EMBO/soda-nel huggingface dataset:
USP33 Deubiquitinates and Stabilizes HIF-2alpha to Promote Hypoxia Response in Glioma Stem Cells (2022)
Figure 2

Figure 2. USP33 stabilizes HIF2α protein in GSCs.

A, B Representative images (A) and statistical quantification (B) of immunofluorescent analyses of USP33 (red) and HIF2α (green) in human primary GBMs. Frozen sections of human GBMs were immunostained with antibodies against USP33 and HIF2α, and counterstained with DAPI to show nuclei (blue). The percentage of USP33+ cells in the HIF2α+ population was quantified. The majority of HIF2α+ cells were positively stained for USP33 in human GBMs. Scale bar, 40 μm. (n = 5 sections; mean ± s.e.m.).

C Immunoblot analysis of HIF2α induction in T4121 GSCs expressing shUSP33 or shNT in response to low oxygen. Twenty-four hours post lentiviral transduction of shUSP33 or shNT, GSCs were incubated under 20% or 5% oxygen for 24 hours and then harvested for the immunoblot analysis. Disruption of USP33 abrogated HIF2α induction in GSCs in response to 5% oxygen.

D Immunoblot analysis of HIF2α induction in T4121 GSCs expressing shNT or shUSP33 in response to CoCl2 mimicking hypoxia. Twenty-four hours post lentiviral transduction of shUSP33 or shNT, GSCs were treated with CoCl2 (300 µM) for 12 hours and then harvested for the immunoblot analysis. Disruption of USP33 abrogated CoCl2-induced HIF2α expression in GSCs.

E Immunoblot analysis of HIF2α protein levels in GSCs expressing ectopic Flag-tagged USP33 in normoxia. Cells were transduced with lentiviruses carrying Flag-tagged USP33 or the control vector, followed by two rounds of puromycin selection. Ectopic expression of USP33 elevated HIF2α protein levels in GSCs cultured under 20% oxygen.

F Immunoblot analysis of ectopic HIF2α protein levels in 293T cells with gradually increased amount of ectopic USP33. 0.5 µg of HA-tagged HIF2α plasmids together with the increased amounts of GFP-tagged USP33 plasmids (0, 0.1, 0.2 or 0.3 μg) were introduced into 293T cells. Forty-eight hours post transfection, levels of ectopic HIF2α-HA and GFP-USP33 were analyzed by immunoblot analysis. Concomitantly increased levels of ectopic HIF2α and USP33 expression indicated the positive regulation of HIF2α protein by USP33.

G Immunoblot analysis of ectopic HIF2α protein levels in 293T cells expressing ectopic wild type (WT) USP33 or the catalytically dead (CD) USP33. HA-tagged HIF2α plasmids (0.5 µg) were introduced into 293T cells alone or together with GFP-tagged WT or CD USP33 plasmids (0.2 µg). Levels of ectopic HIF2α-HA and GFP-USP33 were analyzed 48 hours post transfection. Expression of the wild type USP33 but not the catalytically dead USP33 increased the ectopic HIF2α protein levels.
USP33 Deubiquitinates and Stabilizes HIF-2alpha to Promote Hypoxia Response in Glioma Stem Cells (2022)
Figure 5

Figure 5. USP33 is required for maintaining GSC self-renewal potential under hypoxic and normoxic conditions.

A Immunoblot analysis of USP33 and HIF2α protein levels in T387 GSCs expressing USP33-targeting shRNAs (shUSP33) or non-targeting shRNA (shNT). Targeting USP33 by two distinct shRNA clones through lentiviral infection reduced USP33 and HIF2α expression in GSCs.

B Representative images of tumorsphere formation of T387 GSCs expressing USP33-targeting shRNA (shUSP33) or non-targeting shRNA (shNT). Twenty-four hours after lentiviral infection, T387 GSCs expressing shUSP33 or shNT were planted in 96 well plates at the density of 2,000 cells per well and cultured for 48 hours under normoxia (20% O2) or hypoxia (5% O2). Disruption of USP33 inhibited GSC tumorsphere formation in normoxia and dramatically suppressed GSC tumorsphere formation in hypoxia. Scale bar, 200 μm.

