Fig. 6: LETR1 is a nuclear lncRNA interacting in trans with DNA regions near a subset of differentially expressed genes. | Nature Communications

Fig. 6: LETR1 is a nuclear lncRNA interacting in trans with DNA regions near a subset of differentially expressed genes.

From: LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C

Fig. 6

a Representative images of negative control dapB (bacterial gene), MALAT-1 (nuclear lncRNA), and LETR1 expression using single-molecule RNA Fluorescence In Situ Hybridization (smRNA-FISH) in neonatal LECs derived from two donors. Immunostaining of endothelial cell marker CD31 was used to outline cell shape. Scale bars represent 20 µm. b Quantification of the nuclear (green) and cytoplasmic (black) smRNA-FISH signal of LETR1 in neonatal LECs derived from two donors quantified with ImageJ108. Bars represent percentages displayed as mean values + SD (n = 2). c Pie chart showing the genomic localization of the 2258 LETR1 peaks in protein-coding, overlap between protein-coding and noncoding, noncoding, and intergenic regions according to FANTOM CAT annotations using bedtools116. Magnification shows the distribution of LETR1-binding sites within promoter, exon, or intron of protein-coding genes (1607 genes). LETR1 peaks are listed in Supplementary Data 10. d Venn diagrams showing the overlap between total genes expressed in LECs (TPM and CPM > 0.5) and identified LETR1-ChIRP genes, and the significant overlap between LETR1-ChIRP genes and differentially expressed genes after LETR1-ASOKD. e Circular plot showing genome-wide interactions of LETR1 near the 44 targets generated by Circos117. Scaled chromosomes with their respective cytobands are placed in circle. Major and minor ticks: 50 Mb and 10 Mb; orange and purple lines: interactions between LETR1 locus and its up- and downregulated targets; green line: genomic locus of LETR1. f Heat maps based on expression levels (CAGE-Seq, CPM) in scrambled control ASO and LETR1-ASOKD samples (left, two replicates), as well as in LECs and BECs (right, two replicates) of the 44 LETR1 targets (orange: upregulated; purple: downregulated). Color code for row Z score values on a scale from −1 to +1. Genes were ordered by log2FC values of ASOKD data and according to their differential expression between LECs and BECs.

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