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DEVELOPMENTAL DYNAMICS 212:318–325 (1998) Gene Trap Insertion Into a Novel Gene Expressed During Mouse Limb Development ANDRÉ PIRES-DASILVA AND PETER GRUSS* Department of Molecular Cell Biology, Max Planck Institute of Biophysical Chemistry, Göttingen, Germany ABSTRACT 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 58-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;212:318–325. r 1998 Wiley-Liss, Inc. Key words: hair follicles; mouse embryogenesis; lacZ; apical ectodermal ridge INTRODUCTION The screening for mutants in Drosophila and Caenorhabditis elegans has greatly enhanced our knowledge of molecules involved in the control of development (Nusslein-Volhard and Wieschaus, 1980; Meneely and Herman, 1979). In vertebrates, however, such large screenings have been hampered by the difficulty of identifying the gene when only the mutant is available. An alternative way to identify new genes and their associated mutant phenotypes in mouse is gene trapping (Gossler et al., 1989). Gene trapping is based on the random integration of a reporter gene in the genome, which allows the detection of the expression pattern of the endogenous gene by a simple histochemical procedure. The identification of the ‘‘trapped gene’’ is performed by using a polymerase chain reaction r 1998 WILEY-LISS, INC. (PCR) method that allows cloning of the exon just upstream of the reporter gene (Frohman et al., 1988). In this paper, we report a gene-trap event that shows expression in the limb. The limb has been the subject of studies for decades in the chick, because it is readily accessible to experimental manipulations in ovo. Many genes that are involved in limb development have been identified by homology screening using Drosophila probes (for review, see Tickle 1994). Such an approach has proved to be very fruitful, because many signaling pathways are highly conserved across phyla (Gaunt, 1997). The identification of vertebrate-specific genes, however, has been very limited. Gene trapping allows a large number of genes and their corresponding expression patterns to be obtained in a relatively short time. Thus, this strategy is well suited for screening for novel genes involved in vertebrate limb development. The limb develops along three axes: a proximodistal (Pr/Di) axis that runs between the shoulder and the tips of the digits, an anteroposterior (A/P) axis that extends (e.g., the hand between the little finger and the thumb), and a dorsoventral (D/V) axis that extends from the back of the hand to the palm. Patterning along these axes is determined very early in vertebrate development, even before the limb bud is recognizable. Both ectodermal and mesodermal components are actively involved in maintaining the limb axial polarity. The ectodermal sheath around the limb controls the D/V axis, whereas its most distal part, the apical ectodermal ridge (AER), is required for outgrowth and Pr/Di regionalization (Saunders, 1948; MacCabe et al., 1974). Patterning along the A/P axis is established by a series of reciprocal interactions between the AER and the region of posterior mesoderm known as the zone of polarizing activity (ZPA; Saunders and Gasseling, 1968; Laufer et al., 1994). Recently, progress has been made in characterizing genes that are involved in limb development. The AER, for instance, can be substituted functionally by ectopic administration of members of the fibroblast growth factor (FGF) family (Niswander et al., 1993; Fallon et al., 1994). Regionalization along the A/P axis, however, is less clear. The role of molecules distributed along this axis, such as sonic hedgehog (shh), retinoic acid, and *Correspondence to: Peter Gruss, Department of Molecular Cell Biology, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. Received 11 September 1997; Accepted 17 December 1997 Paddy EXPRESSION IN THE LIMB Hox genes, is not fully understood (Noji et al., 1991; Dolle et al., 1993; Davis and Cappecchi, 1994; Chiang et al., 1996). Thus, characterization of additional molecules is required to fully understand the mechanisms of limb development. Here, we describe a gene-trap insertion into a novel gene, paddy, that has an expression pattern that correlates with multiple roles during limb development and that is expressed in restricted mesodermal domains along the limb axes, which are probably involved in A/P and D/V differentiation processes of the limb pad. The patterns of expression in other tissues, such as the hair follicles, stomach, genital bud, and pharynx, are also discussed. RESULTS Mouse embryonic stem (ES) cells were electroporated with the internal ribosome entry site (IRES)-bGeo vector (see Experimental Procedures) and screened initially for their pattern of expression in vitro in an undifferentiated state. Of approximately 100 G418resistant ES colonies, 80 stained for b-galactosidase (b-gal) activity. The pattern of expression was highly variable among the different ES cell clones maintained in culture. Clones that had fewer than 30% of their cells stained with lacZ were further processed. Twenty of these clones were selected for morula aggregation to generate chimeras. Nine of them were found to contribute to the germ line. Embryos were analyzed for b-gal staining from embryonic day 8.5 (E8.5) to E16.5. One mouse line presented a very restricted expression pattern during embryogenesis. 