Fig. 1: Retention of specific introns correlates with nuclear localization of TERT mRNA and TUG1 lncRNA in hES/iPS cells.

a UCSC Genome Browser showing the TUG1 locus (hg19) and the poly(A)⁺ RNA-seq track from human ES cells from ENCODE. Below, the location of probes used in smRNA FISH. Exon probes, gray; intron probes, magenta. b UCSC Genome Browser showing the TERT locus (hg19) and the poly(A)⁺ RNA-seq track from human ES cells from ENCODE. Below, the location of probes used in smRNA FISH. Exon probes, gray; intron probes, magenta. c Percentage of intron retention of TERT (left) and TUG1 (right) in human iPS cells obtained with vast-tools analysis of RNA-seq data, n = 2 poly(A)⁺ RNA-seq and 1 ribo-depleted RNA-seq. Bars, means across replicates; dots, individual replicates. Introns with insufficient read coverage are shown as black lines in TERT plot. TUG1 intron 2 was absent in the VastDB database. d SmRNA FISH scheme. Co-localizing exon and intron signals are considered as unspliced, exon-only signal as spliced. e Maximum intensity projections of representative images of TUG1 exon/intron smRNA FISH on iPS cells. Exon, gray; intron 1 and 2, magenta. Nucleus, blue, outlined with a dashed circle. Scale bar, 5 μm. Towards the right: quantification of total and unspliced transcripts for each intron in the nucleus (N) and cytoplasm (C), solid line represents the mean; quantity of spliced (exon only, gray) and intron-retained (magenta) transcripts across 50 nuclei, ordered from fewest to most exon count in the nucleus (average PIR shown on top); correlation between nuclear intron and nuclear TUG1 quantity. N = 50 cells, at least two independent RNA FISH stainings. f Maximum intensity projections of representative images of TERT exon/intron smRNA FISH on iPS cells. Exon, gray; introns 2, 11, and 14, magenta. Nucleus, blue, outlined with a dashed circle. Scale bar, 5 μm. Towards the right: quantification of total and unspliced transcripts for each intron, solid line represents the mean; quantity of spliced (exon only, gray) and intron-retained (magenta) transcripts across nuclei, ordered from fewest to most exon count in the nucleus (average PIR is shown on top); correlation between nuclear intron and nuclear TERT quantity. N = 50 cells (intron 14), 51 cells (intron 2 and 11), at least two independent RNA FISH stainings.