Functional Mapping of the Zebrafish Early Embryo Proteome and Transcriptome

Zebrafish is a popular system for
studying vertebrate development
and disease that shows high genetic conservation with humans. Molecular
level studies at different stages of development are essential for
understanding the processes deployed during ontogeny. Here, we performed
comparative analysis of the whole proteome and transcriptome of the
early stage (24 h post-fertilization) zebrafish embryo. We identified
8363 proteins with their approximate cellular abundances (the largest
number of zebrafish embryo proteins quantified thus far), through
a combination of thorough deyolking and extensive fractionation procedures,
before resolving the peptides by mass spectrometry. We performed deep
sequencing of the transcripts and found that the expressed proteome
and transcriptome displayed a moderate correlation for the majority
of cellular processes. Integrative functional mapping of the quantified
genes demonstrated that embryonic developmental systems differentially
exploit transcriptional and post-transcriptional regulatory mechanisms
to modulate protein abundance. Using network mapping of the low-abundance
proteins, we identified various signal transduction pathways important
in embryonic development and also revealed genes that may be regulated
at the post-transcriptional level. Our data set represents a deep
coverage of the functional proteome and transcriptome of the developing
zebrafish, and our findings unveil molecular regulatory mechanisms
that underlie embryonic development.