319 ment by about 1 day, has an expression pattern similar to that seen in the forelimb. D/V of lacZ expression starts at E13.5 (Fig. 1F–I). At this time, mesenchymal cells lining the ventral epithelium of the limb are labelled. No expression is observed in chondrification centers. In subsequent stages of development, expression localizes to the limb pads, which are small elevations in the plantar surface of the hind limb and the palmar surface of the forelimb (Fig. 1J–L). The expression in the forelimb is first observed in the metacarpal region and in the metacarpophalangeal joints at E14.5; later (E15.5), it includes the five digital pads. Tangential sections revealed that staining was restricted to the dermal component of the pad. Hair Follicles Hair follicles, like the limbs, require epitheliomesenchymal interactions to develop (for review, see Hardy, 1992). The first step of development is a thickening of the epithelium, which is thought to induce a mesenchymal condensation of underlying dermal cells. This condensation, called dermal papilla, promotes ingrowth of the epidermis and subsequent proliferation of the adjacent epithelial cells that, later, will form the hair itself. Hair follicles develop in a rostral-to-caudal sequence. The first follicles to appear, those of the vibrissae, are seen at E12.5. LacZ expression is observed in mesenchymal cells that condense to form the dermal papilla (Fig. 2A,B). Pelage hair follicles appear in E14.5 embryos, with the same lacZ expression pattern as that seen in the vibrissae follicles. Stomach, Genital Bud, and Branchial Arc Expression in the Limbs LacZ expression corresponding to paddy activation is first observed at E9.5, when the forelimb bud becomes visible (Fig. 1A,B). Blue staining is restricted to the mesenchymal layer of the bud. Staining is not observed either in the anterior one-third of the limb or in the ectoderm. As the bud elongates, paddy expression is restricted to the posterior half of the limb (Fig. 1C–H). In late limb development, expression includes anterior domains (Fig. 1J), culminating in 5-bromo-4-chloro-3indolyl B-D-galactopyranoside (X-Gal) staining in restricted cells along the whole A/P axis (Fig. 1K). Interestingly, a gradient of expression can be observed along the A/P and Pr/Di axes at E9.5–11.5 (Fig. 1B,C,E). The most posterior domain, which includes the ZPA, has the strongest staining. A dynamic pattern of expression is also observed along the Pr/Di axis. Up to E10.5, no polarization of expression is observed. In later stages, however, cells underlying the AER become progressively negative for X-Gal staining up to the proximal half of the hand/foot plate at E12.5 (Fig. 1H). The proximal expression domain extends to the axilla region until E13.5; later, it remains only in the autopod and the anterior part of the zeugopod. The hind limb, which is delayed in develop- At E9.5, lacZ expression appears at the level of the third and fourth branchial arches (Fig. 1A). The iden- Fig. 1. (Overleaf.) LacZ expression of paddy in the limb in embryos 9.5–15.5 days postcoitum (E9.5–E15.5). B, C, E, H, J, and K show limbs that are oriented with proximal to the left, distal to the right, anterior on the top, and posterior on the bottom of the photomicrograph. A: Whole-mount of an E9.5 embryo exhibiting expression in the branchial arch region (arrowhead) and in the forelimb. B: Higher power magnification of the E9.5 forelimb showing expression restricted to the mesodermal layer. Note that the most anterior region of the limb is negative for lacZ. C: E10.5 forelimb whole-mount showing staining localized predominantly in the posterior half of the limb. D: At E11.5, expression includes the stomach. E: Sagittal section along an E11.5 limb showing strong expression in the region overlapping with the zone of zone of polarizing activity (ZPA). No expression is observed in the apical ectodermal ridge (AER). F: Cross section of an E11.5 limb. There is no sign of dorsoventral (D/V) polarization of the lacZ expression. G: Whole-mount of E12.5 embryo showing staining in whisker follicles and limbs. H: The lacZ expression at E12.5 is detected in a more proximal region of the limb compared with earlier stages. I: At E13.5, staining is polarized along the D/V axis and is restricted to the mesodermal cells lining the ventral surface of the limb. J: Ventral view of an E14.5 limb. K: Ventral view