Gene Trap Insertion Research Articles

The Complete Sequence of a Heterochromatic Island from a Higher Eukaryote

Heterochromatin, constitutively condensed chromosomal material, is widespread among eukaryotes but incompletely characterized at the nucleotide level. We have sequenced and analyzed 2.1 megabases (Mb) of Arabidopsis thaliana chromosome 4 that includes 0.5–0.7 Mb of isolated heterochromatin that resembles the chromosomal knobs described by Barbara McClintock in maize. This isolated region has a low density of expressed genes, low levels of recombination and a low incidence of genetrap insertion. Satellite repeats were absent, but tandem arrays of long repeats and many transposons were found. Methylation of these sequences was dependent on chromatin remodeling. Clustered repeats were associated with condensed chromosomal domains elsewhere. The complete sequence of a heterochromatic island provides an opportunity to study sequence determinants of chromosome condensation.

A retroviral gene trap insertion into the histone 3.3A gene causes partial neonatal lethality, stunted growth, neuromuscular deficits and male sub-fertility in transgenic mice.

Spermatogenesis is a complex developmental pro-cess involving cell division and differentiation. Approximately half of all sterile males have defects in spermatogenesis or sperm function. An insight into the molecular control points regulating this process might help in treating male infertility. Gene trapping in embryonic stem cells and the generation of transgenic mice represents one route to identify genes expressed during spermatogenesis. The trapped gene is tagged with a lacZ reporter gene so that the expression pattern of the gene can be visualized by staining for beta-galactosidase activity. We have screened transgenic mouse lines for expression of trapped genes in the gonads. One such trap event was shown to be in the replacement histone 3.3A gene ( H3.3A ). This gene was expressed ubiquitously during embryonic development until 13.5 days post-coitum and in the adult heart, kidney, brain, testes and ovaries. This mutation resulted in postnatal death of 50% of homozygous mutants. Surviving mutants displayed reduced growth rates when competing with wild-type siblings for food. Mutant mice also had a neuro-muscular deficit and males displayed reduced copulatory activity. When copulations did occur, these resulted in very few pregnancies, suggesting that mutations in the H3.3A gene may contribute to some cases of impaired fertility in man.

Compensation for a gene trap mutation in the murine microtubule-associated protein 4 locus by alternative polyadenylation and alternative splicing.

One of the features expected of the gene trap approach is the functional mutation of a gene, allowing its loss-of-function phenotype analysis. We have mutated the murine microtubule-associated protein 4 (MAP-4) locus by inserting a splice-acceptor gene trap construct. Because the MAP-4 gene has been cloned, sufficient information is available to investigate the efficiency of the gene trap insertion in disrupting the protein-coding region. The fusion mRNA contains the first 905 bases of the MAP-4 mRNA and is expected to code for a truncated, nonfunctional MAP-4 protein missing, among others, the microtubule-binding domain. Activity of the lacZ marker gene of the gene trap construct was observed in all tissues throughout development and in all cells examined in adult animals. However, some cells and tissues showed higher levels of activity than others: for example, blood vessel endothelium, heart, aspects of the developing nervous system, surface ectoderm of embryonic day 11.5 embryos, and the ependymal layer and blood vessel endothelium in adult brain. MAP-4 binds to microtubules and is thought to modulate their stability. It is expressed differentially in different tissues as 5.5-kb, 6.5-kb, 8-kb, 9-kb, and 10-kb mRNA species from a single copy gene in mice. Northern hybridization with a 5', MAP-4-specific probe revealed a 3.3-kb splice variant, which has not been described previously, that was expressed as the most abundant MAP-4 mRNA species in the brain but not in other tissues. Mice homozygous for the reported gene trap insertion in the MAP-4 locus (MAP-4gt/gt) are viable and appear to be phenotypically normal. They exhibited normal levels of all MAP-4 mRNA species in brain and kidney, showing that the simian virus 40-polyadenylation signal of the gene trap construct was ignored and also showing compensation for the gene trap insertion by splicing around the gene trap construct.

Aquarius, a novel gene isolated by gene trapping with an RNA-dependent RNA polymerase motif.

In a retinoic acid (RA) gene trap screen of mouse embryonic stem (ES) cells, a novel gene, named Aquarius (Aqr), was identified and characterized. The promoterless lacZ marker was used to trap the genomic locus and to determine the expression pattern of the gene. Aqr transcripts are strongly induced in response to RA in vitro. During embryogenesis, Aqr is expressed in mesoderm, in the neural crest and its target tissues, and in neuroepithelium. Expression was first detected at 8.5 days postcoitum, when neural crest cells are visible at the lateral ridges of the neural plate. The gene-trapped Aqr locus was transmitted through the mouse germ line in three genetic backgrounds. In the F2 generation, the expected mendelian ratio of 1:2:1 was observed in all backgrounds, indicating that homozygous mice are viable. Homozygotes are normal in size and weight and breed normally. The gene trap insertion, however, does not seem to generate a null mutation, because Aqr transcripts are still present in the homozygous mutant animals. The Aqr open reading frame has weak homology to RNA-dependent RNA polymerases (RRPs) of the murine hepatitis viruses and contains an RRP motif. Aqr was mapped to mouse chromosome 2 between regions E5 through F2 by using fluorescence in situ hybridization analysis.

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

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

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.

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

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

Distribution of a murine protein tyrosine phosphatase BL-beta-galactosidase fusion protein suggests a role in neurite outgrowth.

We have generated a gene trap insertion into the protein tyrosine phosphatase-BL (PTP-BL) locus, which produces a fusion of the N-terminal half of PTP-BL with beta-galactosidase. During development, beta-galactosidase activity was seen in all epithelial cells: strong staining was observed in the stomach and kidney epithelium, the ependymal layer of the central nervous system, and the surface ectoderm. Particularly prominent beta-galactosidase activity was seen in the peripheral nervous system, which correlated with neurite outgrowth. In epithelial cells, staining was seen in the apical portion of the cells. In nerves, beta-galactosidase activity was associated with growth cones as well as with Schwann cells. This suggests that the amino-terminal portion of PTP-BL contains sequences sufficient to target the fusion protein to specific subcellular compartments. In situ hybridization with a PTP-BL probe demonstrated that all tissues in which beta-galactosidase activity was seen were genuine sites of expression of the PTP-BL gene, although differences in the stability of the PTP-BL protein and the PTP-BL-beta-galactosidase fusion protein may exist. The distribution of beta-galactosidase activity in the peripheral nervous system, together with the structure of the wild-type protein, suggests that this phosphatase may have a role in regulation of the cytoskeleton during the development of the peripheral nervous system.

A molecular strategy designed for the rapid screening of gene traps based on sequence identity and gene expression pattern in adult mice.

We have devised a strategy to rapidly screen gene traps in mouse embryonic stem (ES) cells based on DNA sequence information and an in vitro analysis of gene expression. After the initial identification of ES cell clones expressing beta-galactosidase, tagged RNA transcripts were immediately cloned and sequenced in order to determine their identities. Novel gene sequences found were used to probe northern blots to examine the expression patterns of their cognate genes. Our initial characterization of 30 cDNA clones indicated that more than half of the tagged sequences were novel mouse genes and of these 40% showed a restricted pattern of expression in adult mouse tissues. This molecular characterization of gene traps is quick, reliable and well suited for the large-scale screening of mammalian developmental genes. Furthermore, since gene trap insertion frequently disrupts the tagged host gene, the ES cells can be used to produce transgenic animals for a genetic analysis of gene function.

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.

A gene trap approach in mouse embryonic stem cells: the lacZ reported 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.