Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes
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ABSTRACT:
PROVIDER: PRJNA1145971 | ENA |
REPOSITORIES: ENA
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Project description:During oocyte maturation, the transition from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage coincides with dramatic chromatin reconfiguration and transcriptional silencing and is crucial for developmental competence. To study the transcriptome and DNA methylation dynamics during the NSN to SN transition we used single cell (sc)M&T-seq to generate scRNA-seq and sc bisulphite-seq data from GV oocytes, classified as NSN or SN by Hoechst staining of their nuclei. Transcriptome analysis showed a lower number of detected transcripts in SN oocytes as well as downregulation of 576 genes, which were enriched for processes related to mRNA processing. We used the RNA-seq data to generate a classifier, which can infer chromatin stage in scRNA-seq data sets, based on their transcription profile. The classifier was successfully tested in multiple published datasets of mouse models with a known skew in NSN:SN ratios. DNA methylation analysis showed increased methylation in SN compared to NSN oocytes, which was most pronounced in regions with intermediate levels of DNA methylation. Overlap with ChIP-seq data for the histone modifications H3K36me3, H3K4me3 and H3K27me3 showed that regions gaining methylation in SN oocytes are enriched for overlapping H3K36me3 and H3K27me3, which is unusual as these marks do not typically coincide. We believe that these late-methylating SN regions are in regions with high chromatin plasticity and that the overlap of H3K36me3 and H3K27me3 may indicate a transient switch or heterogeneity on a single-cell level.
2025-01-02 | GSE274327 | GEO
Project description:During oocyte maturation, the transition from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage coincides with dramatic chromatin reconfiguration and transcriptional silencing and is crucial for developmental competence. To study the transcriptome and DNA methylation dynamics during the NSN to SN transition we used single cell (sc)M&T-seq to generate scRNA-seq and sc bisulphite-seq data from GV oocytes, classified as NSN or SN by Hoechst staining of their nuclei. Transcriptome analysis showed a lower number of detected transcripts in SN oocytes as well as downregulation of 576 genes, which were enriched for processes related to mRNA processing. We used the RNA-seq data to generate a classifier, which can infer chromatin stage in scRNA-seq data sets, based on their transcription profile. The classifier was successfully tested in multiple published datasets of mouse models with a known skew in NSN:SN ratios. DNA methylation analysis showed increased methylation in SN compared to NSN oocytes, which was most pronounced in regions with intermediate levels of DNA methylation. Overlap with ChIP-seq data for the histone modifications H3K36me3, H3K4me3 and H3K27me3 showed that regions gaining methylation in SN oocytes are enriched for overlapping H3K36me3 and H3K27me3, which is unusual as these marks do not typically coincide. We believe that these late-methylating SN regions are in regions with high chromatin plasticity and that the overlap of H3K36me3 and H3K27me3 may indicate a transient switch or heterogeneity on a single-cell level.
2025-01-02 | GSE274329 | GEO
Project description:During oocyte maturation, the transition from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage coincides with dramatic chromatin reconfiguration and transcriptional silencing and is crucial for developmental competence. To study the transcriptome and DNA methylation dynamics during the NSN to SN transition we used single cell (sc)M&T-seq to generate scRNA-seq and sc bisulphite-seq data from GV oocytes, classified as NSN or SN by Hoechst staining of their nuclei. Transcriptome analysis showed a lower number of detected transcripts in SN oocytes as well as downregulation of 576 genes, which were enriched for processes related to mRNA processing. We used the RNA-seq data to generate a classifier, which can infer chromatin stage in scRNA-seq data sets, based on their transcription profile. The classifier was successfully tested in multiple published datasets of mouse models with a known skew in NSN:SN ratios. DNA methylation analysis showed increased methylation in SN compared to NSN oocytes, which was most pronounced in regions with intermediate levels of DNA methylation. Overlap with ChIP-seq data for the histone modifications H3K36me3, H3K4me3 and H3K27me3 showed that regions gaining methylation in SN oocytes are enriched for overlapping H3K36me3 and H3K27me3, which is unusual as these marks do not typically coincide. We believe that these late-methylating SN regions are in regions with high chromatin plasticity and that the overlap of H3K36me3 and H3K27me3 may indicate a transient switch or heterogeneity on a single-cell level.