C, D Statistical quantifications of tumorsphere numbers (C) and sizes (D) showing the inhibition of tumorsphere formation after disruption of USP33 in T387 GSCs. Disruption of USP33 inhibited tumorsphere formation of GSCs in normoxia, whereas hypoxia further augmented the inhibitory effects of USP33 disruption on GSC tumorsphere formation. Data represent three independent experiments. The presented bars for tumorsphere numbers and sizes were based on 5 and 10 technical replicates, respectively. *, p < 0.05; **, p < 0.01; ***, p < 0.001 (mean ± s.e.m.; two tailed unpaired t-test).

E Cell titer assays showing cell growth of T387 GSCs expressing shUSP33 or shNT in normoxia or hypoxia. GSCs were transduced with shNT or shUSP33 through lentiviral infection for 24 hours, and then split into 96 well plates at the concentration of 2,000 cells per well. Cell titer was determined by the Glo luminescent cell viability assay kit (Promega) at the indicated time points. Disruption of USP33 inhibited GSC growth in normoxia and hypoxia. The experiment has been repeated three times. The presented curves were based on three technical replicates. *, p < 0.05; **, p < 0.01; ***, p < 0.001 (mean ± s.e.m.; two tailed unpaired t-test).

F Representative immunofluorescent staining of the apoptotic marker cleaved caspase 3 in T387 GSCs expressing shUSP33 or shNT in normoxia or hypoxia. GSCs were attached to hESC-Qualified Matrix (Corning) in 6-well plates at the concentration of 50,000 cells per well. Forty-eight hours post infection with shUSP33 or shNT lentiviruses, cells were stained for cleaved caspase 3 (green) and nuclei (blue). Scale bar, 80 μm.

G Statistical quantification of (F) showing relative apoptosis of T387 GSCs expressing shUSP33 or shNT in normoxia or hypoxia. Disruption of USP33 increased the apoptosis of GSCs in normoxia, which was further elevated in hypoxia. Data represent three independent experiments. *, p < 0.05 (mean ± s.e.m.; two tailed unpaired t-test).
USP33 Deubiquitinates and Stabilizes HIF-2alpha to Promote Hypoxia Response in Glioma Stem Cells (2022)
Figure 6

Figure 6. Disrupting USP33 impairs hypoxia response in GSCs in the tumor microenvironment.

A A schematic diagram of the 4HRE-d2GFP fluorescent hypoxia reporter system containing a destabilized GFP (d2GFP) fluorescent reporter under the control of four repetitive cis-acting hypoxia-responsive elements (HRE) followed by a minimum CMV promoter. The hypoxia reporter system was constructed on the backbone of pCDH-CMV-MCS-EF1α-Neo lentiviral vector (System Biosciences).

B Representative images of autonomous fluorescent signals from T387 and T3359 GSCs transduced with 4HRE-d2GFP in response to 5% oxygen. Strong GFP signals were detected under 5% oxygen, whereas no GFP signal was detected under 20% oxygen. Scale bar, 200 μm.

C, D Representative images (C) and statistical quantifications (D) of autonomous fluorescent signals of 4HRE-d2GFP in xenografts derived from or shUSP33- or shNT- expressing T387 GSCs transduced with 4HRE-d2GFP. The reduced fraction of GFP+ tumor cells in the xenografts derived from shUPS33-expressing GSCs relative to the control xenografts indicated that USP33 disruption impaired hypoxia response in tumor cells. Scale bar, 200 μm. ***, p < 0.001 (n = 5 tumors; mean ± s.e.m.; two tailed unpaired t-test).

E, F Representative images (E) and statistical quantifications (F) of autonomous fluorescent signals of 4HRE-d2GFP (green) and immunofluorescent staining of the stem cell marker SOX2 (red) in xenografts derived from T387 GSCs transduced with 4HRE-d2GFP. More GFP signals were detected in the SOX2+ cells compared with the SOX2- cells, suggesting a stronger hypoxia response in GSCs relative to NSTCs. Scale bar, 200 μm. ***, p < 0.001 (n = 5 tumors; mean ± s.e.m.; two tailed unpaired t-test).

G, H Representative images (G) and statistical quantifications (H) of immunofluorescent staining of the apoptotic marker cleaved caspase 3 (red) and autonomous fluorescent signals of 4HRE-d2GFP (green) in xenografts derived from T387 GSCs transduced with 4HRE-d2GFP. The GFP+ population had much less apoptosis relative to the GFP- population, suggesting that hypoxia response inhibited cell apoptosis. Scale bar, 200 μm. (n = 5 tumors for each group; ***, p < 0.001; mean ± s.e.m.; two tailed unpaired t-test).
USP33 Deubiquitinates and Stabilizes HIF-2alpha to Promote Hypoxia Response in Glioma Stem Cells (2022)
Figure 7

Figure 7. Disrupting USP33 inhibited growth of GSC-derived GBM xenografts.

