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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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Members of the Same Synphenotype Group Do Not Necessarily Have the Same Expression PatternsThe six examples shown here are all from the motility defects class. (A–C) Expression patterns of the three members of the swimming in circles synphenotype group. (D–F) Expression patterns of three members of the normal appearance but paralyzed synphenotype group. Members of each group are not expressed in the same patterns and so do not belong to the same synexpression group (see text).
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pgen-0020193-g016: Members of the Same Synphenotype Group Do Not Necessarily Have the Same Expression PatternsThe six examples shown here are all from the motility defects class. (A–C) Expression patterns of the three members of the swimming in circles synphenotype group. (D–F) Expression patterns of three members of the normal appearance but paralyzed synphenotype group. Members of each group are not expressed in the same patterns and so do not belong to the same synexpression group (see text).

Mentions: Genes within a synphenotype group do not necessarily belong to the same synexpression group [20]. This may be illustrated by referring to two synphenotype groups within the class of genes required for normal motility. Thus, of the three genes whose loss-of-activity causes embryos to swim in circles, one (AuroraA) is expressed at highest levels in the head (Figure 16A), another (FrzA) is expressed most strongly in muscle, heart, pronephros, and otic vesicle (Figure 16B), and the third (Mu1a) is expressed in the brain and neural tube but absent from muscle (Figure 16C). Similarly, of the genes whose loss-of-function causes paralysis, one (TEgg043a17) is expressed almost ubiquitously (Figure 16D), another (TNeu053K08) is highly expressed in muscle (Figure 16E), and yet another (TNeu098a04) is most strongly expressed in the posterior neural tube (Figure 16F). These observations are discussed below.


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

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

Members of the Same Synphenotype Group Do Not Necessarily Have the Same Expression PatternsThe six examples shown here are all from the motility defects class. (A–C) Expression patterns of the three members of the swimming in circles synphenotype group. (D–F) Expression patterns of three members of the normal appearance but paralyzed synphenotype group. Members of each group are not expressed in the same patterns and so do not belong to the same synexpression group (see text).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0020193-g016: Members of the Same Synphenotype Group Do Not Necessarily Have the Same Expression PatternsThe six examples shown here are all from the motility defects class. (A–C) Expression patterns of the three members of the swimming in circles synphenotype group. (D–F) Expression patterns of three members of the normal appearance but paralyzed synphenotype group. Members of each group are not expressed in the same patterns and so do not belong to the same synexpression group (see text).
Mentions: Genes within a synphenotype group do not necessarily belong to the same synexpression group [20]. This may be illustrated by referring to two synphenotype groups within the class of genes required for normal motility. Thus, of the three genes whose loss-of-activity causes embryos to swim in circles, one (AuroraA) is expressed at highest levels in the head (Figure 16A), another (FrzA) is expressed most strongly in muscle, heart, pronephros, and otic vesicle (Figure 16B), and the third (Mu1a) is expressed in the brain and neural tube but absent from muscle (Figure 16C). Similarly, of the genes whose loss-of-function causes paralysis, one (TEgg043a17) is expressed almost ubiquitously (Figure 16D), another (TNeu053K08) is highly expressed in muscle (Figure 16E), and yet another (TNeu098a04) is most strongly expressed in the posterior neural tube (Figure 16F). These observations are discussed below.

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.

Show MeSH