Single‐cell RNA‐seq reveals mRNAs and lncRNAs important for oocytes in vitro matured in pigs

Yang, Caixia; Wu, Zi‐Wei; Liu, Xiaoman; Liang, Hao; Gao, Zhuoran; Wang, Yi; Fang, Ting; Liu, Yunhua; Miao, Yi‐Liang; Du, Zhiqiang

doi:10.1111/rda.13901

Cited by 13 publications

(18 citation statements)

References 51 publications

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“…At the translational level, it has been shown that miR-181c in concert with Ago2 can repress the translation of the mitochondrial cyclooxygenase ( Cox1 ) mRNA, determining a remodeling of complex IV in cardiac dysfunction ( 68 , 69 , 78 , 79 ). Noteworthy, Cox1 transcript is among the transcripts induced during oocyte maturation ( 80 ). Similarly, miR-378 can inhibit the mitochondrial expression of Atp6 ( 71 ) that modulates mouse follicle development and oocyte maturation as well as aromatase levels ( 70 ).…”

Section: Mitochondrion-nucleus Crosstalk: a Focus On Ncrnas Acting As Anterograde And Retrograde Signalsmentioning

confidence: 99%

Ovarian Aging: Role of Pituitary-Ovarian Axis Hormones and ncRNAs in Regulating Ovarian Mitochondrial Activity

et al. 2021

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The number of mitochondria in the oocyte along with their functions (e.g., energy production, scavenger activity) decline with age progression. Such multifaceted functions support several processes during oocyte maturation, ranging from energy supply to synthesis of the steroid hormones. Hence, it is hardly surprising that their impairment has been reported in both physiological and premature ovarian aging, wherein they are crucial players in the apoptotic processes that arise in aged ovaries. In any form, ovarian aging implies the progressive damage of the mitochondrial structure and activities as regards to ovarian germ and somatic cells. The imbalance in the circulating hormones and peptides (e.g., gonadotropins, estrogens, AMH, activins, and inhibins), active along the pituitary-ovarian axis, represents the biochemical sign of ovarian aging. Despite the progress accomplished in determining the key role of the mitochondria in preserving ovarian follicular number and health, their modulation by the hormonal signalling pathways involved in ovarian aging has been poorly and randomly explored. Yet characterizing this mechanism is pivotal to molecularly define the implication of mitochondrial dysfunction in physiological and premature ovarian aging, respectively. However, it is fairly difficult considering that the pathways associated with ovarian aging might affect mitochondria directly or by altering the activity, stability and localization of proteins controlling mitochondrial dynamics and functions, either unbalancing other cellular mediators, released by the mitochondria, such as non-coding RNAs (ncRNAs). We will focus on the mitochondrial ncRNAs (i.e., mitomiRs and mtlncRNAs), that retranslocate from the mitochondria to the nucleus, as active players in aging and describe their role in the nuclear-mitochondrial crosstalk and its modulation by the pituitary-ovarian hormone dependent pathways. In this review, we will illustrate mitochondria as targets of the signaling pathways dependent on hormones and peptides active along the pituitary/ovarian axis and as transducers, with a particular focus on the molecules retrieved in the mitochondria, mainly ncRNAs. Given their regulatory function in cellular activities we propose them as potential diagnostic markers and/or therapeutic targets.

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Section: Mitochondrion-nucleus Crosstalk: a Focus On Ncrnas Acting As Anterograde And Retrograde Signalsmentioning

confidence: 99%

Ovarian Aging: Role of Pituitary-Ovarian Axis Hormones and ncRNAs in Regulating Ovarian Mitochondrial Activity

et al. 2021

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“…Third, oocytes are surrounded by granulosa cells, making large-scale cell isolation challenging. Because of the aforementioned reasons, most of the current scRNA-seq studies focus on oocytes at GV, MI, and MII stages with limited cell numbers in each experiment, which makes it hard to compare male and female germ-cell transcriptomes at single-cell level (Ferrero et al, 2019;Zhang T. et al, 2019;Ye et al, 2020;Yu et al, 2020;Yang et al, 2021). It is not until recent years that scRNA-seq was applied to transcriptome studies of early prophase I oocytes (Li et al, 2017;Ge et al, 2020;Niu and Spradling, 2020;Wang et al, 2020).…”

Section: Comparing Meiotic Scrna-seq Studies Between Male and Femalementioning

confidence: 99%

“…oocytes, or comparing abnormal oocytes with normal oocytes at the MII stage (Zhang et al, 2018;Ferrero et al, 2019;Ye et al, 2020;Yang et al, 2021).…”

Section: How Can We Conduct Scrna-seq To Study Meiosis? What Sequencing Strategies To Choose For Meiosis Studies?mentioning

confidence: 99%

The Application of Single-Cell RNA Sequencing in Mammalian Meiosis Studies

Peng

Qiao

2021

Front. Cell Dev. Biol.

