Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development

The
condition of the placenta is a determinant of the short- and
long-term health of the mother and the fetus. However, critical processes
occurring in early placental development, such as trophoblast invasion
and establishment of placental metabolism, remain poorly understood.
To gain a better understanding of the genes involved in regulating
these processes, we utilized a multiomics approach, incorporating
transcriptome, proteome, and phosphoproteome data generated from mouse
placental tissue collected at two critical developmental time points.
We found that incorporating information from both the transcriptome
and proteome identifies genes associated with time point-specific
biological processes, unlike using the proteome alone. We further
inferred genes upregulated on the basis of the proteome data but not
the transcriptome data at each time point, leading us to identify
27 genes that we predict to have a role in trophoblast migration or
placental metabolism. Finally, using the phosphoproteome data set,
we discovered novel phosphosites that may play crucial roles in the
regulation of placental transcription factors. By generating the largest
proteome and phosphoproteome data sets in the developing placenta,
and integrating transcriptome analysis, we uncovered novel aspects
of placental gene regulation.