Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development

Abstract

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 multi-omics approach, incorporating transcriptome, proteome, and phosphoproteome data generated from mouse placental tissue collected at two critical developmental timepoints. We found that incorporating information from both the transcriptome and proteome identifies genes associated with timepoint-specific biological processes, unlike using the proteome alone. We further inferred genes upregulated based on the proteome data but not the transcriptome data at each timepoint, leading us to identify 27 genes that we predict to have a role in trophoblast migration or placental metabolism. Finally, using the phosphoproteome dataset, we discovered novel phosphosites that may play crucial roles in the regulation of placental transcription factors. By generating the largest proteome and phosphoproteome datasets in the developing placenta, and integrating transcriptome analysis, we uncovered novel aspects of placental gene regulation.

Transcriptomic and proteomic analyses between small yellow follicles and the smallest hierarchical follicles reveal a role of VLDLR in chicken follicle selection

“…In this study, by association analysis between the transcriptome and the proteome, we found that the expression changes of most genes are inconsistent at the mRNA and protein levels, which is consistent with other studies showing that most genes can exhibit differential expression at the transcript and protein level [39][40][41][42][43]…”

Transcriptomic and proteomic analyses between small yellow follicles and the smallest hierarchical follicles reveal a role of VLDLR in chicken follicle selection

“…In this study, by association analysis between the transcriptome and the proteome, we found that the expression changes of most genes are inconsistent at the mRNA and protein levels, which is consistent with other studies showing that most genes can exhibit differential expression at the transcript and protein level [39][40][41][42][43], suggesting that it is necessary to analyze the function of genes at both levels.…”

Transcriptomic and proteomic analyses of ovarian follicles reveal the role of VLDLR in chicken follicle selection

“…In this study, by association analysis between the transcriptome and the proteome, we found that the expression changes of most genes are inconsistent at the mRNA and protein levels, which is in line with the results of other studies showing that most genes can exhibit differential expression at the transcript and protein levels [38,39], and this suggests that it is necessary to analyze the functions of genes at both levels.…”