Fig. 7

Sex-biased and TCPOBOP-responsive lncRNAs: select examples. a Robust male-biased (left) and female-biased lncRNAs (right) (Table S4A, column J) and their expression levels across five subcellular compartments (data based on Tables S2A-S2C). Solid lines indicate expression level in livers of the dominant sex, and dashed lines indicate expression in the opposite sex. Also see Table S3A. b and c UCSC genome browser screen shots highlighting individual sex-biased genes. The first two tracks in each panel describe the chromatin state (CS) in untreated male and female liver (red = inactive state, green = enhancer state, purple = actively transcribed state; see key of all 14 chromatin states at bottom right, based on [47]). Also shown are tracks indicating the TAD structure (horizontal bar, in c), as marked, followed by the Merged DHS track, which marks DHS that are female-biased (pink vertical bars), male-biased (blue bars) and sex-independent (gray bars). Tracks presenting RefSeq gene structures (blue) and lncRNA structures (green) follow. b Three female-biased lncRNAs and two female-biased PCGs (red asterisks, pink boxes), all within a TAD that also contains the male-biased gene Slc27a28 (blue box) (see Table S6A). Shown at the bottom are four tracks with normalized RNA-seq reads in the nucleoplasmic fraction for vehicle-treated male and female liver on the forward and reverse strands, as indicated. c TAD containing many Cyp2c genes and lncRNAs. The 4th track from top shows a predicted intra-TAD (iTAD) loop (long pink horizontal bar) that is found in female liver only. The genomic region shown is divided into 3 regions whose genes are either up regulated (green boxes) or down regulated (red box) by TCPOBOP exposure (see Table S6B). The first segment includes 5 up-regulated genes, including Cyp2c55, which is induced by TCPOBOP > 200-fold. The strongest of the two induced lncRNAs in this segment, lnc15004, is also induced 200-fold and is a robust TCPOBOP-responsive lncRNA. The middle segment contains 4 lncRNAs and 5 PCGs, all of which are repressed by TCPOBOP, and the third segment contains three PCGs and two lncRNAs up regulated by TCPOBOP, including the robustly responsive lncRNA, lnc15014 (80-fold induction)