Stoichiometry of the Cre recombinase bound to the lox recombining site.

The site-specific recombinase Cre from bacteriophage P1 binds and carries out recombination at a 34 bp lox site. The lox site consists of two 13 bp inverted repeats, separated by an 8 bp spacer region. Both the palindromic nature of the site and the results of footprinting and band shift experiments suggest that a minimum of two Cre molecules bind to a lox site. We report here experiments that demonstrate the absolute stoichiometry of the Cre-lox complex to be one molecule of Cre bound per inverted repeat, or two molecules per lox site.     

Site-directed integration of the cre gene mediated by Cre recombinase using a combination of mutant lox sites

The Cre-lox system is an important tool for genetic manipulation. To promote integrative reactions, two strategies using mutant lox sites have been developed. One is the left element/right element (LE/RE)-mutant strategy and the other is the cassette exchange strategy using heterospecific lox sites such as lox511 or lox2272. We compared the recombination efficiencies using these mutant lox sites in embryonic stem (ES) cells, and found that the combination of the LE/RE mutant and lox2272 showed high recombination efficiency and stability of the recombined structure. Taking advantage of this stability, we successfully integrated the cre gene into the mutant lox sites by Cre-mediated recombination. Germ line chimeric mice were produced from the cre-integrated ES cell clones, and Cre-expressing mouse lines were established. The inserted cre gene was stably maintained through the generations. This cre knock-in system using the LE/RE-lox2272 combination should be useful for the production of various cre mice for gene targeting or gene trapping.     

A new location to split Cre recombinase for protein fragment complementation

We have previously described a recombinase‐mediated gene stacking system in which the Cre recombinase is used to remove lox‐site flanked DNA no longer needed after each round of Bxb1 integrase‐mediated site‐specific integration. The Cre recombinase can be conveniently introduced by hybridization with a cre‐expressing plant. However, maintaining an efficient cre‐expressing line over many generations can be a problem, as high production of this DNA‐binding protein might interfere with normal chromosome activities. To counter this selection against high Cre activity, we considered a split‐cre approach, in which Cre activity is reconstituted after separate parts of Cre are brought into the same genome by hybridization. To insure that the recombinase‐mediated gene stacking system retains its freedom to operate, we tested for new locations to split Cre into complementing fragments. In this study, we describe testing four new locations for splitting the Cre recombinase for protein fragment complementation and show that the two fragments of Cre split between Lys244 and Asn245 can reconstitute activity that is comparable to that of wild‐type Cre.     

一种新的用于删除选择标记基因的Cre/lox系统

设计了一种新的诱导型Cre/lox系统,并在转基因烟草(Nicotianatabacum L.)中进行了验证.在诱导剂的作用下,位于同向lox位点之间的选择标记基因(hpt)和重组酶基因(Cre)在烟草愈伤组织中被删除.在该系统中,Cre基因在玉米乙酰苯胺类化合物诱导启动子(In5-2)的控制下表达.对转基因后代的分子检测结果表明,不论是否加入了诱导剂,目的基因(gus)均被整合到烟草基因组中;在诱导剂处理的48株转基因烟草To代中,45株的hpt基因被删除了.该系统只使用一个载体,克服了二次转化系统带来的问题.     

一种新的用于删除选择标记基因的Cre／lox系统

设计了一种新的诱导型Cre/lox系统,并在转基因烟草(NicotianatabacumL.)中进行了验证。在诱导剂的作用下,位于同向lox位点之间的选择标记基因(hpt)和重组酶基因(Cre)在烟草愈伤组织中被删除。在该系统中,Cre基因在玉米乙酰苯胺类化合物诱导启动子(In5-2)的控制下表达。对转基因后代的分子检测结果表明,不论是否加入了诱导剂,目的基因(gus)均被整合到烟草基因组中;在诱导剂处理的48株转基因烟草T0代中,45株的hpt基因被删除了。该系统只使用一个载体,克服了二次转化系统带来的问题。     