of an E15.5 limb showing 5-bromo-4-chloro-3-indolyl B-D-galactopyranoside (X-Gal) staining in the limb pads. L: Cross section of an E15.5 limb with lacZ expression in the ventral dermis. a, Anterior; p, posterior; d, dorsal; v, ventral; pr, proximal; di, distal; st, stomach; ect, ectoderm. Scale bars 5 500 µm in A,D,G–L, 150 µm in B,C,E,F. A B a C ect di pr p D E AER a F v ZPA st G d p pr I H v d di J d L K v Figure 1. A B C D E F Fig. 2. Paddy is expressed in the hair follicles (A,B), stomach (C), pharynx (D), and genital bud (F,H). A: Section of an E12.5 embryo showing X-Gal staining in the condensing mesenchymal cells underlying the epithelium of the hair vibrissae. B: Later, at E13.5, expression is detected exclusively in the dermal papilla. C:. Blue staining is observed in the pyloric region of the stomach at E11.5 D: E11.5 sagittal section showing signal in the epithelium lining the pharynx. E: Genital bud of an E12.5 embryo with lacZ expression in mesenchymal cells at the tip of the bud. F: In later stages (E13.5), expression continues in the tip. Scale bars 5 150 µm. 322 PIRES-DASILVA AND GRUSS Fig. 3. Sequence obtained by 58-rapid amplification of cDNA ends (RACE) of paddy limb RNA. tity of these cells was not determined. At around E10.5, expression of lacZ begins to be detected in parts of the digestive system. More specifically, staining is detected in the pyloric region of the developing stomach (Fig. 2C) and in the epithelium of the midgut (not shown). Later in development, at E11.5, blue staining is observed in the epithelium lining the pharynx (Fig. 2C). In no other stage is staining detected in this region. Expression in the genital bud starts at E10.5 and extends until E13.5 (Fig. 2E,F). LacZ expression is observed exclusively in the mesodermal component of the bud. X-Gal staining is detected in more distal regions as the genital bud develops. 58-Rapid Amplification of cDNA Ends Sequence Total RNA of heterozygous E12.5 limbs was prepared to amplify 58 sequences flanking the lacZ gene. A 258 base pair (bp) fragment was obtained that did not show any similarity to the sequences described previously (Fig. 3), and the open reading frame (ORF) that was found did not show similarity to any protein domain. Therefore, it is very likely that this sequence derives from an uncharacterized gene. The evidence that this amplified sequence corresponds to the cDNA of the trapped gene is supported by the following data. First, Southern blot analysis using an enzyme that cuts the gene-trap vector in only one site shows that there is reporter gene integration in only one locus (Fig. 4A). Second, reverse transcriptase (RT)-PCR between the amplified sequence and the gene-trap vector sequence shows a single band of the expected size in RNA derived from the limbs but not from tissues that are negative for X-Gal staining, e.g., the brain (Fig. 4B). Third, the sequence is spliced correctly with the reporter gene, ruling out the possibility of a product derived from a nonspecific PCR amplification (data not shown). Homozygous Mice Are Apparently Normal Homozygous animals were identified by quantitative Southern blot analysis. Preliminary data reveal that they were born at the expected Mendelian ratio and did not show any obvious morphological phenotype compared with their heterozygous or wild type litter mates. DISCUSSION Here, we present the characterization of a gene-trap event with expression in the branchial arches, stomach, limbs, hair follicles, and genital bud. The short 58-RACE sequence available does not allow us to assign a possible function for the trapped gene, although its spatiotemporal pattern of expression suggests multiple roles during development. Expression is first detected at E9.5, when it is restricted to the forelimbs and branchial arches. Later in development, X-Gal staining is observed sequentially in hind limbs and stomach at E10.5, in vibrissae follicles and genital bud at E11.5–E12.5, and in pellage hair follicles at E14.5. Paddy in Limb Development The determination of limb asymmetry depends on a series of epitheliomesenchymal interactions that occur very early during limb development. Classical experiments have shown that inversion of the ectodermal sheath along the D/V axis promotes concomitant mesoderm polarity inversion along the same axis (MacCabe et al., 1974; Geduspan and MacCabe, 1987, 1989). Recent studies have provided information about molecules that are important for dorsal determination. Wnt-7a, for instance, is expressed in dorsal ectoderm during early stages of mouse and chick limb development (Dealey et al., 1993; Parr et al., 1993). Its functional inactivation results in the transformation of dorsal limb structures toward a ventral phenotype (Parr and McMahon, 1995). Wnt-7a signaling activates genes that encode transcription factors in dorsal mesoderm. One such gene is Lmx1, a member of the Lim gene