Fig 2: Knockdown of KAP1 resulted in a reduction in influenza virus replication. A549 cells were transfected twice with negative control siRNA (Allstars NC) or two siRNAs targeting human Kap1 (siKAP1 1#; siKAP1 2#). (A) qPCR to confirm the relatively low level of mRNA expression in siKAP1-treated A549 cells. (B) Western blotting with anti-KAP1 or anti-β-actin antibody to confirm the knockdown efficiency. (C) Cell viability of siRNA-treated cells was determined by using CellTiter-Glo reagent. (D) Virus growth in siRNA-treated A549 cells infected with WSN virus at an MOI of 0.001 and the supernatant was collected at 48h post-infection. (h.p.i: hours post-infection). Means ± SD of triplicate experiments is shown in (A,C,D). ** p < 0.01 (two-way ANOVA followed by Dunnett’s test).

Fig 3: Single‐nuclei RNA‐seq of cortical tissue from Emx1‐Cre/Trim28‐KO animals and their littermates AA schematic of the workflow for the single‐nuclei RNA‐seq of cortical tissue from Emx1‐Cre/Trim28‐KO animals and their littermates.BUMAP showing the unbiased clustering analysis with seven different cell clusters.C, DUMAP and pie charts showing the distribution of Trim28‐KO and control cells over the seven different clusters. There were no major differences in proportions of the different cell clusters between Emx1‐Cre/Trim28‐KO animals and controls.E–HA selection of significant cell‐type‐specific changes in gene expression between Emx1‐Cre/Trim28‐KO animals and controls as revealed by single‐nuclei RNA‐seq. The black dots represent the mean value (Wilcoxon rank sum test, (P‐adj value < 0.01), n = 2. For a full list, see Table EV2.

Fig 4: Deletion of Trim28 during brain development results in aberrant TE expression in the adult brain A schematic of the breeding scheme resulting in highly efficient conditional deletion of Trim28‐KO during cortical development and analyzing the adult tissue 3 months later by IHC and RNA‐seq.IHC for Trim28 in the adult cortex revealed that the protein was lost in cells exposed to Cre‐activity during brain development (GFP+ cells). Scale bars: low magnification 75 μm, high magnification 20 µm.RNA‐seq analysis of the expression of TE families using TEtranscriptsSignificantly upregulated TE families upon the Trim28‐KO, in which the families with the highest fold change are listed.RNA‐seq analysis of full length MMERVK10Cs in the adult tissue. The location of the full length MMERVK10Cs is indicated as a thick black line under each histogram.

Fig 5: Effects of point mutations in the KRAB binding site and KAP1 binding and silencing. See also Fig EV3 Surface plasmon resonance (SPR) KAP1‐KRAB binding assay. MBP‐KRAB was immobilized on the chip. WT or R311E KAP1 RBCC were flowed over the chip. Data points are shown in dark red or blue; fits are shown as light red or blue lines. See Fig EV3 for binding kinetics constants.Position of the mutations in the KRAB‐KAP1 interface.LINE‐1 reporter repression with single point mutants and a previously described KRAB binding‐deficient KAP1 variant containing four mutations in the CC domain (CCmut; V293S/K296A/M297A/L300S).SVA reporter repression with the same set of mutants as in (B). Data were normalized to KAP1 KO cells transfected with an empty vector (EV). Data information: In (C) and (D), data are presented as fold‐repression of reporter luciferase luminescence. Error bars represent standard error of the mean between measurements (n = 3). Data are representative of at least three independent (biological replicate) experiments. Lower panels: Western blots of cell lysates from KAP1 KO HEK293T cells transfected with each of the variants or empty vector. Uncropped blots available in Source Data. Source data are available online for this figure.