Single-cell analysis of Non-CG methylation dynamics and gene expression in human oocyte maturation

ABSTRACTOocyte maturation is a coordinated process that is tightly linked to reproductive potential. A better understanding of gene regulation during human oocyte maturation will not only answer an important question in biology, but also facilitate the development of in vitro maturation technology as a fertility treatment. We generated single-cell transcriptome and use previously published single-cell methylome data from human oocytes at different maturation stages to investigate how genes are regulated during oocyte maturation, focusing on the potential regulatory role of non-CG methylation. DNMT3B, a gene encoding a key non-CG methylation enzyme, is one of the 1000 genes upregulated in mature oocytes, which may be at least partially responsible for the increased non-CG methylation as oocytes mature. Non-CG differentially methylated regions (DMRs) between mature and immature oocytes have multiple binding motifs for transcription factors, some of which bind with DNMT3B and may be important regulators of oocyte maturation through non-CG methylation. Over 98% of non-CG DMRs locate in transposable elements, and these DMRs are correlated with expression changes of the nearby genes. Taken together, this data indicates that global non-CG hypermethylation during oocyte maturation may play an active role in gene expression regulation, potentially through the interaction with transcription factors.

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Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation

PLoS ONE ◽

10.1371/journal.pone.0241698 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241698

Author(s):

Bo Yu ◽

Naresh Doni Jayavelu ◽

Stephanie L. Battle ◽

Jessica C. Mar ◽

Timothy Schimmel ◽

...

Keyword(s):

Transcription Factors ◽

Single Cell ◽

Oocyte Maturation ◽

Gene Expression Regulation ◽

Single Cell Analysis ◽

Reproductive Potential ◽

Cpg Methylation ◽

Fertility Treatment ◽

Human Oocyte

Oocyte maturation is a coordinated process that is tightly linked to reproductive potential. A better understanding of gene regulation during human oocyte maturation will not only answer an important question in biology, but also facilitate the development of in vitro maturation technology as a fertility treatment. We generated single-cell transcriptome and used our previously published single-cell methylome data from human oocytes at different maturation stages to investigate how genes are regulated during oocyte maturation, focusing on the potential regulatory role of non-CpG methylation. DNMT3B, a gene encoding a key non-CpG methylation enzyme, is one of the 1,077 genes upregulated in mature oocytes, which may be at least partially responsible for the increased non-CpG methylation as oocytes mature. Non-CpG differentially methylated regions (DMRs) between mature and immature oocytes have multiple binding motifs for transcription factors, some of which bind with DNMT3B and may be important regulators of oocyte maturation through non-CpG methylation. Over 98% of non-CpG DMRs locate in transposable elements, and these DMRs are correlated with expression changes of the nearby genes. Taken together, this data indicates that global non-CpG hypermethylation during oocyte maturation may play an active role in gene expression regulation, potentially through the interaction with transcription factors.

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Single-cell analysis reveals a nestin+ tendon stem/progenitor cell population with strong tenogenic potentiality

Science Advances ◽

10.1126/sciadv.1600874 ◽

2016 ◽

Vol 2 (11) ◽

pp. e1600874 ◽

Cited By ~ 42

Author(s):

Zi Yin ◽

Jia-jie Hu ◽

Long Yang ◽

Ze-Feng Zheng ◽

Cheng-rui An ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Cell Population ◽

Single Cell Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cell Analysis ◽

Nestin Expression

The repair of injured tendons remains a formidable clinical challenge because of our limited understanding of tendon stem cells and the regulation of tenogenesis. With single-cell analysis to characterize the gene expression profiles of individual cells isolated from tendon tissue, a subpopulation of nestin+ tendon stem/progenitor cells (TSPCs) was identified within the tendon cell population. Using Gene Expression Omnibus datasets and immunofluorescence assays, we found that nestin expression was activated at specific stages of tendon development. Moreover, isolated nestin+ TSPCs exhibited superior tenogenic capacity compared to nestin− TSPCs. Knockdown of nestin expression in TSPCs suppressed their clonogenic capacity and reduced their tenogenic potential significantly both in vitro and in vivo. Hence, these findings provide new insights into the identification of subpopulations of TSPCs and illustrate the crucial roles of nestin in TSPC fate decisions and phenotype maintenance, which may assist in future therapeutic strategies to treat tendon disease.

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Changes in the Mitochondria-Related Nuclear Gene Expression Profile during Human Oocyte Maturation by the IVM Technique

Cells ◽

10.3390/cells11020297 ◽

2022 ◽

Vol 11 (2) ◽

pp. 297

Author(s):

Zhi-Yong Yang ◽

Min Ye ◽

Ya-Xin Xing ◽

Qi-Gui Xie ◽

Jian-Hong Zhou ◽

...

