cells in vitro  (Precision X-Ray)

Journal: bioRxiv

Article Title: TET1 non-catalytic activity shapes the chromatin landscape that directs de novo methylation establishment in the male germline

doi: 10.1101/2025.10.29.685418

Figure Lengend Snippet: A) MA-plot for differential expression analysis of total RNA-seq in Tet1 -/- prospermatogonia vs WT (n=3, FDR ≤ 0.05, ≥2-fold change). B) Top five enriched GO biological process terms for downregulated DEGs in Tet1 -/- prospermatogonia. C) Top five enriched GO biological process terms for upregulated DEGs in Tet1 -/- prospermatogonia. D) Chromatin states assigned by ChromHMM using public datasets for CTCF, Pol II, and histone modifications across spermatogonial stem cells (SSC), spermatogonia (SPG), pachytene spermatocytes (PS), round spermatids (RS), and sperm (datasets used are in supplemental table). Chromatin state assignment is based on Encode consortium convention . E) Classes of repetitive elements enriched in regions with H3K4me3 loss. F) Top ten enriched GO biological process terms for regions with H3K4me3 gain.

Article Snippet: Ribosomal RNA-depleted total RNA libraries were generated using the SMART-Seq Total RNA Pico Input Kit with UMIs with ZapR Mammalian (Takara Bio) from 5 ng input according to the manufacturer’s protocol.

Techniques: Quantitative Proteomics, RNA Sequencing

Journal: bioRxiv

Article Title: TET1 non-catalytic activity shapes the chromatin landscape that directs de novo methylation establishment in the male germline

doi: 10.1101/2025.10.29.685418

Figure Lengend Snippet: A) Scatter plot of significantly altered H3K4me3 peaks in Tet1 -/- prospermatogonia (vs WT) at gene promoters and their associated gene expression changes as measured by total RNA-seq. Differentially expressed genes (FDR ≤ 0.05, ≥2-fold change) are highlighted with blue (downregulated) or red (upregulated) dots. B) Enrichment of H3K4me3 peaks lost or gained in Tet1 -/- prospermatogonia across chromatin states during spermatogenesis (SSC: spermatogonial stem cells; SPG: spermatogonia; PS: pachytene spermatocyte; RS: round spermatid), using ChromHMM. Chromatin states assignment is based on the ENCODE consortium projects and are defined in C) Motif enrichment for regions with H3K4me3 loss after masking repetitive elements. D) Motif enrichment for regions with H3K4me3 gain.

Article Snippet: Ribosomal RNA-depleted total RNA libraries were generated using the SMART-Seq Total RNA Pico Input Kit with UMIs with ZapR Mammalian (Takara Bio) from 5 ng input according to the manufacturer’s protocol.

Techniques: Gene Expression, RNA Sequencing