基于Cre重组酶体系的鸡卵清蛋白基因打靶载体的构建

利用胚胎干细胞基因打靶技术制备转基因鸡是研制鸡输卵管反应器的最佳技术路线。为建立基于Cre/loxp系统的鸡卵清蛋白基因(Ovalbumingene,OV)位点的双交换打靶载体系统,本研究克隆了鸡的OV基因7.8kb片段,并与克隆的内部核糖体进入位点(IRES)、人工合成的含有Cre重组酶识别位点变异体交换盒m2/loxp71EGFPloxp66,一起构建了含有Hsvtk负筛选标记的针对鸡卵清蛋白基因位点的敲入型共表达基因打靶载体pSSCm2/71EGFP66IRESOV7.8;以猪β干扰素基因(βInterferon,IFNβ)为目的基因构建了穿梭载体pMDm2/66MCSIFNMCSLoxp71,经过限制酶酶切及部分测序鉴定,所构建载体结构正确。进一步将它们共转化组成性表达Cre的细菌BM25.8,验证了loxp突变位点对重组反应的有效性     

A new approach for the identification and cloning of genes: the pBACwich system using Cre/lox site-specific recombination

With current plant transformation methods ( Agrobacterium, biolistics and protoplast fusion), insertion of DNA into the genome occurs randomly and in many instances at multiple sites. Associated position effects, copy number differences and multigene interactions can make gene expression experiments difficult to interpret and plant phenotypes less predictable. An alternative approach to random integration of large DNA fragments into plants is to utilize one of several site-specific recombination (SSR) systems, such as Cre/ lox. Cre has been shown in numerous instances to mediate lox site-specific recombination in animal and plant cells. By incorporating the Cre/ lox SSR system into a bacterial artificial chromosome (BAC) vector, a more precise evaluation of large DNA inserts for genetic complementation should be possible. Site-specific insertion of DNA into predefined sites in the genome may eliminate unwanted 'position effects' caused by the random integration of exogenously introduced DNA. In an effort to make the Cre/ lox system an effective tool for site-directed integration of large DNAs, we constructed and tested a new vector potentially capable of integrating large DNA inserts into plant and fungal genomes. In this study, we present the construction of a new BAC vector, pBACwich, for the system and the use of this vector to demonstrate SSR of large DNA inserts (up to 230 kb) into plant and fungal genomes.     

A mutational analysis of the bacteriophage P1 recombinase Cre

Bacteriophage P1 encodes a 38,600 Mr site-specific recombinase, Cre, that is responsible for reciprocal recombination between sites on the P1 DNA called loxP. Using in vitro mutagenesis 67 cre mutants representing a total of 37 unique changes have been characterized. The mutations result in a wide variety of phenotypes as judged by the varying ability of each mutant Cre protein to excise a lacZ gene located between two loxP sites in vivo. Although the mutations are found throughout the entire cre gene, almost half are located near the carboxyl terminus of the protein, suggesting a region critical for recombinase function. DNA binding assays using partially purified mutant proteins indicate that mutations in two widely separated regions of the protein each result in loss of heparin-resistant complexes between Cre and a loxP site. These results suggest that Cre may contain two separate domains, both of which are involved in binding to loxP.     

Sequence of the loxP site determines the order of strand exchange by the Cre recombinase

Conservative site-specific recombinases of the integrase family carry out recombination via a Holliday intermediate. The Cre recombinase, a member of the integrase family, was previously shown to initiate recombination by cleaving and exchanging preferentially on the bottom strand of its loxP target sequence. We have confirmed this strand bias for an intermolecular recombination reaction that used wild-type loxP sites and Cre protein. We have examined the sequence determinants for this strand preference by selectively mutating the two asymmetric scissile base-pairs in the lox site (those immediately adjacent to the sites of cleavage by Cre). We found that the initial strand exchange occurs preferentially next to the scissile G residue. Resolution of the Holliday intermediate thus formed takes place preferentially next to the scissile A residue. Lys86, which contacts the scissile nucleotides in the Cre-lox crystal structures, was important for establishing the strand preference in the resolution of the loxP-Holliday intermediate, but not for the initiation of recombination between loxP sites.     

A test for ectopic exchange catalyzed by Cre recombinase in maize

A maize line expressing Cre recombinase as well as the recipient line without the transgene were assayed for evidence of ectopic recombination within the maize genome. Such a test is valuable for understanding the action of Cre as well as for its use to recombine two target lox sites present in the chromosomes. Pollen examination and seed set tests of material expressing Cre provided no evidence of ectopic recombination, which would be manifested in the production of translocations or inversions and result in pollen abortion and reduced seed set. Root-tip chromosome karyotype analysis was also performed on material with and without Cre expression. Chromosomal aberrations in Cre+ material were not observed above the background level.     

