(A) Schematic of subnuclear fractionation protocol. RNA (red) and associated proteins are solubilized by serial biochemical extraction procedures from TIG-1 nuclei and a pie chart of RNA (average by mass, n=2) extracted for each fraction. (B-D) Relative abundance of XIST, NEAT1, and GAPDH RNAs in transcripts per million (TPM) from RNA-seq. Error bars represent SEM. (E) Enrichment of GENCODE lncRNAs in the CDNI relative to NS fraction. Blue dots indicate significant enrichment (p < 0.05). (F) Boxplot of RNA enrichment grouped by subtype in the CDNI and NS fractions. RNAs binned by mean abundance. (G) SYBR Safe stained 1.5% agarose gel of DNA isolated from CDNI material after DNase I digestion. (H) Relative abundance of lncRNAs in CDNI and CDNS fractions. (I) Stacked bar graph of RNA-seq mapping to Repeatmasker repeats. (J) Bar graph of RNA-seq mapping to indicated repeats relative to their abundance in the genome (LC, low complexity; SR, simple repeats; amb, ambiguous). (K) Percent of CDNI and NS RNA-seq mapping to genomic features. (L) Distribution of total read normalized intron coverage in NS (red) and CDNI (blue) fractions. (M) Distribution of exon-intron splice ratios derived from analysis of spliced and unspliced intron-exon junction read depth (spliced/spliced+unspliced depth) in NS (red) or CDNI (blue) fractions.