Functional mapping of the zebrafish early embryo proteome and transcriptome
Alli Shaik, Asfa
Li, Rachel Hai Xia
Carney, Tom J.
Date of Issue2014
Lee Kong Chian School of Medicine
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.
Journal of proteome research
© 2014 American Chemical Society. This is the author created version of a work that has been peer reviewed and accepted for publication by Journal of Proteome Research, American Chemical Society. It incorporates referee’s comments but changes resulting from the publishing process, such as copyediting, structural formatting, may not be reflected in this document. The published version is available at: [http://dx.doi.org/10.1021/pr5005136].