family (Riddle et al., 1995; Vogel et al., 1995). Less is known, however, about the molecular cues that determine ventral polarity. The functional inactivation of engrailed-1 (En-1) has shown that this gene is required for limb ventralization (Loomis et al., 1996). Molecules in the mesoderm component that respond to En-1 signal, however, are not known. Paddy is expressed in both surfaces early in development, making it unlikely that it has a role in early patterning decisions. Its later expression (from E14.5 onward), however, suggests a function that is related to the differentiation process of the plantar/palmar surface of the limbs. Paddy, then, is probably activated in response to signals from ventral mesenchyme, which then pattern the ectoderm. Possible roles for the expression in the pad dermis are the guidance of nerve fibers or the elevation of the epidermal surface. To our knowledge, Pax-9 is the only known gene with overlapping expres- Paddy EXPRESSION IN THE LIMB 323 able to respecify the limb pattern when it is grafted to more anterior positions (Saunders and Gasseling, 1968). The biochemical nature of the molecule that confers this activity is not yet known, although candidates are available. For example, shh, which is expressed in the ZPA region, is able to specify posterior identity when it is expressed in anterior regions of the limb bud (Riddle et al., 1993). The fact that paddy has a similar expression, although it occurs in a broader domain, suggests that it has a role along this axis. It has been hypothesized that a gradient of positional information is required to specify different identities (Wolpert, 1969). Paddy is expressed in a graded manner, suggesting that the level of expression is important for its function. A reciprocal signaling cascade has been shown to occur between the AER and the ZPA (Laufer et al., 1994). Shh, which is expressed in the ZPA, is thought to activate Fgf-4 in the AER. Further maintenance of shh expression in the distal domain of the limb is then controlled by Fgf-4. Consequently, the shh expression domain is found subjacent to the AER as the limb grows out distally. The continued shh expression in distal regions may be important to activate and maintain the expression of HoxD and Bmp genes, which then pattern the digits. Paddy expression, however, does not seem to depend on AER/ZPA signalling in late stages, because its expression domain moves proximally rather than distally as the limb develops. Thus, it can be hypothesized that paddy is activated in response to polarizing signals only in early limb development. The limb develops following a proximodistal progression of differentiation (Saunders, 1948). Accordingly, the expression of paddy in proximal regions of the limb correlates with a role in girdle/humerus differentiation. Paddy in Hair Follicle Development Fig. 4. The 58-RACE corresponds to the cDNA of the trapped gene. A: Southern blot of DNAs digested with NcoI and hybridized with lacZ probe. In the transgenic mice (asterisks), only one band of 3 Kb was detected. B: Reverse transcriptase-polymerase chain (RT-PCR) reaction of samples derived from E12.5 transgenic animals. RNA were isolated from the limb (left lane) and from the brain (right lane). PCR was performed with primers that anneal to the gene-trap vector and the 58-RACE sequence (top) and for GAPDH (bottom). sion patterns in these late stages (E14.5–E16.5) of limb development (Neubuser et al., 1995). The function of Pax-9 in these stages, however, is unknown. The onset of expression of paddy along the A/P axis correlates with the timing of this axial polarity determination. The ZPA, which is comprised of a population of mesenchymal cells in the posterior part of the limb, is The hair follicles arise in a stepwise process: The dermal mesenchyme initiates the thickening and ingrowth of the overlying epithelium (Hardy, 1992), the mesenchymal cells then aggregate and form the dermal papilla, and the adjacent epithelial cells are stimulated by the dermal papilla to divide rapidly, forming the ‘‘hair matrix.’’ Cells derived from the hair matrix will later differentiate into hair cells and inner root sheath cells. There are only a few molecules that are known to be involved in these induction processes. The expression of Bmp-4 in the condensing mesenchyme, for example, could be involved in epithelial invagination (Bitgood and McMahon, 1995). The fact that paddy has an expression pattern similar to Bmp-4 suggests that it could have a similar or related role. Other possible functions are the aggregation of mesenchymal cells and the innervation of the hair follicle. Paddy Expression Suggests Many Roles During Development In summary, paddy is a new gene with restricted expression domains in several tissues. The expression in the limb suggests that paddy may be involved in the 324 PIRES-DASILVA AND GRUSS determination of A/P and D/V