ZFIN ID: ZDB-PUB-140918-1
Functional mapping of the zebrafish early embryo proteome and transcriptome
Alli Shaik, A., Wee, S., Li, R.H., Li, Z., Carney, T.J., Mathavan, S., Gunaratne, J.
Date: 2014
Source: Journal of Proteome Research   13(12): 5536-50 (Journal)
Registered Authors: Carney, Tom, Li, Zhen, Mathavan, S.
Keywords: none
MeSH Terms:
  • Animals
  • Embryo, Nonmammalian/metabolism*
  • Protein Interaction Mapping
  • Protein Interaction Maps
  • Proteome/genetics
  • Proteome/metabolism*
  • Spectrometry, Mass, Electrospray Ionization
  • Tandem Mass Spectrometry
  • Transcriptome*
  • Zebrafish/genetics
  • Zebrafish/metabolism*
  • Zebrafish Proteins/genetics
  • Zebrafish Proteins/metabolism*
PubMed: 25230361 Full text @ J. Proteome Res.
Zebrafish is a popular system for studying vertebrate development and disease, and shows high genetic conservation with humans. Molecular level studies at different stages of development are essential for understanding the mechanisms deployed during ontogeny. Here, we performed comparative analysis of whole proteome and transcriptome at early-stage (24 hours post fertilization) zebrafish embryo. We identified 8363 proteins with their approximate cellular abundances (the largest number of zebrafish embryos 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 amounts. Using network mapping of the low abundant 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.