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Trapping Genes

In the Literature.

Here GNN posts abstracts to articles related to the feature story Building a Better Gene Trap.


Gene trap integrations expressed in the developing heart: insertion site affects splicing of the PT1-ATG vector.

We describe the characterisation of three gene trap integrations in embryonic stem cells in which the lacZ reporter gene is repressed by retinoic acid (RA) in vitro and is expressed in the developing heart in vivo. In one of these, the gene trap vector has integrated into a gene that is located on chromosome 17 and is homologous to the human transcription factor gene, TFEB. Embryonic and adult cardiac expression of both the fusion transcript and the endogenous gene was confirmed. However, we show that the integration has not resulted in a null allele, because wild type transcripts, possibly resulting from splicing around the vector, are observed in homozygous tissue. The other two cardiac-expressing gene trap integrations have occurred into exons on chromosomes 1 and 5 and have used cryptic donor sites within the vector to generate functional fusion transcripts. One of these exon integrations results in a lethal neonatal phenotype.

Dev Dyn 1998 Jun;212(2):267-76.

Gene trap insertion into a novel gene expressed during mouse limb development.

Gene trapping is a useful method to identify new genes involved in development. Here we describe the spatiotemporal expression of a gene identified in a gene-trap screen. This gene is first expressed at 9.5 days postcoitum (E9.5) in the forelimbs and in the branchial arches region. At E11.5, expression was detected in the stomach, genital bud, and pharyngeal epithelium. At later stages, expression includes the hair follicles, whereas the expression in the stomach and pharynx disappears. We performed 5'-rapid amplification of cDNA ends (RACE) to amplify and clone a partial cDNA of the endogenous sequence fused to the lacZ reporter gene. The sequence did not reveal any similarity to known sequences and was named paddy. The expression pattern suggests multiple roles during limb development. The early phase of expression, for instance, correlates with anteroposterior (A/P) regionalization. In contrast to other molecules involved in A/P polarization, paddy expression fades away distally as the bud elongates. This suggests that expression of paddy in late stages does not depend on apical ectodermal ridge (AER) and zone of polarizing activity (ZPA) signaling and is probably involved in posterior determination in more proximal regions of the limb.

Dev Dyn 1998 Jun;212(2):318-25.

Rapid sequence analysis of gene trap integrations to generate a resource of insertional mutations in mice.

Gene trapping in murine embryonic stem cells is a proven method for the simultaneous identification and mutation of genes in the mouse. Gene trap vectors are designed to detect insertions within genes through the production of a fusion mRNA transcript, making the identification of the endogenous gene possible by 5' rapid amplification of cDNA ends (RACE). Although the amplification of specific cDNAs can be achieved rapidly, cloning and screening of informative-sized cDNAs has proven to be time consuming. To eliminate the need for cloning, we have developed a method for solid-phase sequencing of 5' RACE products. More than 150 independent gene trap cell lines were analyzed, and sequence information was obtained for every line successfully amplified by RACE. With the vector used in this study, 40% of the cell lines were found to contain properly spliced gene trap events. The remaining lines were either spliced inefficiently or contained deletions of the vector. These results highlight the advantage of sequencing gene trap integrations before further characterization. This work now paves the way for large-scale gene trap screens in mice and should greatly acGNNte the functional analysis of the mammalian genome.

Genome Res 1997 Mar;7(3):293-8.

Capturing genes encoding membrane and secreted proteins important for mouse development.

A strategy based on the gene trap was developed to prescreen mouse embryonic stem cells for insertional mutations in genes encoding secreted and membrane-spanning proteins. The "secretory trap" relies on capturing the N-terminal signal sequence of an endogenous gene to generate an active beta-galactosidase fusion protein. Insertions were found in a cadherin gene, an unc6-related laminin (netrin) gene, the sek receptor tyrosine kinase gene, and genes encoding two receptor-linked protein-tyrosine phosphatases, LAR and PTP kappa. Analysis of homozygous mice carrying insertions in LAR and PTP kappa showed that both genes were effectively disrupted, but neither was essential for normal embryonic development.

Proc Natl Acad Sci U S A 1995 Jul 3;92(14):6592-6.

Characterization of a gene trap insertion into a novel gene, cordon-bleu, expressed in axial structures of the gastrulating mouse embryo.

We have used a gene trap (GT) vector and embryonic stem (ES) cell chimeras to screen for insertions of the lacZ reporter gene into transcription units that are spatially and temporally regulated during early mouse embryogenesis. GT vectors which can act as both a reporter and a mutagen have been previously used to isolate new genes that are essential for mouse development. In this paper we describe a GT insertion which displays a very restricted pattern of expression in the gastrulating embryo. beta-Galactosidase activity was first detected at 7.5 days post-coitum (E7.5) in the node region of the embryo and extended to the midline structures at E8.0. At E9.5 expression was restricted to the floor plate, the notochord, the roof of the gut, and the liver anlage. Expression appeared in the somites at E10.0 and later became more widespread. We used rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR) to clone a partial 360 base pair (bp) cDNA representing an endogenous sequence and containing an open reading frame (ORF) fused in frame to the lacZ reporter gene. The sequence showed no homology to any known protein or protein domain. An overlapping 1,200 bp fragment from a wild-type cDNA library was cloned and it detected the same pattern of expression as the reporter gene in E7.5, E8.5, and E9.5 wild-type embryos. It hybridized to a 5.4 kb lacZ fusion transcript and to an endogenous transcript of 6.5 kb. The gene was mapped to chromosome 11 and was named cordon-bleu (cobl). No phenotype was detected in mice homozygous for the insertion. However, the insertion may not cause a complete disruption of the gene function. The pattern of expression of cobl is very similar to that of hepatic nuclear factor 3 beta (HNF3 beta) and sonic hedgehog (Shh), both of which are involved in axial patterning. Therefore, the product of the cobl gene may also prove to be an important component of the genetic pathway regulating vertebrate axis formation.

Dev Genet 1995;17(2):141-54.

A gene trap approach in mouse embryonic stem cells: the lacZ reporter is activated by splicing, reflects endogenous gene expression, and is mutagenic in mice.

We have confirmed that the gene trap vector pGT4.5 creates spliced fusion transcripts with endogenous genes and prevents the synthesis of normal transcripts at the site of integration. cDNA was prepared to the lacZ fusion transcript in three ES cell lines to recover endogenous exon sequences upstream of lacZ. Each of the clones detected a unique-sized endogenous transcript, as well as the fusion transcript in the ES cell line from which the clone was derived. Sequence analysis of these clones and larger clones isolated from a random-primed cDNA library showed that the splice acceptor was used properly. For two insertions, the expression patterns of the lacZ reporter and the associated endogenous gene were compared in situ at three embryonic stages and were found to be similar. Three gene trap insertions were transmitted into the germ line, and abnormalities were observed with two of the three insertions in the homozygous state. RNA obtained from mice homozygous for the two mutant gene trap insertions was analyzed for normal endogenous transcripts and negligible amounts were detected, indicating that little splicing around the gene trap insertion occurred. This work demonstrates the capacity of the gene trap vector to generate lacZ fusion transcripts, to accurately report endogenous gene expression, and to mutate the endogenous gene at the site of integration.

Genes Dev 1992 Jun;6(6):903-18.

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