Journal: bioRxiv

Article Title: Decoding the pituitary gonadotrope regulatory architecture governing the preovulatory surge in vivo

doi: 10.1101/2025.11.18.689023

Figure Lengend Snippet: (A) Spherical representation of gonadotrope cell organisation, with pseudotime (θ axis, blue dashed line) and latent time (ϕ axis, red dashed line). Each gonadotrope cell’s pseudotime and latent time values were projected onto a circular space, and smoothed models were used to combine them into a single trajectory (solid black line). Individual cells are shown as coloured points by sampling stage: D2 10 am (blue), PE 10 am (green), PE 6 pm (red), and E 10 am (yellow). The projection of cells onto this periodic model defines a new time value, the “regulatory time,” capturing the cyclical progression of cellular states across the estrus cycle. (B) Ordering of pituitary gonadotrope cells according to pseudotime, latent time or regulatory time, with colours corresponding to the sampling stage. The upper panel shows the expected distribution according to the stage of sample collection. (C-E) Heatmaps of DAEs ( C ), GDVs ( D ) and DEGs ( E ) in gonadotrope cells across regulatory time. The upper panel shows gonadotrope cell distribution according to regulatory time. Signals are shown for each region or gene (lines) across the regulatory time (columns). The heatmap colour scale represents the relative signal (Z-score) in gonadotrope cells across the regulatory time. DAEs, GDVs and DEGs are clustered based on their respective accessibility (Cluster A1 to A5), velocity (Cluster V1 to V5) or expression profiles (Cluster E1 to E4). A dotted line indicates the transition between early to late PE, framing the preovulatory surge. (F) Identification of differentially regulated genes in gonadotrope cells across the estrus cycle. A gene was considered differentially regulated if associated with a DAE and displaying differential velocity and expression across regulatory time. The Venn diagram represents the overlap between GDV, DEG and DAE-associated genes. (G) Mean temporal trajectories of chromatin accessibility, mRNA velocity and mRNA abundance for each identified pair of gene and DAE (n = 1816 pairs). Mean ± SEM signals are plotted across the regulatory time. ATAC and RNA data are rescaled to a common amplitude (left y-axis) for comparison, while velocity is shown on its native scale (right y-axis).

Article Snippet: Nuclei purified from frozen hemi-pituitaries collected in the four above-mentioned females were processed using the Single Cell Multiome ATAC + Gene Expression platform (10x Genomics), followed by high-throughput sequencing.

Techniques: Sampling, Expressing, Comparison

Journal: Nature Cell Biology

Article Title: Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells

doi: 10.1038/s41556-025-01767-x

Figure Lengend Snippet: a , Representative top views, side views and 3D reconstructions of LaminB1-RFP-tagged hiPS cells subjected to compression (scale bars, 10 µm; images representative of six independent experiments). b , UMAP of scRNA- and scATAC-seq from hiPS cells subjected to compression for timepoints indicated. c , A heatmap of predicted regulons enriched in compressed cells from SCENIC+ analyses of the multiome data. d , A schematic of experimental outline for genome-wide mapping of H3K27ac changes. e , f , Heatmap ( e ) and metaplot ( f ) analysis of mean H3K27ac levels at active promoters and predicted active enhancer regions. Note reduction in H3K27ac enrichment at promoters across all conditions and at enhancers in cells compressed in basal medium or exposed to hypertonic shock. g , UpSet plot showing an overlap of enhancers decommissioned in compression and hypertonic shock conditions. h , Venn diagram and Reactome pathway enrichment of compression-specific and shared decommissioned enhancers as defined in g . i , A schematic of the experimental outline for the quantification of the nascent transcriptome. 4sU, 4-thiouridine. j , Quantification of RNA synthesis across conditions from TTseq. Note reduced synthesis across all conditions compared with pluripotency medium condition ( n = 3 biological replicates per condition). k , Quantification of total changes in nascent RNA production across conditions relative to the pluripotency medium condition ( n = log 2 FC of 19,288 genes computed from 3 biological replicates; Tukey’s box plots show 75th, 50th and 25th percentiles). l , A heatmap of z scores from altered nascent RNA levels of relevant transcripts from TTseq quantified by DESeq2. Note increased levels of IEGs specifically in cells compressed in pluripotency medium while key pluripotency and growth factor regulators are repressed. Comp, compression; Hyper, hypertonic; Rec, recovery; pluri, pluripotency.

Article Snippet: Two biological replicates were prepared for each condition and sequenced using the Chromium Single Cell Multiome platform (10x Genomics).

Techniques: Genome Wide