A In vivo bioluminescent imaging analysis of intracranial tumor growth in mice bearing GBM xenografts derived from the T387 GSCs expressing shUSP33 or shNT. Two thousand GSCs transduced with luciferase and shUSP33 or shNT were implanted into mouse brains through intracranial injection. Representative bioluminescent images on day 7, day 15 and day 30 post-transplantation of GSCs were shown. Disruption of USP33 delayed tumor growth of intracranial GBM xenografts.

B Kaplan-Meier survival curves of mice bearing GBMs derived from T387 GSCs expressing shUSP33 or shNT from (A). Disruption of USP33 extended the survival of mice bearing GSC-derived GBM tumors. (n= 5 mice for each group; shUSP33#42 vs shNT, p = 0.0185; shUSP33#45 vs shNT, p = 0.0027; two-tailed log-rank test).

C, D Immunofluorescent analysis (C) and statistical quantifications (D) of the apoptotic marker cleaved caspase 3 in xenografts derived from T387 GSCs expressing shUSP33 or shNT. Disruption of USP33 in GSCs dramatically elevated apoptosis in GBM tumors. Scale bar, 80 μm. (n = 5 tumors for each group; ***, p < 0.001; mean ± s.e.m.; two tailed unpaired t-test).

E, F Immunofluorescent analysis (E) and statistical quantifications (F) of the cell proliferation marker Ki67 in xenografts derived from T387 GSCs expressing shUSP33 or shNT. Disruption of USP33 in GSCs reduced cell proliferation in GBM xenografts. Scale bar, 80 μm. (n = 5 tumors for each group; ***, p < 0.001; mean ± s.e.m.; two tailed unpaired t-test).

G, H Immunofluorescent analysis (G) and statistical quantifications (H) of the vascular endothelial cell marker Glut1 in xenografts derived from T387 GSCs expressing shUSP33 or shNT. Disruption of USP33 in GSCs reduced vessel intensity in GBM xenografts. Scale bar, 80 μm. (n = 5 tumors for each group; ***, p < 0.001; mean ± s.e.m.; two tailed unpaired t-test).
The inhaled corticosteroid ciclesonide blocks coronavirus RNA replication by targeting viral NSP15 (2020)
Figure 2:

Antiviral effects of steroids on SARS-CoV-2.(a) Intracellular SARS-CoV-2 RNA (6 hpi). VeroE6/TMPRSS2 cells were infected with SARS-CoV-2 at MOI = 1 in the presence of 10□μM compounds for 6 h. Cellular viral RNA was quantified by real-time PCR using the E gene primer/probe set. (b) Culture Medium SARS-CoV-2 RNA (27 hpi). VeroE6/TMPRSS2 cells were infected with SARS-CoV-2 at MOI = 0.01 in the presence of ciclesonide for 27 h. Viral RNA in culture medium was quantified by real-time PCR using the E gene primer/probe set. Cell viability in the presence of ciclesonide was quantified at 27 hpi by WST assay.
Improvement of islet transplantation by the fusion of islet cells with functional blood vessels (2020)
Figure 1

Figure 1: Generation of PI+MVF.

A A neutral red-stained mouse pancreas is excised and digested with collagenase. Islets are then separated by hand picking and further digested into single islet cells. Scale bars: 10 mm (left image); 200 µm (middle image); 60 µm (right image).

B Epidydimal fat pads are isolated and processed mechanically and enzymatically. The obtained mixture, containing MVF and ECM, is filtrated for the purification of MVF. Scale bars: 20 mm (left image); 25 µm (right image).

C Western blots of CD31, α-SMA and GAPDH in whole cell extracts of eEND, HDMEC, HUVEC and MVF.

D Immunofluorescence stainings of CD31 / α-SMA and CD31 / PDGFR-β in MVF. Cell nuclei are stained with Hoechst 33342 (blue). Scale bar: 20 µm.

E Schematic illustration of PI+MVF generation. By means of liquid overlay technique, 2,000 pancreatic islet cells and 200 MVF are cocultured for 5 days.

F PI and PI+MVF on days -5, -3 and 0. Scale bar: 200 µm.

G Surface morphology of FI, CI, PI and PI+MVF on day 0 as visualized by scanning electron microscopy. Scale bar: 50 µm.
Improvement of islet transplantation by the fusion of islet cells with functional blood vessels (2020)
Figure 2

Figure 2: Viability of FI, CI, PI and PI+MVF.