Cre recombinase-mediated inversion using lox66 and lox71: method to introduce conditional point mutations into the CREB-binding protein

CREB-binding protein (CBP) is a multifunctional cofactor implicated in many intracellular signal transduction pathways. We aimed to investigate the involvement of CBP in the cAMP response element-binding protein (CREB)-mediated pathway. The point mutation Tyr658Ala in the CREB-binding domain (CBD) was shown to abolish the binding activity of CBP to phospho-CREB, the activated form of CREB. By using a mutant Cre/loxP recombination system, this point mutation was aimed to be generated in the mouse genome in a tissue- and time-specific manner. A targeting construct in which CBD exon 5 and inverted exon 5* containing the point mutation flanked by two mutant loxP sites (lox66 and lox71) oriented in a head-to-head position was generated. When Cre recombinase is present, the DNA flanked by the two mutant loxP sites is inverted, forming one loxP and one double mutated loxP site. As the double mutated loxP site shows low affinity for Cre recombinase, the favorable reaction leads to a product where the mutated exon 5* is placed into the position to be correctly transcribed and spliced. Inversion was observed to be complete in both bacteria and mouse embryonic stem cells. Our results indicate that this Cre- mediated inversion method is a valuable tool to introduce point mutations in the mouse genome in a regulatable manner.     

Use of an internal ribosome entry site for bicistronic expression of Cre recombinase or rtTA transactivator

Conditional gene targeting depends on tissue and time specificity of recombination events. Endogenous promoters are often used to drive various transgenic constructs. To avoid the problems associated with reconstituting a specific expression pattern in transgenic animals by this method, we tested the internal ribosome entry site of the encephalomyocarditis virus, to enable linkage of the Cre recombinase or rtTA trans-activator to 3' untranslated ends of endogenous genes. Here we report that these constructs function effectively in COS cells. The data suggest that these cassettes will be appropriate for 3' targeting of mouse genes.     

Multiplex Cre/lox recombination permits selective site-specific DNA targeting to both a natural and an engineered site in the yeast genome.

Variant lox sites having an altered spacer region (heterospecific lox sites) are not proficient for Cre-mediated recombination with the canonical 34 bp loxP site, but can recombine with each other. By placing different heterospecific lox sites at different genomic locations, Cre can catalyze independent DNA recombination events at multiple loci in the same cell without concern that unwanted inter-locus recombination events will be generated. Such heterospecific lox sites also allow Cre to specifically target efficient integration of exogenous DNA to endogenous lox-like sequences that naturally occur in the genome. Specific targeting occurs only with a DNA vector carrying a heterospecific lox site in which the spacer region has been redesigned to match the 'spacer' region of the targeted chromosomal element. Moreover, in cells expressing a catalytically active Cre recombinase, naturally occurring lox-like sequences can exhibit almost 20% mitotic recombination. Thus, in the same cell, heterospecific lox sites can be used independently at multiple loci for integration, for deletion and for enhanced mitotic recombination, thereby increasing the repertoire of genomic manipulations catalyzed by the Cre recombinase.     

A functional trait approach to identifying life history patterns in stochastic environments

Temporal variation in demographic processes can greatly impact population dynamics. Perturbations of statistical coefficients that describe demographic rates within matrix models have, for example, revealed that stochastic population growth rates (log(λ_s)) of fast life histories are more sensitive to temporal autocorrelation of environmental conditions than those of slow life histories. Yet, we know little about the mechanisms that drive such patterns. Here, we used a mechanistic, functional trait approach to examine the functional pathways by which a typical fast life history species, the macrodetrivore Orchestia gammarellus, and a typical slow life history species, the reef manta ray Manta alfredi, differ in their sensitivity to environmental autocorrelation if (a) growth and reproduction are described mechanistically by functional traits that adhere to the principle of energy conservation, and if (b) demographic variation is determined by temporal autocorrelation in food conditions. Opposite to previous findings, we found that O. gammarellus log(λ_s) was most sensitive to the frequency of good food conditions, likely because reproduction traits, which directly impact population growth, were most influential to log(λ_s). Manta alfredi log(λ_s) was instead most sensitive to temporal autocorrelation, likely because growth parameters, which impact population growth indirectly, were most influential to log(λ_s). This differential sensitivity to functional traits likely also explains why we found that O. gammarellus mean body size decreased (due to increased reproduction) but M. alfredi mean body size increased (due to increased individual growth) as food conditions became more favorable. Increasing demographic stochasticity under constant food conditions decreased O. gammarellus mean body size and increased log(λ_s) due to increased reproduction, whereas M. alfredi mean body and log(λ_s) decreased, likely due to decreased individual growth. Our findings signify the importance of integrating functional traits into demographic models as this provides mechanistic understanding of how environmental and demographic stochasticity affects population dynamics in stochastic environments.     

Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans

Regulation of pre-mRNA splicing is achieved through the interaction of RNA sequence elements and a variety of RNA-splicing related proteins (splicing factors). The splicing machinery in humans is not yet fully elucidated, partly because splicing factors in humans have not been exhaustively identified. Furthermore, experimental methods for splicing factor identification are time-consuming and lab-intensive. Although many computational methods have been proposed for the identification of RNA-binding proteins, there exists no development that focuses on the identification of RNA-splicing related proteins so far. Therefore, we are motivated to design a method that focuses on the identification of human splicing factors using experimentally verified splicing factors. The investigation of amino acid composition reveals that there are remarkable differences between splicing factors and non-splicing proteins. A support vector machine (SVM) is utilized to construct a predictive model, and the five-fold cross-validation evaluation indicates that the SVM model trained with amino acid composition could provide a promising accuracy (80.22%). Another basic feature, amino acid dipeptide composition, is also examined to yield a similar predictive performance to amino acid composition. In addition, this work presents that the incorporation of evolutionary information and domain information could improve the predictive performance. The constructed models have been demonstrated to effectively classify (73.65% accuracy) an independent data set of human splicing factors. The result of independent testing indicates that in silico identification could be a feasible means of conducting preliminary analyses of splicing factors and significantly reducing the number of potential targets that require further in vivo or in vitro confirmation.     

Identification of the structural and functional domains of the large serine recombinase TnpX from Clostridium perfringens

Members of the large serine resolvase family of site-specific recombinases are responsible for the movement of several mobile genetic elements; however, little is known regarding the structure or function of these proteins. TnpX is a serine recombinase that is responsible for the movement of the chloramphenicol resistance elements of the Tn4451/3 family. We have shown that TnpX binds differentially to its transposon and target sites, suggesting that resolvase-like excision and insertion were two distinct processes. To analyze the structural and functional domains of TnpX and, more specifically, to define the domains involved in protein-DNA and protein-protein interactions, we conducted limited proteolysis studies on the wild-type dimeric TnpX(1-707) protein and its functional truncation mutant, TnpX(1-597). The results showed that TnpX was organized into three major domains: domain I (amino acids (aa) 1-170), which included the resolvase catalytic domain; domain II (aa 170-266); and domain III (aa 267-707), which contained the dimerization region and two separate regions involved in binding to the DNA target. A small polypeptide (aa 533-587) was shown to bind specifically to the TnpX binding sites providing further evidence that it was the primary DNA binding region. In addition, a previously unidentified DNA binding site was shown to be located between residues 583 and 707. Finally, the DNA binding and multerimization but not the catalytic functions of TnpX could be reconstituted by recombining separate polypeptides that contain the N- and C-terminal regions of the protein. These data provide evidence that TnpX has separate catalytic, DNA binding, and multimerization domains.     

A genome-wide approach to identifying novel-imprinted genes

Genomic imprinting is an epigenetic process in which the copy of a gene inherited from one parent (maternal or paternal) is consistently silenced or expressed at a significantly lower level than the copy from the other parent. In an effort to begin a systematic genome-wide screen for imprinted genes, we assayed differential allelic expression (DAE) at 3,877 bi-allelic protein-coding sites located in 2,625 human genes in 67 unrelated individuals using genotyping microarrays. We used the presence of both over- and under-expression of the reference allele compared to the alternate allele to identify candidate-imprinted genes. We found 61 genes with at least twofold DAE plus “flipping” of the more highly expressed allele between reference and alternate across heterozygous samples. Sixteen flipping genes were genotyped and assayed for DAE in an independent data set of lymphoblastoid cell lines from two CEPH pedigrees. We confirmed that PEG10 is paternally expressed, identified one gene (ZNF331) with multiple lines of data indicating it is imprinted, and predicted several additional imprinting candidate genes. Our findings suggest that there are at most several hundred genes in the human genome that are universally imprinted. With samples of mRNA from appropriate tissues and a collection of informative cSNPs, a genome-wide search using this methodology could expand the list of genes that undergo genomic imprinting in a tissue- or temporal-specific manner. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.