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. 2024 May 9;22(1):qzad004.
doi: 10.1093/gpbjnl/qzad004.

GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice

Jianting An  1   2   3   4   5 , Jing Wang  1   2   3   4 , Siming Kong  1   2   3   4   5 , Shi Song  1   2   3   4 , Wei Chen  1   2   3   4 , Peng Yuan  1   2   3   4 , Qilong He  1   2   3   4 , Yidong Chen  1   2   3   4 , Ye Li  1   2   3   4 , Yi Yang  1   2   3   4 , Wei Wang  1   2   3   4   5 , Rong Li  1   2   3   4 , Liying Yan  1   2   3   4 , Zhiqiang Yan  1   2   3   4 , Jie Qiao  1   2   3   4   5   6
Affiliations

GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice

Jianting An et al. Genomics Proteomics Bioinformatics. .

Abstract

Gametogenesis plays an important role in the reproduction and evolution of species. The transcriptomic and epigenetic alterations in this process can influence the reproductive capacity, fertilization, and embryonic development. The rapidly increasing single-cell studies have provided valuable multi-omics resources. However, data from different layers and sequencing platforms have not been uniformed and integrated, which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and spermatogenesis. Here, we develop GametesOmics, a comprehensive database that integrates the data of gene expression, DNA methylation, and chromatin accessibility during oogenesis and spermatogenesis in humans and mice. GametesOmics provides a user-friendly website and various tools, including Search and Advanced Search for querying the expression and epigenetic modification(s) of each gene; Tools with Differentially expressed gene (DEG) analysis for identifying DEGs, Correlation analysis for demonstrating the genetic and epigenetic changes, Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors (TFs), and MethylView for studying the genomic distribution of epigenetic modifications. GametesOmics also provides Genome Browser and Ortholog for tracking and comparing gene expression, DNA methylation, and chromatin accessibility between humans and mice. GametesOmics offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development, and can be accessed at http://gametesomics.cn/.

Keywords: Epigenomics; Gametogenesis; Oogenesis; Spermatogenesis; Transcriptomics.

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Conflict of interest statement

The authors have declared no competing interests.

Figures

Figure 1
Figure 1
The framework of GametesOmics A. Data collection of multi-omics sequencing data. B. The custom pipeline to process the collected data for downstream applications and display in GametesOmics. C. The tools provided by GametesOmics. WCG sites includes ACG or TCG and GCH sites includes GCA, GCC or GCT. GEO, Gene Expression Omnibus; SRA, Sequence Read Archive; ENA, European Nucleotide Archive; RNA-seq, RNA sequencing; BS-seq, bisulfite sequencing; COOL-seq, chromatin overall omic-scale landscape sequencing; TF, transcription factor; DEG, differentially expressed gene.
Figure 2
Figure 2
Screening the regulatory factors of spermatids in humans and mice A. UMAP plot showing the mouse spermatogenesis trajectory. Developmental stages are marked by different colors. “spermatids.steps3to4” stage is highlighted. B. Heatmap showing the expression of stage-specific genes of the “spermatids.steps3to4” stage in mouse spermatogenesis. C. Bubble plot showing the top 5 TFs enriched in the promoters of stage-specific genes of the “spermatids.steps3to4” stage, with selected Rfx2 motif displayed below. D. UMAP plot showing the human spermatogenesis trajectory. Developmental stages are marked by different colors. “spermatids.2” stage is highlighted. E. Heatmap showing the expression of stage-specific genes of the “spermatids.2” stage in human spermatogenesis. F. Bubble plot showing the top 5 TFs enriched in the promoters of stage-specific genes of the “spermatids.2” stage, with selected ATF2 motif displayed below. G. Line plot showing the expression of PACRG, MORN3, GAPDHS, and CREM during human spermatogenesis. UMAP, Uniform Manifold Approximation and Projection; RPM, reads of exon model per million mapped reads.
Figure 3
Figure 3
Screening the key genes involved in oocyte growth in humans and mice A. Volcano plot showing the fold changes and P values of DEGs between GO1 and FGO in humans and mice. B. Venn diagram of the highly expressed DEGs in humans and mice at the GO1 stage. C. GO enrichment of the unique highly expressed DEGs in human GO1 stage. D. GO enrichment of the unique highly expressed DEGs in mouse GO1 stage. E. GO enrichment of the overlapping highly expressed DEGs in human and mouse GO1 stages. F. The gene expression levels (showed by the box plot), the DNA methylation tracks (showed by UCSC Genome Browser in blue), and the chromatin accessibility tracks (showed by UCSC Genome Browser in purple) of SIRT1/Sirt1 in human and mouse oogenesis. G. The gene expression levels (showed by the box plot), the DNA methylation tracks (showed by UCSC Genome Browser in blue), and the chromatin accessibility tracks (showed by UCSC Genome Browser in purple) of SMAD4/Smad4 in human and mouse oogenesis. H. The gene expression levels (showed by the box plot), the DNA methylation tracks (showed by UCSC Genome Browser in blue), and the chromatin accessibility tracks (showed by UCSC Genome Browser in purple) of ESR2/Esr2 in human and mouse oogenesis. GO1, growing oocyte I; GO2, growing oocyte II; GO3, growing oocyte III; M I, metaphase I oocyte, M II, metaphase II oocyte; NGO, non-growing oocytes; FGO, fully-grown oocyte; GO, Gene Ontology; UCSC, University of California Santa Cruz.
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