polarities, probably in a different signaling pathway than those described thus far. Its relatively late expression polarization along the D/V axis suggests that paddy is more likely to act in late differentiation processes rather than in axis determination. The absence of a phenotype can be explained in a number of ways. There is the possibility, for instance, that alternative splicing is occurring. This would generate the wild type transcript that rescues the phenotype. Other possibilities include integration in a part of the gene that does not interfere in its function or the presence of related genes with overlapping functions. EXPERIMENTAL PROCEDURES Generation of Gene-Trapped ES Cell Clones and Mouse Chimeras The vector IRESbGeo contains an IRES between the splice-acceptor site and the bgeo sequence (Chowdhury et al., 1997). Gene-trapped ES clones were produced by electroporating 1 3 107 R1 ES cells (Nagy et al., 1993) with 25 µg of vector linearized at the SacI site. ES cell colonies resistant for G418 were selected, picked, and expanded essentially as described by Wurst and Joyner (1993). Clones positive for lacZ activity were aggregated with morulas to generate chimeric mice (Nagy et al., 1993). Chimeras with a strong contribution from ES cells, as judged by coat color, were tested for contribution to the germ line by crossing to NMRI mice. X-Gal Staining of Mouse Embryos In all animals, the day on which the vaginal plug was detected was considered to be day 0.5 of gestation (E0.5). Embryos were fixed in 1% formaldehyde, 0.2% glutaraldehyde, and 0.02% NP-40 at 4°C for 30–120 min and then washed twice in phosphate-buffered saline (PBS) at room temperature. Staining in X-Gal solution (1 mg/ml X-Gal, 5 mM K3Fe(CN)6, 5 mM K4Fe(CN)6, 2 mM MgCl2) was performed at 30°C overnight to reveal lacZ activity. Embryos processed for paraffin sections were postfixed in 4% paraformaldehyde overnight at 4°C and counterstained with neutral red. Quantitative Southern Blot Heterozygous mice for the vector integration were identified by Southern blot analysis on genomic DNA digested with BamHI and hybridized with a 32P-labeled lacZ probe. In the presently described mouse line, there are about four tandem integrations in one locus (data not shown). The offspring of heterozygous matings were genotyped by adding a second probe, Fkh-5, which was used as an internal control (Wehr, 1996). The homozygous animals had a higher lacZ:Fkh-5 ratio than the heterozygous animals. 58-RACE, RT-PCR, and Sequence Analysis Total RNA was prepared from E12.5 limbs by using TRIzol reagent (GIBCO-BRL, Gaithersburg, MD). Ge- nomic DNA was removed by DNAseI (BoehringerMannheim, Mannheim, Germany) digestion. 58-RACE was performed by using the GIBCO kit (catalog no. 18374–025; GIBCO-BRL) following the manufacturer’s instructions. The primer PB1 (58-AGGGAGAGGGGCGGATT-38), which hybridizes to the IRES sequence, was used for the RT reaction. Nested PCRs were performed with primers PB2 (58-CGATGATCTTCCGGGTACCGAGCT-38) and PB3 (58-TACCGAGCTCCTGTGCCAGACTCT-38) under the following conditions: 94°C for 45 sec, 57°C for 25 sec, and 72°C for 2 min using 1 unit of Taq DNA polymerase in Taq buffer for 30 cycles. PCR products were cloned into pGEM-T vector (Promega, Madison, WI) and sequenced by dideoxy chain termination using T7 DNA polymerase (Pharmacia, Uppsala, Sweden). The sequences of seven clones were analyzed by using the software from Genetics Computer Group (Madison, WI) and were compared with GenBank/EMBL sequence data links. All clones presented the same sequence. To confirm that the 58-RACE sequence corresponded to the trapped gene, an RT-PCR was performed using RNA isolated from the limbs and brains of E12.5 transgenic embryos, as identified previously by Southern blot. RT was performed with the first-strand cDNA synthesis kit (Pharmacia) by using random hexamer primers. The primers for the PCR amplification of the derived cDNAs were as follows: AS31 (58-TGCGGTTGAGGCTCACTT-38) derived from the 58-RACE sequence positions 18–29; AS32 (58-ATCTTCCGGGTACCGAGC-38) derived from the gene-trap vector sequence; GAPDH, a typical ‘‘housekeeping gene,’’ was used as an internal control; GAPDH 58 primer (58-ACCACAGTCCATGCCATCAC-38; positions 566–585); and GAPDH 38 primer (58-TCCACCACCCTGTTGCTGTA-38; positions 998–1,017). The DNA fragments produced after 25 or 30 amplification cycles with an annealing temperature of 60°C were 420 bp and 451 bp, respectively. ACKNOWLEDGMENTS We thank R. Scholz for ES cell aggregation; F. Cecconi for helping with the 58-RACE; and C. Tickle, K. Ewan, and G. Alvarez-Bolado for critically reading the paper. This research was funded by AmGen Inc. and the Max Planck Society. REFERENCES Bitgood MJ, McMahon AP. Hedgehog and Bmp genes are coexpressed at many diverse sites of cell-cell interaction in the mouse embryo. Dev. 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