Pervasive 3′-UTR Isoform Switches During Mouse Oocyte Maturation

Abstract

Oocyte maturation is the foundation for developing healthy individuals of mammals. Upon germinal vesicle breakdown, oocyte meiosis resumes and the synthesis of new transcripts ceases. To quantitatively profile the transcriptomic dynamics after meiotic resumption throughout the oocyte maturation, we generated transcriptome sequencing data with individual mouse oocytes at three main developmental stages: germinal vesicle (GV), metaphase I (MI), and metaphase II (MII). When clustering the sequenced oocytes, results showed that isoform-level expression analysis outperformed gene-level analysis, indicating isoform expression provided extra information that was useful in distinguishing oocyte stages. Comparing transcriptomes of the oocytes at the GV stage and the MII stage, in addition to identification of differentially expressed genes (DEGs), we detected many differentially expressed transcripts (DETs), some of which came from genes that were not identified as DEGs. When breaking down the isoform-level changes into alternative RNA processing events, we found the main source of isoform composition changes was the alternative usage of polyadenylation sites. With detailed analysis focusing on the alternative usage of 3′-UTR isoforms, we identified, out of 3,810 tested genes, 512 (13.7%) exhibiting significant switches of 3′-UTR isoforms during the process of moues oocyte maturation. Altogether, our data and analyses suggest the importance of examining isoform abundance changes during oocyte maturation, and further investigation of the pervasive 3′-UTR isoform switches in the transition may deepen our understanding on the molecular mechanisms underlying mammalian early development.

Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications

“…ScAPAtrap [271], Sierra [272], dynamic analysis of alternative polyadenylation (APA) from single-cell RNA-seq (scDaPars) [273], SCAPTURE [274], and single cell alternative polyadenylation using expectation-maximization (SCAPE) [275], for example, take advantage of the fact that sequencing reads in 3' tagbased scRNA-seq are distributed near the polyadentation sites of individual transcripts to analyze alternative polyadentation and differential usage of 3'UTR isoforms between cells or cell types. Alternative UTR isoform usage is an important post-transcriptional regulatory mechanism in many physiological and pathological processes, affecting the rate of RNA degradation and the status of translation [276,277]. Currently, many research groups have been combining scRNA-seq with long-read sequencing technologies to enable high-confidence isoform profiling at the single-cell level [278][279][280].…”

Editorial: Reproductive genomics

“…Recently, considerable efforts have been devoted to achieving better understanding of the molecular networks, regulatory programs, and germline-soma or soma-soma communications during gametogenesis and embryogenesis. In particular, the rapid advancement of highthroughput sequencing technologies and ultra-low-input (or even single-cell) omics approaches have accelerated novel discoveries in reproductive development e.g., (Wang et al, 2018;Qiao et al, 2020;Xu K. et al, 2021;He et al, 2021b;Tyser et al, 2021;Yan et al, 2021;Wu et al, 2022;Xiong et al, 2022). Towards this direction, Qian et al profiled the transcriptomes of 14,315 single testicular cells from adult zebrafish testes by single-cell RNA sequencing (scRNA-seq) using the 10x Genomics Chromium platform, identified ten distinguishable cell types with novelly revealed marker genes, and characterized interactions between somatic cells and germ cells through ligand-receptor analysis.…”

“…Recently, considerable efforts have been devoted to achieving better understanding of the molecular networks, regulatory programs, and germline-soma or soma-soma communications during gametogenesis and embryogenesis. In particular, the rapid advancement of high-throughput sequencing technologies and ultra-low-input (or even single-cell) omics approaches have accelerated novel discoveries in reproductive development e.g., ( Wang et al, 2018 ; Qiao et al, 2020 ; Xu K. et al, 2021 ; He et al, 2021b ; Tyser et al, 2021 ; Yan et al, 2021 ; Wu et al, 2022 ; Xiong et al, 2022 ). Towards this direction, Qian et al .…”