Asfa Alli Shaik†,1, Sheena Wee†,1, Rachel Hai Xia Li1, Zhen Li2, Tom J. Carney1,3, Sinnakaruppan Mathavan2 and Jayantha Gunaratne*, 1,3,4
(† These authors equally contributed to this work)
1 Institute of Molecular and Cell Biology, Agency for Science Technology and Research, 61 Biopolis Drive, Singapore 138673
2 Genome Institute of Singapore, Agency for Science Technology and Research, 60 Biopolis Street, Singapore 138672
3 Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
4 Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, 117597, Singapore
Published online in Journal of Proteome Research on 17th September 2014
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.
Functional modulation of protein and transcripts in the developing embryo. Proteins and mRNAs were grouped into seven groups based on abundance values as follows: high protein and mRNA, low protein and mRNA, moderate protein and mRNA, high protein and moderate-to-low mRNA, low protein and moderate-to-high mRNA, low mRNA and moderate-to-high, and high mRNA and moderate-to-low protein. The clustered GO biological process terms enriched in at least one of the seven groups are depicted on the heat map. The red arrow corresponds to high abundance of quantified proteins or transcripts, the green arrow, low, and the black symbol, moderate. The shaded red triangle corresponds to moderate-to-high protein or transcript abundances, and the shaded green triangle represents moderate-to-low protein or transcript abundances. High (yellow) and low (blue) in the heat map represent statistical over- or under-representation, respectively.
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