轻且最具活力的转座子。（5）转座子的串联重复特征分析表明,BovB在0—600 bp,L1_BT在1 500—2 700 bp的序列分别发生了大量的串联重复,与consensus序列的一致性分别达93%和87%以上,且两段区域均为非编码区。【结论】重复序列在牛亚科物种中具有相似的分布特征, non-LTR是牛亚科物种TRs-related TEs的重要来源,且SINE/Core-RTE（主要为BOV-A2）为牛亚科物种最年轻且最具活力的转座子;同时串联重复序列又可作为转座子内部结构的组成部分,表明串联重复序列与转座子在基因组的进化过程相互影响、相互作用。     

Waxy allele diversity in waxy maize landraces of Yunnan Province,China

Waxy maize is one of the main fresh-eating maize types, and a mutation of the waxy gene causes the waxy character of maize grains.  China is rich in waxy maize landraces, and Yunnan and its surrounding areas, are the place of origin and genetic diversity center of Chinese waxy maize.  The six known waxy alleles of Chinese waxy maize are wx-D7, wx-D10, wx-Cin4, wx-124, wx-Reina, and wx-Xuanwei.  The mutation sites of these alleles all occur in the coding region of the waxy gene, however, the mechanism by which the waxy characteristic is caused by the mutation in the regulatory region has only been reported rarely in maize.  In this study, 405 waxy maize landraces from Yunnan were used as materials to identify the insertion and deletion of a large sequence fragment in the upstream ~3.5 kb regulatory region of the waxy gene by molecular marker detection.  Three different waxy alleles were identifed in this study: wx-PIF/Harbinger, wx-hAT and wxElote2.  These three types of mutations all represented transposons inserted into the regulatory region of the waxy gene.  Wx-PIF/Harbinger was a 304-bp MITE class transposon insertion belonging to the PIF/Harbinger family, while wx-hAT was a 560-bp MITE class transposon insertion belonging to the hAT family, and wx-Elote2 was a 6 560-bp LTR-like transposon insertion.  In this study, the alleles were identifed for more than 70% of the waxy maize landraces in Yunnan, which provids a basis for the utilization of these waxy maize landraces.     

Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome

The completion of the draft sequence of the rhesus macaque genome allowed us to study the genomic composition and evolution of transposable elements in this representative of the Old World monkey lineage, a group of diverse primates closely related to humans. The L1 family of long interspersed elements appears to have evolved as a single lineage, and Alu elements have evolved into four currently active lineages. We also found evidence of elevated horizontal transmissions of retroviruses and the absence of DNA transposon activity in the Old World monkey lineage. In addition, approximately 100 precursors of composite SVA (short interspersed element, variable number of tandem repeat, and Alu) elements were identified, with the majority being shared by the common ancestor of humans and rhesus macaques. Mobile elements compose roughly 50% of primate genomes, and our findings illustrate their diversity and strong influence on genome evolution between closely related species.     

Regulation of the timing of transposable element excision during maize development

The ability of transposable elements (TEs) to insert into or excise out of a genetic locus can be regulated by genetic, environmental, and developmental factors. Tissue- or organ-specific activity of TEs is a frequent and well-characterized example of spatial, developmental regulation. Regulation of the timing of TE activity during ontogeny is less well understood. To analyze timing, TE-induced variegation was quantified in the aleurone of maize kernels, a tissue composed of only a single layer of cells, and sector sizes were assigned to specific cell divisions in aleurone development. Three TE families, Mu, Spm, and Ac/Ds, were studied at two genetic loci. It was found that the frequency of transposon excision changes drastically (up to 30-fold increase or equivalent decrease) during the proliferation of the aleurone. Moreover, these changes occur at the same cell divisions in all three TE families. These results suggest that the timing of TE excision during maize development can be controlled by the host.