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Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides.

Rana AA, Collart C, Gilchrist MJ, Smith JC - PLoS Genet. (2006)

Bottom Line: MOs were designed to complement sequence between -80 and +25 bases of the initiating AUG codons of the target mRNAs, and the specificities of many were tested by (i) designing different non-overlapping MOs directed against the same mRNA, (ii) injecting MOs differing in five bases, and (iii) performing "rescue" experiments.About 65% of the MOs caused X. tropicalis embryos to develop abnormally (59% of those targeted against novel genes), and we have divided the genes into "synphenotype groups," members of which cause similar loss-of-function phenotypes and that may function in the same developmental pathways.Analysis of the expression patterns of the 202 genes indicates that members of a synphenotype group are not necessarily members of the same synexpression group.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.

ABSTRACT
To identify novel genes involved in early development, and as proof-of-principle of a large-scale reverse genetics approach in a vertebrate embryo, we have carried out an antisense morpholino oligonucleotide (MO) screen in Xenopus tropicalis, in the course of which we have targeted 202 genes expressed during gastrula stages. MOs were designed to complement sequence between -80 and +25 bases of the initiating AUG codons of the target mRNAs, and the specificities of many were tested by (i) designing different non-overlapping MOs directed against the same mRNA, (ii) injecting MOs differing in five bases, and (iii) performing "rescue" experiments. About 65% of the MOs caused X. tropicalis embryos to develop abnormally (59% of those targeted against novel genes), and we have divided the genes into "synphenotype groups," members of which cause similar loss-of-function phenotypes and that may function in the same developmental pathways. Analysis of the expression patterns of the 202 genes indicates that members of a synphenotype group are not necessarily members of the same synexpression group. This screen provides new insights into early vertebrate development and paves the way for a more comprehensive MO-based analysis of gene function in X. tropicalis.

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The Five Members of the Ventral Defects Phenotypic ClassThis class can be subdivided into two synphenotype groups, as indicated in Figure 3 and Table 4. All embryos are shown at the tadpole stage (stage 35–41).
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pgen-0020193-g010: The Five Members of the Ventral Defects Phenotypic ClassThis class can be subdivided into two synphenotype groups, as indicated in Figure 3 and Table 4. All embryos are shown at the tadpole stage (stage 35–41).

Mentions: This class contains five genes whose loss-of-function phenotypes are characterized by defects in ventral tissues (Figure 10). Its members can be divided into two synphenotype groups, those with ventral oedema at the tadpole stage (n = 4) and those with a reduction in ventral tissue (n = 1). The former group may exhibit defects in heart or kidney development, or osmoregulation; the latter may show defects in ventral patterning.


Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides.

Rana AA, Collart C, Gilchrist MJ, Smith JC - PLoS Genet. (2006)

The Five Members of the Ventral Defects Phenotypic ClassThis class can be subdivided into two synphenotype groups, as indicated in Figure 3 and Table 4. All embryos are shown at the tadpole stage (stage 35–41).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1636699&req=5

pgen-0020193-g010: The Five Members of the Ventral Defects Phenotypic ClassThis class can be subdivided into two synphenotype groups, as indicated in Figure 3 and Table 4. All embryos are shown at the tadpole stage (stage 35–41).
Mentions: This class contains five genes whose loss-of-function phenotypes are characterized by defects in ventral tissues (Figure 10). Its members can be divided into two synphenotype groups, those with ventral oedema at the tadpole stage (n = 4) and those with a reduction in ventral tissue (n = 1). The former group may exhibit defects in heart or kidney development, or osmoregulation; the latter may show defects in ventral patterning.

Bottom Line: MOs were designed to complement sequence between -80 and +25 bases of the initiating AUG codons of the target mRNAs, and the specificities of many were tested by (i) designing different non-overlapping MOs directed against the same mRNA, (ii) injecting MOs differing in five bases, and (iii) performing "rescue" experiments.About 65% of the MOs caused X. tropicalis embryos to develop abnormally (59% of those targeted against novel genes), and we have divided the genes into "synphenotype groups," members of which cause similar loss-of-function phenotypes and that may function in the same developmental pathways.Analysis of the expression patterns of the 202 genes indicates that members of a synphenotype group are not necessarily members of the same synexpression group.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.

ABSTRACT
To identify novel genes involved in early development, and as proof-of-principle of a large-scale reverse genetics approach in a vertebrate embryo, we have carried out an antisense morpholino oligonucleotide (MO) screen in Xenopus tropicalis, in the course of which we have targeted 202 genes expressed during gastrula stages. MOs were designed to complement sequence between -80 and +25 bases of the initiating AUG codons of the target mRNAs, and the specificities of many were tested by (i) designing different non-overlapping MOs directed against the same mRNA, (ii) injecting MOs differing in five bases, and (iii) performing "rescue" experiments. About 65% of the MOs caused X. tropicalis embryos to develop abnormally (59% of those targeted against novel genes), and we have divided the genes into "synphenotype groups," members of which cause similar loss-of-function phenotypes and that may function in the same developmental pathways. Analysis of the expression patterns of the 202 genes indicates that members of a synphenotype group are not necessarily members of the same synexpression group. This screen provides new insights into early vertebrate development and paves the way for a more comprehensive MO-based analysis of gene function in X. tropicalis.

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