Fig. 1: MTR4 destabilizes 3XTs.
From: The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons
a Schematic illustration of the identification of RNAs destabilized by MTR4. (left) To identify transcript variant repertoire upregulated upon MTR4 depletion, HeLa cells transfected with siCont or siMTR4 were subjected to short- and long-read sequencing, as presented in Supplementary Fig. 1b. Pale-colored boxes are transcripts identified in this study. (right) To identify the transcript variant stabilized by MTR4 depletion, HeLa cells transfected with siCont or siMTR4 were treated with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), a transcription inhibitor, for the indicated times and then subjected to 3′-sequencing to estimate stability. By combining these data, MTR4-target transcripts were determined. b Schematic representation of two types of 3′ eXtended Transcript (3XT) and 3′ eXtended Regions (3XRs). The middle exon is the exon other than the first or last exon in annotated transcripts. 3XTs are transcripts that have an extended last exon with (multi-exon 3XT) or without (mono-exon 3XT) splicing events. c A violin plot from NanoBlot results displaying the distribution of sequenced read lengths of a representative 3XT. ATP23 (left, blue) and HECTD2 (right, red) are examples of genes with mono- and multi- exon 3XTs, respectively. Arrowheads indicate the lengths of ATP23 (blue) and HECTD2 (red) 3XT. d qRT-PCR analysis of mono- (blue) and multi-exon (red) 3XT expression in HeLa cells transfected with siRNA targeting MTR4. Results are expressed as the mean ± s.d. (n = 3 biologically independent replicates). Paired two-sided Student’s t-test; *p < 0.05. The exact p-values are ATP23 3XT: p = 0.00916 (siCont vs siMTR4#1), p = 0.00074 (siCont vs siMTR4#2), TP53TG1 3XT: p = 0.00077 (siCont vs siMTR4#1), p = 0.00227 (siCont vs siMTR4#2), USP45 3XT: p = 0.00792 (siCont vs siMTR4#1), p = 0.01991 (siCont vs siMTR4#2), HECTD2 3XT: p = 0.00441 (siCont vs siMTR4#1), p = 0.00667 (siCont vs siMTR4#2), SPRED2 3XT: p = 0.00794 (siCont vs siMTR4#1), p = 0.00122 (siCont vs siMTR4#2), KCTD13 3XT: p = 0.02597 (siCont vs siMTR4#1), p = 0.02677 (siCont vs siMTR4#2). Source data are provided as a Source Data file.
