Fig. 4

Differential expression of lncRNAs and PCGs across nuclear subcellular fractions. Subcellular fraction bias between: a nucleoplasm (NP) and the chromatin-bound (CB) fraction; or b within the chromatin-bound fraction, between polyA-selected and non-polyA selected RNA, based on an edgeR adjusted p-value < 0.001 in at least one of the four biological conditions assayed (Table S2B and Table S2C, columns D and E). Gray dots are PCGs, red dots are lncRNAs; numbers of genes whose transcripts are enriched in each fraction are shown above and below the dashed line, respectively. For any gene showing a significant bias in more than one biological condition, data is shown for the condition with the highest FPKM value. In b, green box encompasses CBnPAs-biased genes with log2 fold-change < − 6, which are further analyzed in e and in f.  c and d, Distributions of gene lengths (c) and percent intronic length (d) for chromatin-bound biased, non-compartment-biased (UB, unbiased) and CBnPAs-biased, graphed separately for lncRNAs and PCGs; also see Table S1D, columns M-Q. Significant differences for PCGs are as marked; no significant differences were seen for lncRNAs. See Figure S4 for corresponding data for NP-biased vs CB-biased genes, and Figure S5 for CB-biased genes, with vs without polyA selection. e and f, Normalized expression for the 506 lncRNAs (e) and 26 PCGs (f) that were very strongly CBnPAs-biased (genes from green box in b) across all 4 biological conditions (marked at top), for each of 5 subcellular fractions (columns from left to right within each condition: Cytoplasm, Nucleus, Nucleoplasm, Chromatin-bound, and Chromatin-bound non-PolyA-selected). See data in Table S2C, columns AD-AS. Data are shown for expression of each gene (row), normalized to the highest expression of that gene in a single condition and fraction. Seventeen of the 506 lncRNAs show sex-biased expression (Table S3A), and 19 show TCPOBOP-responsiveness (Table S3B) in at least one fraction. g and h, Distribution of expression values (FPKM) for the subsets of 6387 lncRNAs (g) and 12,233 PCGs (h) expressed at FPKM > 1 in at least one of the 5 subcellular fractions. The maximum expression of the gene across the four biological conditions is graphed for each subcellular fraction. Only a subset of the lncRNAs and PCGs were expressed at FPKM > 1 in each fraction (gene count numbers below each column). Based on expression data in Tables S2A-S2C. Median FPKM values (black horizontal midline) and IQR (error bars) are marked. Red horizontal lines compare lncRNAs, or PCGs, between fractions: adjusted p-value < 0.05 (*), or < 0.0001 (**)