Shifts in domain positioning relative to speckles are small and correlate with changes in expression of cell type–specific genes. (A,B) Scatterplots show change in scaled SON TSA-seq scores (1−100 range) averaged over each domain (y-axis) with a significant score change for domains closer to speckles in HFFc6 (A) or H1 (B) as a function of scaled TSA-seq scores averaged over each domain (x-axis) in H1 (top) or HFFc6 (bottom). (C,G) Scatter plots show scaled SON TSA-seq scores (1−100 range) in H1 hESCs (y-axis) versus HFFc6 (x-axis) for protein-coding genes (dots) that are up-regulated in HFF (C) or in H1 (G): top panels: all up-regulated genes; middle panels: up-regulated genes in regions closer to nuclear speckles in HFFc6 (C) or in H1 (G); bottom panels: up-regulated genes in regions that are not closer to nuclear speckles. Red dashed lines represent thresholds for statistically significant changes in scaled HFFc6 versus H1 SON TSA-seq scores. (D,H) Comparison of log₂-fold changes in gene expression for protein-coding genes significantly up-regulated in HFF (D, HFF/ H1) or in H1 (H, H1/HFF) for: up-regulated genes in regions closer to nuclear speckles in HFFc6 (D, left, blue) or in H1 (H, left, blue) versus up-regulated genes in regions that are not closer to nuclear speckles in HFFc6 (D, right, orange) or in H1 (H, right, orange) (Welch's t-test). Box plots show median (inside line), 25th (box bottom), and 75th (box top) percentiles, 75th percentile to highest value within 1.5-fold of box height (top whisker), and 25th percentile to lowest value within 1.5-fold of box height (bottom whisker). (E,F,I,J) Top Gene Ontology (GO) terms for protein-coding genes up-regulated in HFF (E,F) or in H1 (I,J) for up-regulated genes in regions closer to nuclear speckles in HFFc6 (E) or in H1 (I) versus up-regulated genes in regions not closer to nuclear speckles in HFFc6 (F) or in H1 (J). Abbreviated GO terms: (E) ECM: extracellular matrix organization; apop regu: negative regulation of apoptotic process; (F) chromatin silenc: chromatin silencing at rDNA; rep-dep nuc assem: DNA replication-dependent nucleosome assembly; (I) homoph cell adhes: homophilic cell adhesion via plasma membrane adhesion molecules; antigen proces: antigen processing and presentation of peptide or polysaccharide antigen via MHC class II; nerv sys dev: nervous system development; (J) chem synap transmis: chemical synaptic transmission; ion transmem transp: ion transmembrane transport; synap assem regu: positive regulation of synapse assembly; neurotransmitter regu: calcium ion-regulated exocytosis of neurotransmitter.