Journal: Nature Cell Biology

Article Title: The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate

doi: 10.1038/s41556-025-01703-z

Figure Lengend Snippet: ( a ) Dendrogram and heatmap of individual LAP2β CUT & RUN replicates (3 per condition) showing similarity of replicates for each genotype. ( b ) Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) values ( b ) and differences ( c ) between numbers of LAP2β domain states used in HMM domain calling. ( d ) Spike-in-controlled LAP2β tracks across a 50 Mb segment of chromosome 12 and corresponding 2-state HMM domain calls for 3 replicates of LAP2β CUT & RUN in WT mESCs. ( e ) Overlap between individual replicate LAP2β domains called by 2-state HMM in WT mESCs determined by multiinter package (Bedtools). ( f ) Comparison of LAP2β and LB1 domain protein-coding genes defined in this study versus previously defined LAD-resident protein-coding genes (determined by LB1 ChIP-seq) in mESCs in 2i + LIF culture conditions (PMID 29033129). ( g ) Number of LAP2β and LB1 domains identified in WT mESCs. ( h ) Genomic length of LAP2β and LB1 domains in WT mESCs.

Article Snippet: mES cells were cultured at 37 °C in 5% CO 2 under normoxic conditions in serum-free 2i + LIF medium (N2B27 basal medium, 3 μM CHIR-99021 (Selleckchem, S1263), 1 μM PD0325901 (Selleckchem, S1036), 10 3 U ml −1 LIF (Millipore Sigma, ESG1107), 55 μM β-mercaptoethanol (Gibco, 21985023) and 1× penicillin–streptomycin (GenClone, 25-512)).

Techniques: Comparison, ChIP-sequencing

Journal: Nature Cell Biology

Article Title: The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate

doi: 10.1038/s41556-025-01703-z

Figure Lengend Snippet: ( a ) Dendrogram and heatmap of individual H3K9me2 CUT & RUN replicates (3 per condition) showing similarity of replicates for each genotype. ( b ) Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) values ( b ) and differences ( c ) between numbers of H3K9me2 domain states used in HMM domain calling. ( d ) Spike-in-controlled H3K9me2 tracks across a 50 Mb segment of chromosome 12 and corresponding 2-state HMM domain calls for 3 replicates of H3K9me2 CUT & RUN in WT mESCs. ( e ) Overlap between individual replicate H3K9me2 domains called by 2-state HMM in WT mESCs determined by multiinter package (Bedtools). ( f ) Breakdown of WT mESC H3K9me2 domain genes, defined as those genes at least 90% within an H3K9me2 domain, by gene class. # indicates that lncRNAs are significantly depleted compared to the mouse genome (two-sided χ 2 test, p < 0.0001) while * indicates that pseudogenes are significantly enriched in H3K9me2 domains compared to the mouse genome (two-sided χ 2 test, p < 0.0001). ( g ) Overlap of H3K9me2 domain protein-coding genes defined in this study versus in a previous list of protein-coding genes within H3K9me2 domains identified by ChiP-seq in mESCs in 2i + LIF culture conditions (PMID 29033129). ( h ) Number of H3K9me2 domains identified across genotypes. ( i ) Genomic length of H3K9me2 domains across genotypes. ( j ) Kernel density plot showing distribution of spike-in-controlled H3K8me2 signal across genotypes.

Article Snippet: mES cells were cultured at 37 °C in 5% CO 2 under normoxic conditions in serum-free 2i + LIF medium (N2B27 basal medium, 3 μM CHIR-99021 (Selleckchem, S1263), 1 μM PD0325901 (Selleckchem, S1036), 10 3 U ml −1 LIF (Millipore Sigma, ESG1107), 55 μM β-mercaptoethanol (Gibco, 21985023) and 1× penicillin–streptomycin (GenClone, 25-512)).

Techniques: ChIP-sequencing