Interrogating the transcriptome of oocytes and preimplantation embryos

Cellular Stress Responses in Oocytes: Molecular Changes and Clinical Implications

The oocyte may be exposed to several sources of stress during its growth and maturation, which may lead to reduced fertility. Unfolded protein responses (UPRs) play a central role to maintain cell survival and repair. Transcription of heat shock proteins (HSPs) is a key element to facilitate reestablishment of cellular homeostasis. Unlike somatic cells, cellular mechanisms by which oocytes can sense and respond to stress are not well described. In here, we provide an overview about the impact of cellular stress, particularly due to lipotoxicity, oxidative stress, and heat stress on oocyte developmental competence. Next, we focus on the expression of HSPs in oocytes and their potential role in UPRs in oocytes and embryos. This is based on a comprehensive shotgun proteomic analysis of mature bovine oocytes performed in our laboratory, as well as a literature review. The topic is discussed in light of our understanding of similar mechanisms in other cell types and the limited transcriptional activity in oocytes. More fundamental research is needed both at the transcriptomic and proteomic levels to further understand cell stress response mechanisms in oocytes and early developing embryos, their critical interactions, and their long-term effects. Strategies to provide targeted external support to prevent or reduce cell stress levels during oocyte maturation or early embryo development under maternal metabolic stress conditions should be developed to maximize the odds of producing good quality embryos and guarantee optimal viability.

Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism

The oocyte-to-embryo transition (OET) is thought to be mainly driven by post-transcriptional gene regulation. However, expression of both RNAs and proteins during the OET has not been comprehensively assayed. Furthermore, specific molecular mechanisms that regulate gene expression during OET are largely unknown. Here, we quantify and analyze transcriptome-wide, expression of mRNAs and thousands of proteins in Caenorhabditis elegans oocytes, 1-cell, and 2-cell embryos. This represents a first comprehensive gene expression atlas during the OET in animals. We discovered a first wave of degradation in which thousands of mRNAs are cleared shortly after fertilization. Sequence analysis revealed a statistically highly significant presence of a polyC motif in the 3' untranslated regions of most of these degraded mRNAs. Transgenic reporter assays demonstrated that this polyC motif is required and sufficient for mRNA degradation after fertilization. We show that orthologs of human polyC-binding protein specifically bind this motif. Our data suggest a mechanism in which the polyC motif and binding partners direct degradation of maternal mRNAs. Our data also indicate that endogenous siRNAs but not miRNAs promote mRNA clearance during the OET.

Normalization of RNA-sequencing data from samples with varying mRNA levels

Methods for normalization of RNA-sequencing gene expression data commonly assume equal total expression between compared samples. In contrast, scenarios of global gene expression shifts are many and increasing. Here we compare the performance of three normalization methods when polyA⁺ RNA content fluctuates significantly during zebrafish early developmental stages. As a benchmark we have used reverse transcription-quantitative PCR. The results show that reads per kilobase per million (RPKM) and trimmed mean of M-values (TMM) normalization systematically leads to biased gene expression estimates. Biological scaling normalization (BSN), designed to handle differences in total expression, showed improved accuracy compared to the two other methods in estimating transcript level dynamics. The results have implications for past and future studies using RNA-sequencing on samples with different levels of total or polyA⁺ RNA.