Skip to main content
. 2021 Jul 1;35(13-14):992–1004. doi: 10.1101/gad.348508.121

Figure 6.

Figure 6.

YTHDC1 regulates the alternative splicing of HIV-1 RNAs. Viral transcript spliced isoforms in infected siCtrl, siDC1, and +DC1 cells 48 hpi were analyzed by PrimerID RNA-seq. n = 3. (A) Schematic of HIV-1 splice donors and acceptors relative to the three major classes of spliced viral RNAs. Top arrows depict the primers used to amplify sequences for RNA-seq, including the common 5′ forward primer in blue, the reverse 4-kb primer in green, and the reverse 1.8-kb primer in red spanning the D4/A7 splice junction. A random reverse primer was also used but is not shown. (B) Spliced transcripts are given as a percentage of all transcripts (1.8-kb + 4-kb class read counts/total read counts). (C) Percent of fully spliced transcripts over all spliced transcripts (1.8-kb/[1.8-kb + 4-kb] read counts). (D–F) Splice acceptor usage assayed using the common forward primer in conjunction with the random reverse primer (D), 1.8-kb reverse primer (E), and 4-kb reverse primer (F). Use of acceptor A3 results in long transcripts that are biased against when amplifying using the 1.8- or 4-kb reverse primers, A3 usage is thus only shown with the random reverse primer. (G) Percent occurrence of D1/A7 splices. (H) Percent occurrence of A2-using spliced RNAs that subsequently splice from D3. Statistical analysis used Student's t-test. Error bars indicate SD. (*) P < 0.05, (**) P < 0.01.