Fig. 5: MSR-originating transcripts are attenuated by the Integrator complex.
From: Transcriptional competence defines the heterochromatin nucleating potential of isolated MSR units
a ChIP-qPCR for INTS11 and INTS12 at the Chr2/116 integration site in two independent mESC clones for HB, L5’UTR3, CMV3 or MSR3 insertions. Asterisks indicate statistically significant differences when compared to the HB control (mean±SD) (***p = 0.0002, ****p < 0.0001, ns = not significant, one-way ANOVA, Dunnett’s test). n = 3 independent experiments. b RT-qPCR transcript analysis at the Chr2/116 integration site in one mESC clone for HB, L5’UTR3, CMV3 or MSR3 insertions 48 hrs after knock-down of Ints11. Asterisks indicate statistically significant differences when compared to the negative control (unspecific siRNA knock-down) (mean±SD) (****p < 0.0001, ns = not significant, two-way ANOVA, Å ĂdĂ¡k’s test). n = 3 independent experiments. c Heat maps of RNA-seq (total RNA, 150 bp paired-end) for MSR transcripts (left panel), and ChIP-seq for H3K9me3 (middle panel) and HP1α (right panel) in mouse ES cells. Data are shown at 0 h and 24 h following depletion of INTS11-degron. MSR sequences were classified into two groups based on sequence identity (95–100% conservation to MSR DNA consensus and below 95% conservation to MSR DNA consensus). Within each group, the signals were ordered according to their level of enrichment. Western blot analysis for the depletion of INTS11 is shown on top. Blot was probed with α-HA antibody and GAPDH was used as loading control. MSR transcripts and ChIP-seq reads are aligned and binned according to their sequence identity (decreasing from 100% to 95% and then to 75%) with the MSR DNA consensus sequence. Two biological replicates are shown for each analysis.
