1. The nuclear RNA degradation landscape of mESCs.
The nuclear RNA degradation landscape of mESCs. (A) Half-lives of mRNAs and lincRNAs, calculated from RNA-seq decay curves following actinomycin D–mediated transcription shut-off. Messenger RNAs are shown in black, lincRNAs in red, and lincRNAs highlighted in this study in green. A running median trend line for mRNAs is shown in blue. (B) Box plot summary of lincRNA and mRNA half-lives (bar = median; notches = 1.58 × IQR/sqrt(n)), with the distributions tested for similarity using the Wilcoxon rank sum test. The three plots show low expressed (<40 normalised counts), high expressed (>40 normalised counts), or all transcripts (left to right). (C) Length of non-genome-encoded oligonucleotide tails detected on RNA fragments captured by Mtr4 CRAC. Oligo(A) tails correspond to degradation intermediates and oligo(C/G/T) tails are shown as a negative control. (D) Metaplots showing the distribution of Pol II Native Elongating Transcript sequencing (NET-seq) (top) and Mtr4 CRAC (middle) RNA fragments around the start and end of mRNA exons and introns (first three and the last exon shown). Mtr4 CRAC RNA fragments with non-genome-encoded 3′ oligo(A) tails, corresponding to initial Mtr4 recruitment sites, are shown separately (bottom). (E) An example of Mtr4 CRAC reads mapping near the 3′ end of an intron (β-actin intron 1). Individual sequencing reads corresponding to fragments with 3′ oligo(A) tails are shown as red bars, with an alignment of these sequences below (highlighting in red the non-genome-encoded oligo(A) tails). (F) Total distribution of RNA fragments bound to Pol II (NET-seq) or Mtr4 (CRAC) around mRNA TSSs, in the sense (top) and antisense (bottom) directions. “Sense PROMPTs” are defined as short, prematurely terminated transcripts originating from TSSes in the sense direction and “antisense PROMPTs” are similar transcripts that arise in the upstream antisense orientation (see diagram). Mtr4 A-tailed read (as for D) distributions are shown in green. See also Fig S5.
Alex C Tuck et al. LSA 2018;1:e
© 2018 Tuck et al.