2025-01-02 | GSE274300 | GEO
Project description:The transition of chromatin configuration in mammalian oocytes from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) is critical for acquiring the developmental competence. However, the genomic and epigenomic features underlying this process remain poorly understood. In the present study, we first establish the chromatin accessibility landscape of mouse oocyte from NSN to SN stage. Through the integrative analysis of multi-omics, we find that establishment of DNA methylation in oocytes is independent on the dynamics of chromatin accessibility. In contrast, histone H3K4me3 status is closely associated with the dynamics of accessible-regions during configuration transition. Furthermore, by focusing on the actively transcribed genes in NSN and SN oocytes, we discover that chromatin accessibility coupled with histone methylation (H3K4me3 and H3K27me3) participates in the transcriptional control during phase transition. In sum, our data serve as a broad resource for probing configuration transition in oocytes, and provide the potential evidence to elucidate the mechanism determining chromatin dynamics and oocyte quality.
2025-01-08 | GSE261972 | GEO
Project description:The transition of chromatin configuration in mammalian oocytes from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) is critical for acquiring the developmental competence. However, the genomic and epigenomic features underlying this process remain poorly understood. In the present study, we first establish the chromatin accessibility landscape of mouse oocyte from NSN to SN stage. Through the integrative analysis of multi-omics, we find that establishment of DNA methylation in oocytes is independent on the dynamics of chromatin accessibility. In contrast, histone H3K4me3 status is closely associated with the dynamics of accessible-regions during configuration transition. Furthermore, by focusing on the actively transcribed genes in NSN and SN oocytes, we discover that chromatin accessibility coupled with histone methylation (H3K4me3 and H3K27me3) participates in the transcriptional control during phase transition. In sum, our data serve as a broad resource for probing configuration transition in oocytes, and provide the potential evidence to elucidate the mechanism determining chromatin dynamics and oocyte quality.
2025-01-08 | GSE262346 | GEO
Project description:The transition of chromatin configuration in mammalian oocytes from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) is critical for acquiring the developmental competence. However, the genomic and epigenomic features underlying this process remain poorly understood. In the present study, we first establish the chromatin accessibility landscape of mouse oocyte from NSN to SN stage. Through the integrative analysis of multi-omics, we find that establishment of DNA methylation in oocytes is independent on the dynamics of chromatin accessibility. In contrast, histone H3K4me3 status is closely associated with the dynamics of accessible-regions during configuration transition. Furthermore, by focusing on the actively transcribed genes in NSN and SN oocytes, we discover that chromatin accessibility coupled with histone methylation (H3K4me3 and H3K27me3) participates in the transcriptional control during phase transition. In sum, our data serve as a broad resource for probing configuration transition in oocytes, and provide the potential evidence to elucidate the mechanism determining chromatin dynamics and oocyte quality.
2025-01-08 | GSE262265 | GEO
Project description:The transition of chromatin configuration in mammalian oocytes from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) is critical for acquiring the developmental competence. However, the genomic and epigenomic features underlying this process remain poorly understood. In the present study, we first establish the chromatin accessibility landscape of mouse oocyte from NSN to SN stage. Through the integrative analysis of multi-omics, we find that establishment of DNA methylation in oocytes is independent on the dynamics of chromatin accessibility. In contrast, histone H3K4me3 status is closely associated with the dynamics of accessible-regions during configuration transition. Furthermore, by focusing on the actively transcribed genes in NSN and SN oocytes, we discover that chromatin accessibility coupled with histone methylation (H3K4me3 and H3K27me3) participates in the transcriptional control during phase transition. In sum, our data serve as a broad resource for probing configuration transition in oocytes, and provide the potential evidence to elucidate the mechanism determining chromatin dynamics and oocyte quality.
2025-01-08 | GSE262263 | GEO
Project description:We selected NSN and SN GV oocytes based on FBL-GFP localization, and performed transcriptome profiling of single NSN and SN GV oocytes, and MII oocytes in vitro matured from NSN and SN GV oocytes.
2021-03-27 | GSE163935 | GEO
Project description:Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes [Bisulfite-Seq]
| PRJNA1145906 | ENA
Project description:Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes [ChIP-Seq]
| PRJNA1145970 | ENA