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Meiosis is a cellular division process that produces gametes for sexual reproduction. Disruption of complex events throughout meiosis, such as synapsis and homologous recombination, can lead to infertility and aneuploidy. To reveal the molecular mechanisms of these events, transcriptome studies of specific substages must be conducted. However, conventional methods, such as bulk RNA-seq and RT-qPCR, are not able to detect the transcriptional variations effectively and precisely, especially for identifying cell types and stages with subtle differences. In recent years, mammalian meiotic transcriptomes have been intensively studied at the single-cell level by using single-cell RNA-seq (scRNA-seq) approaches, especially through two widely used platforms, Smart-seq2 and Drop-seq. The scRNA-seq protocols along with their downstream analysis enable researchers to accurately identify cell heterogeneities and investigate meiotic transcriptomes at a higher resolution. In this review, we compared bulk RNA-seq and scRNA-seq to show the advantages of the scRNA-seq in meiosis studies; meanwhile, we also pointed out the challenges and limitations of the scRNA-seq. We listed recent findings from mammalian meiosis (male and female) studies where scRNA-seq applied. Next, we summarized the scRNA-seq analysis methods and the meiotic marker genes from spermatocytes and oocytes. Specifically, we emphasized the different features of the two scRNA-seq protocols (Smart-seq2 and Drop-seq) in the context of meiosis studies and discussed their strengths and weaknesses in terms of different research purposes. Finally, we discussed the future applications of scRNA-seq in the meiosis field.

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“…Single-cell RNA-seq raw data for three GV oocytes (GV1, GV2 and GV3) and three MII oocytes (MII1, MII2 and MII3) were downloaded from GSE16 0334 that we have previously deposited in NCBI GEO repository (http://www.ncbi.nlm.nih.gov/geo/; Yang et al, 2021).…”

Section: Acquisition and Processing Of Raw Datamentioning

confidence: 99%

Global 3′‐untranslated region landscape mediated by alternative polyadenylation during meiotic maturation of pig oocytes

Mou

Fang

et al. 2021

Reprod Domestic Animals

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Alternative polyadenylation affects the length and composition of 3′-untranslated region (3′-UTR) and regulates mRNA stability or translational activity to affect important biological processes. However, global 3′-UTR landscape and its relationship with gamete maturation remain less studied. Here, we analysed our previously reported single-cell RNA-seq data of germinal vesicle and metaphase II stage oocytes in pigs to systematically catalogue the 3′-UTR dynamics during oocyte maturation. Two softwares (DaPars and APAtrap) were employed and identified 110 and 228 mRNAs with significantly different 3′-UTRs (adjusted p ≤ .05), respectively. Gene enrichment analyses found signalling pathways related with biological processes of female gametophyte production, methyltransferase activity and mRNA surveillance (DaPars) and cell cycle process, regulation of ERK1 and ERK2 cascade, regulation of translation, spindle organization, kinetochore, condensed chromosome and progesteronemediated oocyte maturation (APAtrap), respectively. Moreover, 18 of 110 mRNAs (|△PDUI| ≥ 0.25 and |log 2 PDUI ratio| ≥ 0.59) and 15 of 228 mRNAs (Perc. diff. ≥ 0.5) were with greater difference of 3′-UTR length or abundance, and integrative genomics viewer analysis further identified 4 (Alg10, Hadhb, Hsd17b4 and Sbds) of 18 mRNAs to be with 3′-UTR length differed ≥150 bp and 6 (Gcc1, Hnrnpa2b1, Lsm6, Prpf18, Sfr1 and Ust) of 15 mRNAs to be with 3′-UTR abundance extremely differed. Furthermore, the location, sequences and number of cis-elements were predicted, which were shown to derange cytoplasmic polyadenylation element, poly(A) site and microRNA binding sites within 3′-UTRs of Alg10, Hadhb, Hsd17b4 and Sbds mRNAs.Taken together, global 3′-UTR landscape changes dynamically with oocyte meiotic maturation, potentially involved in regulating oocyte meiotic process in pigs.

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Single‐cell RNA‐seq reveals mRNAs and lncRNAs important for oocytes in vitro matured in pigs

Cited by 13 publications

References 51 publications

Ovarian Aging: Role of Pituitary-Ovarian Axis Hormones and ncRNAs in Regulating Ovarian Mitochondrial Activity

Ovarian Aging: Role of Pituitary-Ovarian Axis Hormones and ncRNAs in Regulating Ovarian Mitochondrial Activity

The Application of Single-Cell RNA Sequencing in Mammalian Meiosis Studies

Global 3′‐untranslated region landscape mediated by alternative polyadenylation during meiotic maturation of pig oocytes

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