Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes
Abstract Background During the latter stages of their development, mammalian oocytes under dramatic chromatin reconfiguration, transitioning from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage, and concomitant transcriptional silencing. Although the NSN-SN transition is known...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | BMC Molecular and Cell Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12860-024-00527-3 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559036477046784 |
|---|---|
| author | Hannah Demond Soumen Khan Juan Castillo-Fernandez Courtney W. Hanna Gavin Kelsey |
| author_facet | Hannah Demond Soumen Khan Juan Castillo-Fernandez Courtney W. Hanna Gavin Kelsey |
| author_sort | Hannah Demond |
| collection | DOAJ |
| description | Abstract Background During the latter stages of their development, mammalian oocytes under dramatic chromatin reconfiguration, transitioning from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage, and concomitant transcriptional silencing. Although the NSN-SN transition is known to be essential for developmental competence of the oocyte, less is known about the accompanying molecular changes. Here we examine the changes in the transcriptome and DNA methylation during the NSN to SN transition in mouse oocytes. Results 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 (scBS-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 compared with NSN oocytes as well as downregulation of 576 genes, which were enriched for processes related to mRNA processing. We used the transcriptome data to generate a classifier that can infer chromatin stage in scRNA-seq datasets. The classifier was successfully tested in multiple published datasets of mouse models with a known skew in NSN: SN ratios. Analysis of the scBS-seq data showed increased DNA methylation in SN compared to NSN oocytes, which was most pronounced in regions with intermediate levels of methylation. Overlap with chromatin immunoprecipitation and sequencing (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 an unusual combination, as these marks do not typically coincide. Conclusions We characterise the transcriptome and DNA methylation changes accompanying the NSN-SN transition in mouse oocytes. We develop a classifier that can be used to infer chromatin status in single-cell or bulk RNA-seq data, enabling identification of altered chromatin transition in genetic knock-outs, and a quality control to identify skewed NSN-SN proportions that could otherwise confound differential gene expression analysis. We identify late-methylating regions in SN oocytes that are associated with an unusual combination of chromatin modifications, which may be regions with high chromatin plasticity and transitioning between H3K27me3 and H3K36me3, or reflect heterogeneity on a single-cell level. |
| format | Article |
| id | doaj-art-fa2782ce103844c890d87d0d3320f767 |
| institution | Kabale University |
| issn | 2661-8850 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Molecular and Cell Biology |
| spelling | doaj-art-fa2782ce103844c890d87d0d3320f7672025-01-05T12:49:48ZengBMCBMC Molecular and Cell Biology2661-88502025-01-0126111510.1186/s12860-024-00527-3Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytesHannah Demond0Soumen Khan1Juan Castillo-Fernandez2Courtney W. Hanna3Gavin Kelsey4Epigenetics Programme, Babraham InstituteEpigenetics Programme, Babraham InstituteEpigenetics Programme, Babraham InstituteEpigenetics Programme, Babraham InstituteEpigenetics Programme, Babraham InstituteAbstract Background During the latter stages of their development, mammalian oocytes under dramatic chromatin reconfiguration, transitioning from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage, and concomitant transcriptional silencing. Although the NSN-SN transition is known to be essential for developmental competence of the oocyte, less is known about the accompanying molecular changes. Here we examine the changes in the transcriptome and DNA methylation during the NSN to SN transition in mouse oocytes. Results 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 (scBS-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 compared with NSN oocytes as well as downregulation of 576 genes, which were enriched for processes related to mRNA processing. We used the transcriptome data to generate a classifier that can infer chromatin stage in scRNA-seq datasets. The classifier was successfully tested in multiple published datasets of mouse models with a known skew in NSN: SN ratios. Analysis of the scBS-seq data showed increased DNA methylation in SN compared to NSN oocytes, which was most pronounced in regions with intermediate levels of methylation. Overlap with chromatin immunoprecipitation and sequencing (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 an unusual combination, as these marks do not typically coincide. Conclusions We characterise the transcriptome and DNA methylation changes accompanying the NSN-SN transition in mouse oocytes. We develop a classifier that can be used to infer chromatin status in single-cell or bulk RNA-seq data, enabling identification of altered chromatin transition in genetic knock-outs, and a quality control to identify skewed NSN-SN proportions that could otherwise confound differential gene expression analysis. We identify late-methylating regions in SN oocytes that are associated with an unusual combination of chromatin modifications, which may be regions with high chromatin plasticity and transitioning between H3K27me3 and H3K36me3, or reflect heterogeneity on a single-cell level.https://doi.org/10.1186/s12860-024-00527-3OocyteTranscriptionChromatinDNA methylationHistonesscRNA-seq |
| spellingShingle | Hannah Demond Soumen Khan Juan Castillo-Fernandez Courtney W. Hanna Gavin Kelsey Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes BMC Molecular and Cell Biology Oocyte Transcription Chromatin DNA methylation Histones scRNA-seq |
| title | Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes |
| title_full | Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes |
| title_fullStr | Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes |
| title_full_unstemmed | Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes |
| title_short | Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes |
| title_sort | transcriptome and dna methylation profiling during the nsn to sn transition in mouse oocytes |
| topic | Oocyte Transcription Chromatin DNA methylation Histones scRNA-seq |
| url | https://doi.org/10.1186/s12860-024-00527-3 |
| work_keys_str_mv | AT hannahdemond transcriptomeanddnamethylationprofilingduringthensntosntransitioninmouseoocytes AT soumenkhan transcriptomeanddnamethylationprofilingduringthensntosntransitioninmouseoocytes AT juancastillofernandez transcriptomeanddnamethylationprofilingduringthensntosntransitioninmouseoocytes AT courtneywhanna transcriptomeanddnamethylationprofilingduringthensntosntransitioninmouseoocytes AT gavinkelsey transcriptomeanddnamethylationprofilingduringthensntosntransitioninmouseoocytes |