Keyword(s):

Oocyte Maturation ◽

Single Cell Analysis ◽

Nuclear Gene ◽

Mature Stage ◽

Human Oocyte ◽

Acid Oxidation ◽

Developmental Needs ◽

Nuclear Gene Expression

To address which mitochondria-related nuclear differentially expressed genes (DEGs) and related pathways are altered during human oocyte maturation, single-cell analysis was performed in three oocyte states: in vivo matured (M-IVO), in vitro matured (M-IVT), and failed to mature in vitro (IM-IVT). There were 691 DEGs and 16 mitochondria-related DEGs in the comparison of M-IVT vs. IM-IVT oocytes, and 2281 DEGs and 160 mitochondria-related DEGs in the comparison of M-IVT vs. M-IVO oocytes, respectively. The GO and KEGG analyses showed that most of them were involved in pathways such as oxidative phosphorylation, pyruvate metabolism, peroxisome, and amino acid metabolism, i.e., valine, leucine, isoleucine, glycine, serine, and threonine metabolism or degradation. During the progress of oocyte maturation, the metabolic pathway, which derives the main source of ATP, shifted from glucose metabolism to pyruvate and fatty acid oxidation in order to maintain a low level of damaging reactive oxygen species (ROS) production. Although the immature oocytes could be cultured to a mature stage by an in vitro technique (IVM), there were still some differences in mitochondria-related regulations, which showed that the mitochondria were regulated by nuclear genes to compensate for their developmental needs. Meanwhile, the results indicated that the current IVM culture medium should be optimized to compensate for the special need for further development according to this disclosure, as it was a latent strategy to improve the effectiveness of the IVM procedure.

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Modular Derivation and Unbiased Single-cell Analysis of Regional Human Hindbrain And Spinal Neurons Enables Discovery of Nuanced Transcriptomic Patterns along Developmental Axes

10.1101/2021.10.14.464440 ◽

2021 ◽

Author(s):

Nisha R. Iyer ◽

Junha Shin ◽

Stephanie Cuskey ◽

Yucheng Tian ◽

Noah R. Nichol ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Single Cell Analysis ◽

Expression Patterns ◽

Gene Expression Pattern ◽

In Vitro Models ◽

Consensus Clustering ◽

Neuronal Diversity ◽

Regional Specificity

Our inability to derive the vast neuronal diversity of the posterior central nervous system (pCNS) using human pluripotent stem cells (hPSCs) poses a major impediment to understanding human neurodevelopment and disease in the hindbrain and spinal cord. Here we establish a modular differentiation paradigm that recapitulates patterning along both the rostrocaudal (R/C) and dorsoventral (D/V) axes of the pCNS, enabling derivation of any neuronal phenotype with discrete regional specificity. First, neuromesodermal progenitors (NMPs) with discrete Hox profiles are efficiently converted to pCNS progenitors (pCNSPs). Then by tuning D/V signaling, pCNSPs are directed to ventral Shh-dependent MNs (MNs) and locomotor interneurons (INs) or dorsal TGF-β-dependent proprioceptive INs and TGF-β-independent sensory INs. We applied D/V protocols to NMPs spanning the R/C axis for expansive single-cell RNA-sequencing (scRNAseq) analysis. By implementing a novel computational pipeline comprising sparse non-negative matrix factorization, consensus clustering, and combinatorial gene expression pattern identification, we detect hundreds of transcriptional markers within region-specific neuronal phenotypes, enabling discovery of gene expression patterns along the developmental axes. These findings highlight the potential of these resources to advance a mechanistic understanding of pCNS development, expand the potential and accuracy of in vitro models, and inform novel regenerative therapeutic strategies.

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Single-cell transcriptome and cell-specific network analysis reveal the reparative effect of neurotrophin-4 in preantral follicles grown in vitro

Reproductive Biology and Endocrinology ◽

10.1186/s12958-021-00818-w ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Yingchun Guo ◽

Peigen Chen ◽

Tingting Li ◽

Lei Jia ◽

Yi Zhou ◽

...

Keyword(s):

Network Analysis ◽

Single Cell ◽

Fertility Preservation ◽

Oocyte Maturation ◽

Human Oocyte ◽

Preantral Follicle ◽

Preantral Follicles ◽

Reparative Effect ◽

Human And Mouse

Abstract Background In-vitro-grow (IVG) of preantral follicles is essential for female fertility preservation, while practical approach for improvement is far from being explored. Studies have indicated that neurotrophin-4 (NT-4) is preferentially expressed in human preantral follicles and may be crucial to preantral follicle growth. Methods We observed the location and expression of Tropomyosin-related kinase B (TRKB) in human and mouse ovaries with immunofluorescence and Western blot, and the relation between oocyte maturation and NT-4 level in follicular fluid (FF). Mice model was applied to investigate the effect of NT-4 on preantral follicle IVG. Single-cell RNA sequencing of oocyte combined with cell-specific network analysis was conducted to uncover the underlying mechanism of effect. Results We reported the dynamic location of TRKB in human and mouse ovaries, and a positive relationship between human oocyte maturation and NT-4 level in FF. Improving effect of NT-4 was observed on mice preantral follicle IVG, including follicle development and oocyte maturation. Transcriptome analysis showed that the reparative effect of NT-4 on oocyte maturation might be mediated by regulation of PI3K-Akt signaling and subsequent organization of F-actin. Suppression of advanced stimulated complement system in granulosa cells might contribute to the improvement. Cell-specific network analysis revealed NT-4 may recover the inflammation damage induced by abnormal lipid metabolism in IVG. Conclusions Our data suggest that NT-4 is involved in ovarian physiology and may improve the efficiency of preantral follicle IVG for fertility preservation.

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Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression

Biochemistry and Cell Biology ◽

10.1139/o05-062 ◽

2005 ◽

Vol 83 (4) ◽

pp. 535-547 ◽

Cited By ~ 7

Author(s):

Gareth N Corry ◽

D Alan Underhill

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcription Factors ◽

Transcriptional Activation ◽

Current Knowledge ◽

Nuclear Architecture ◽

Subnuclear Localization ◽

Modular Structures

To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein–protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.Key words: transcription, subnuclear localization, chromatin, gene expression, nuclear architecture.

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