Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression

Fernando Faunes, Natalia Sánchez, Javier Castellanos, Ismael A. Vergara, Francisco Melo, Juan Larraín

Resultado de la investigación: Article

9 Citas (Scopus)

Resumen

Background: Recent evidence from global studies of gene expression indicates that transcriptomes are more complex than expected. Xenopus has been typically used as a model organism to study early embryonic development, particularly dorso-ventral patterning. In order to identify novel transcripts involved in dorso-ventral patterning, we compared dorsal and ventral transcriptomes of Xenopus tropicalis at the gastrula stage using serial analysis of gene expression (SAGE). Results: Of the experimental tags, 54.5% were confidently mapped to transcripts and 125 showed a significant difference in their frequency of occurrence between dorsal and ventral libraries. We selected 20 differentially expressed tags and assigned them to specific transcripts using bioinformatics and reverse SAGE. Five mapped to transcripts with known dorso-ventral expression and the frequency of appearance for these tags in each library is in agreement with the expression described by other methods. The other 15 tags mapped to transcripts with no previously described asymmetric expression along the dorso-ventral axis. The differential expression of ten of these novel transcripts was validated by in situ hybridization and/or RT-PCR. We can estimate that this SAGE experiment provides a list of at least 86 novel transcripts with differential expression along the dorso-ventral axis. Interestingly, the expression of some novel transcripts was independent of β-catenin. Conclusions: Our SAGE analysis provides a list of novel transcripts with differential expression in the dorso-ventral axis and a large number of orphan tags that can be used to identify novel transcripts and to improve the current annotation of the X. tropicalis genome.

Idioma originalEnglish
Número de artículoR15
PublicaciónGenome Biology
Volumen10
N.º2
DOI
EstadoPublished - 11 feb 2009

Huella dactilar

Gastrula
Xenopus
gene expression
Gene Expression
Transcriptome
transcriptome
Libraries
orphan
Catenins
bioinformatics
embryonic development
Computational Biology
in situ hybridization
Embryonic Development
In Situ Hybridization
embryogenesis
genome
reverse transcriptase polymerase chain reaction
analysis
Genome

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Citar esto

Faunes, Fernando ; Sánchez, Natalia ; Castellanos, Javier ; Vergara, Ismael A. ; Melo, Francisco ; Larraín, Juan. / Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression. En: Genome Biology. 2009 ; Vol. 10, N.º 2.
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Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression. / Faunes, Fernando; Sánchez, Natalia; Castellanos, Javier; Vergara, Ismael A.; Melo, Francisco; Larraín, Juan.

En: Genome Biology, Vol. 10, N.º 2, R15, 11.02.2009.

Resultado de la investigación: Article

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