EXOSC10 sculpts the transcriptome during the growth-to-maturation transition in mouse oocytes

Wu, Di; Dean, Jurrien

doi:10.1101/663377

Cited by 3 publications

(6 citation statements)

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“…Single oocyte RNA-seq has high reproducibility To estimate the reproducibility of mouse oocyte RNA-seq, we obtained several published datasets from single or pooled oocytes at GV (geminal vesicle) and MII (meiosis II) stages which are the beginning and ending of oocyte maturation, respectively [6][7][8][9][10]. We processed all raw sequencing files in parallel.…”

Section: Resultsmentioning

confidence: 99%

“…4a). However, ERCC normalization dramatically altered the results in cross-stage comparison in the GSE141190 dataset [7]. The absence of genes showing increased abundance is consistent to the absence of transcription during oocyte maturation, suggesting that external spike-in molecules provide better normalization for libraries with variated transcriptome size [7].…”

Section: External and Internal Normalization For Cross-stage Comparisonmentioning

confidence: 99%

“…It has been long known that the transcriptome undergoes dramatic decrease during mammalian oocyte maturation [7,10,13]. Presumably, identification of the decreased and stable RNA in this process could add understanding to the molecular regulation of oocyte development and quality control.…”

Section: External and Internal Normalization For Cross-stage Comparisonmentioning

confidence: 99%

“…Since single oocyte RNA-seq was introduced [4], it has become increasingly popular for multi-omic studies in mice. These advances provide greater understanding of developmental and genetic variation as well as detailed information in the co-regulation of transcripts that affect oocyte quality and ageing [5][6][7]. However, there has been no direct evaluation of single oocyte RNA-seq compared to pooled oocytes, or any discussion of different analytical methods.…”

Section: Introductionmentioning

confidence: 99%

“…2a-b) which determines duplicates by both UMI and insert reads. The N8 UMI, capable of distinguishing up to 65,536 molecules, is sufficient to distinguish the ~20,000 different RNAs expressed in mouse oocytes [3,7]. On average, the number of reads of the Dedup (UMI-based) samples were 43%±15% of their Original (without deduplication) samples ( Fig.…”

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Oocytes, a single cell and a tissue

Dean

2020

Preprint

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Development of single cell sequencing allows detailing the transcriptome of individual oocytes. Here, we compare different RNA-seq datasets from single and pooled mouse oocytes and show higher reproducibility using single oocyte RNA-seq. We further demonstrate that UMI (unique molecular identifiers) based and other deduplication methods are limited in their ability to improve the precision of these datasets. Finally, for normalization of sample differences in cross-stage comparisons, we propose that external spike-in molecules are comparable to using the endogenous genes stably expressed during oocyte maturation. The ability to normalize data among single cells provides insight into the heterogeneity of mouse oocytes. KeywordsMouse single oocyte RNA-seq; cross-stage normalization; oocyte heterogeneity (GV) stage. ConstGenes or ERCC normalization should become standards for cross-stage comparison in future single oocyte sequencing studies. Results and discussionSingle oocyte RNA-seq has high reproducibility To estimate the reproducibility of mouse oocyte RNA-seq, we obtained several published datasets from single or pooled oocytes at GV (geminal vesicle) and MII (meiosis II) stages which are the beginning and ending of oocyte maturation, respectively [6][7][8][9][10]. We processed all raw sequencing files in parallel. Due to the different distribution of transcripts from all the samples, we only took the coding reads for comparison ( Fig. 1a; Table S1). Interestingly, single oocyte RNA-seq (GSE141190, GSE96638, GSE44183) had higher correlation within the group than when compared to pooled oocytes of the same stage (Fig. 1b). In addition, MII stages exhibit higher deviation of poly(A) vs RiboMinus sequencing results, possibly due to the existence of dormant RNAs and hyper polyadenylated mRNAs being actively translated (Fig. 1b) [11]. By principal component clustering, single oocyte groups show higher similarity, though experiments/methods dominate the difference (Fig. 1c-d). Thus, we concluded that single oocyte sequencing can generate highly reproducible and consistent results. Deduplication improved the single oocyte RNA-seq limitedlySingle cell RNA-seq is susceptible to a range of biases, including gene capture, reverse transcription and cDNA amplification [12]. The incorporation of UMI (unique molecular identifiers) significantly improves single cell sequencing reproducibility by quantifying reads with more precision [3]. To test whether UMI also benefits single oocyte RNA-seq, we re-analyzed the GSE141190 RiboMinus RNA-seq results using UMI quantification ( Fig. 2a-b) which determines duplicates by both UMI and insert reads. The N8 UMI, capable of distinguishing up to 65,536 molecules, is sufficient to distinguish the ~20,000 different RNAs expressed in mouse oocytes [3,7]. On average, the number of reads of the Dedup (UMI-based) samples were 43%±15% of their Original (without deduplication) samples ( Fig. 2c-d; Table S2). After filtering out low-count genes, the linear regression of gene counts in Original a...

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Section: Resultsmentioning

confidence: 99%

Section: External and Internal Normalization For Cross-stage Comparisonmentioning

confidence: 99%

Section: External and Internal Normalization For Cross-stage Comparisonmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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Oocytes, a single cell and a tissue

Dean

2020

Preprint

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Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Quio

Schleiffer

Mechtler

et al. 2020

Preprint

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Post-transcriptional mechanisms are crucial for the regulation of gene expression.These mechanisms are particularly important during rapid developmental transitions such as the oocyte-to-embryo transition, which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions, changes to the RNA content are solely dependent on RNA degradation.Although several mechanisms that promote RNA decay during embryogenesis have been identified, it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte-to-embryo transition. Here, we focused on the auxiliary 3'-to-5' degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults, yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte-toembryo transition, transcriptome profiling identified stage-specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type, suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis-regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall, our results provide first insights into the physiological role of vertebrate Ski7 as an important posttranscriptional regulator during the oocyte-to-embryo transition.

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Translational Control of Xenopus Oocyte Meiosis: Toward the Genomic Era

Meneau

Dupré

Jessus

et al. 2020

Cells

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The study of oocytes has made enormous contributions to the understanding of the G2/M transition. The complementarity of investigations carried out on various model organisms has led to the identification of the M-phase promoting factor (MPF) and to unravel the basis of cell cycle regulation. Thanks to the power of biochemical approaches offered by frog oocytes, this model has allowed to identify the core signaling components involved in the regulation of M-phase. A central emerging layer of regulation of cell division regards protein translation. Oocytes are a unique model to tackle this question as they accumulate large quantities of dormant mRNAs to be used during meiosis resumption and progression, as well as the cell divisions during early embryogenesis. Since these events occur in the absence of transcription, they require cascades of successive unmasking, translation, and discarding of these mRNAs, implying a fine regulation of the timing of specific translation. In the last years, the Xenopus genome has been sequenced and annotated, enabling the development of omics techniques in this model and starting its transition into the genomic era. This review has critically described how the different phases of meiosis are orchestrated by changes in gene expression. The physiological states of the oocyte have been described together with the molecular mechanisms that control the critical transitions during meiosis progression, highlighting the connection between translation control and meiosis dynamics.

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EXOSC10 sculpts the transcriptome during the growth-to-maturation transition in mouse oocytes

Cited by 3 publications

References 59 publications

Oocytes, a single cell and a tissue

Oocytes, a single cell and a tissue

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Translational Control of Xenopus Oocyte Meiosis: Toward the Genomic Era

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