Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes

Abstract

Oocyte growth is a key step in forming mature eggs that are ready to be fertilized. The states and modifications of chromatin represent critical sources of information for this process. However, the dynamics and interrelations of these chromatin characteristics remain elusive. In this study, we developed an improved scCOOL-seq technique (iscCOOL-seq), which is a multi-omics, single-cell and single-base resolution method with high mapping rates, and explored the chromatin accessibility landscape and its relationship to DNA methylation in growing mouse oocytes. The most dramatic change in chromatin accessibility occurs during oocyte growth initiation, accompanied with prominent transcriptome alterations and an elevated variation in DNA methylation levels among individual oocytes. Unlike CpG islands (CGIs), partially methylated domains (PMDs) are associated with a low density of nucleosome-depleted regions (NDRs) during the whole maturation period. Surprisingly, highly expressed genes are usually associated with NDRs at their transcriptional end sites (TESs). In addition, genes with de novo methylated gene bodies during oocyte maturation are already open at their promoters before oocyte growth initiation. Furthermore, epigenetic and transcription factors that might be involved in oocyte maturation are identified. Our work paves the way for dissecting the complex, yet highly coordinated, epigenetic alterations during mouse oocyte growth and the establishment of totipotency.

Dynamics of the Transcriptome and Accessible Chromatin Landscapes During Early Goose Ovarian Development

“…Therefore, we integrated RNA-seq and ATAC-seq to unravel the transcriptional networks regulating early avian ovarian development. Our results showed that the most extensive changes in both the ovarian transcriptome and chromatin accessibility took place during the transition from mid-to late embryogenesis (P0 vs. E15), indicating that transcriptional activity of target genes is strongly associated with the accessibility of functional genomic regions (i.e., transcription factor occupancy) that is finely tuned at the chromatin level, which was concordant with previous findings in a range of vertebrate species (Stergachis et al, 2014;Ackermann et al, 2016;Lowdon et al, 2016;Miyamoto et al, 2018;Gu et al, 2019). As revealed by ATAC-seq analysis, the majority (>90%) of developmental stage-selective peaks was present in intronic and intergenic regions, whereas less than 4% of peaks occurred in regions around TSS and TTS.…”

“…Although understanding how gene regulatory networks control the orderly progression of these events remains a long-standing challenge, recent advances in determining dynamic gene expression and chromatin accessibility changes in human and mouse ovarian tissues and cells using next generation sequencing-based epigenomic techniques (e.g., RNAseq, CHIP-seq, DNase-seq, and ATAC-seq) are contributing to the identification of key genes, cis-regulatory elements, and organism-specific regulatory systems (Apostolou and Hochedlinger, 2013;Barragan et al, 2017;Guo et al, 2017;Yu et al, 2017;Miyamoto et al, 2018;Gu et al, 2019). Therefore, we integrated RNA-seq and ATAC-seq to unravel the transcriptional networks regulating early avian ovarian development.…”

“…Over the last 20 years, with the urge demand for solving the infertility problems related to early ovarian development, the improved experimental systems, and the advent of high-throughput sequencing technologies, considerable progresses have been made in understanding the critical molecular events during early follicle development, including perinatal oocyte loss, primordial follicle formation, and the primordial-to-secondary follicle transition, as well as the underlying molecular mechanisms in a range of mammalian species (Wang et al, 2017). One of the most exciting progresses in the first decade is the illustration of the pivotal roles of intra-ovarian factors (especially oocyte-derived ones) and oocyte-somatic cell interaction during primordial follicle formation and development (Guigon and Magre, 2006;Hsueh et al, 2015), and these events have recently been demonstrated to be associated with dynamic reorganization of open chromatin in both oocytes and somatic cells (Apostolou and Hochedlinger, 2013;Miyamoto et al, 2018;Gu et al, 2019). In contrast, there is almost a paucity of information about the accessible chromatin dynamic profiles during ovarian development in birds, although some epigenetic changes, such as chromatin remodeling, cytosine methylation, histone modification, and non-coding RNAs, have been evidenced to regulate avian ovarian cell functions (Krasikova et al, 2012;Guioli and Lovell-Badge, 2016;Li et al, 2019).…”

Human Developmental Cell Atlas: milestones achieved and the roadmap ahead

“…CITE-seq, REAP-seq 35,36 ; multi-parameter protein analysis e.g. mass cytometry, MICS, CODEX, MIBI 37 ; combinations of DNA modifications, chromatin accessibility and DNA conformation 38 as well as legacy knowledge of embryonic cell type definitions augmented by information from multiple animal models across evolutionary time. Multi-omics data sets from identical cells will refine cell type definitions and function as a scaffold to align single modality genomics datasets.…”

The 5.8S pre‐rRNA maturation factor, M‐phase phosphoprotein 6, is a female fertility factor required for oocyte quality and meiosis

“…Meiosis is regulated by numerous fertility factors, among which maturation-promoting factor (MPF, composed of cyclin B and cdk1), 1 spindle checkpoint proteins 2 Based on recent knowledge, researchers agree that oocyte maturation should include cytoplasmic, nuclear and epigenetic maturation, [6][7][8] and further studies are required to completely resolve the mechanism. Recently, researchers identified many potential female fertility factors through transcriptome [8][9][10][11] and proteome-wide [12][13][14] analyses. For loss-of-function studies, besides small interfering RNA knockdown, the protein-depletion method using specific antibodies and trim21-mediated protein degradation provided a powerful tool, 15 which we have applied successfully to IVM oocytes.…”