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Fig. 4 | BMC Genomics

Fig. 4

From: De novo annotation of lncRNA HOTAIR transcripts by long-read RNA capture-seq reveals a differentiation-driven isoform switch

Fig. 4

Remodeling of the HOTAIR isoform pool during adipogenesis. a Schematic representation of HOTAIR 5’ exons (exons E1 to E5) showing novel HOTAIR exons and 9 alternative TSSs detected by PacBio Capture-Seq. b Cumulative number of long-reads for each HOTAIR starting exon. c Heatmap of the proportion of isoforms expressed at each time in the adipogenesis time course. Matching full length reads from PacBio long-read Capture-Seq are compared with each time point. d, e Proportion of read coverage for each start exon quantified from long-read data for (d) HOTAIR isoforms cumulating > 500 reads over the time course and (e) E3- and E3.1-starting isoforms. f Normalized short-read RNA-seq read count per kilobase of exon sequence for E3 and E3.1 exons during differentiation, quantified with featureCounts with strict parameters (-f -g exon_id -p -s 2 -O –fraction -B -C) (n = 3, ***p < 0.001 paired t-test with Benjamini–Hochberg adjusted p value) g Semi-quantitative RT-PCR analysis of HOTAIR expression using primers located in HOTAIR exons E3.1-E4 and E3-E5. SF3A1 is shown as a loading control. A representative image from one of three independent experiments is shown for adipogenesis (left) and osteogenesis (right); see also Additional file 1 Fig. S3b,c. RT-: no reverse transcriptase control; NTC: no template control. Full-length gels are presented in Additional file 4 Fig. S4,5,6

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