A Neutral red and trypan blue stainings of FI, CI, PI and PI+MVF. CI incubated for 24 h with 0.2% H2O2 served as control. Scale bar: 100 µm.

B Representative flow cytometric scatterplots of propidium iodide / annexin V-stained cells from PI+MVF and CI+H2O2 (positive control).

C Quantitative analysis of propidium iodide / annexin V-stained cells from FI, CI, PI, PI+MVF and CI+H2O2 subdivided in necrotic, necroptotic, apoptotic and vital cells in % of total cell number (n = 3 each).

D Schematic illustration of the mitochondrial ROS-sensor mito-roGFP2-Orp1. The fluorescence maximum of this sensor shifts from 488 nm to 405 nm with increasing mitochondrial H2O2 levels, as shown by representative fluorescence images of FI. Scale bar: 70 µm.

E Quantitative analysis of the ROS sensor ratio (405 nm / 488 nm) of FI, CI, PI and PI+MVF (n = 25 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI.

F Representative Western blot analysis of β-actin and HO-1 in whole cell extracts from FI, CI, PI and PI+MVF.

G Quantitative analysis of HO-1 expression in FI, CI, PI and PI+MVF (n = 3 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI.

H Representative immunofluorescence stainings of HO-1 / insulin and HO-1 / CD31 in PI+MVF. Cell nuclei are stained with Hoechst 33342 (blue). Scale bar: 50 µm.

I Representative Western blot analysis of β-actin and HO-1 in whole cell extracts from PI and MVF.

Data information: Exact P-values are specified in Appendix Table S1.
Improvement of islet transplantation by the fusion of islet cells with functional blood vessels (2020)
Figure 4

Figure 4: Microvasculature and angiogenic activity of CI, FI, PI and PI+MVF.

A Representative immunofluorescence stainings of insulin and CD31 in CI, FI, PI and PI+MVF. Cell nuclei are stained with Hoechst 33342 (blue). Scale bar: 100 µm.

B Quantitative analysis of CD31-positive cells in FI, CI, PI and PI+MVF in % of all islet or islet organoid cells (n = 20 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI.

C Representative Western blot analysis of CD31 and β-actin in whole cell extracts from CI, FI, PI and PI+MVF.

D Quantitative analysis of CD31 expression in FI, CI, PI and PI+MVF in % of FI (n = 3). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI.

E Confocal microscopic images of CD31 and cell nuclei (blue) in PI+MVF, demonstrating endothelial cells (arrowheads). Scale bar: 100 µm.

F Representative immunofluorescence staining of Ki67 and CD31 in PI+MVF. Cell nuclei are stained with Hoechst 33342 (blue). Arrows mark endothelial cells expressing Ki67. Scale bar: 100 µm.

G Quantitative analysis of CD31 / Ki67-positive cells in FI, CI, PI and PI+MVF in % of all endothelial cells (n = 10 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI.

H Flow cytometric analysis of BrdU-positive cells from PI+MVF treated with DMSO (vehicle) or linsitinib during the entire fusion process (n = 5 each). Mean ± SD. Unpaired Student's t-test was used for statistical analysis. *P < 0.05 vs. vehicle.

I Representative Western blot analysis of pAkt, Akt, pERK1/2 and ERK1/2 from MVF cell extracts. MVF were treated with vehicle or insulin for 3 h.

J, K Quantitative analysis of pERK1/2 / ERK1/2 (J) and pAkt / Akt (K) ratio in PI+MVF treated with vehicle or insulin for 3 h. Data are expressed as relative intensities (n = 3 each). Mean ± SD. Unpaired Student's t-test was used for statistical analysis. *P < 0.05 vs. vehicle.

L Representative bright field image of angiogenic sprouting from PI+MVF on 3 day of the sprouting assay. Scale bar: 150 µm. Insert: Immunofluorescence staining of insulin (red) and CD31 (green) of sprouted PI+MVF. Cell nuclei are stained with Hoechst 33342 (blue). Scale bar: 30 µm.

M Quantitative analysis of sprouting area of FI, CI, PI and PI+MVF in % of the initial size (day 0) (n = 10 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI.

Data information: Exact P-values are specified in Appendix Table S1.
Improvement of islet transplantation by the fusion of islet cells with functional blood vessels (2020)
Figure 5

Figure 5: Generation of hPI+MVF.

A Schematic illustration of human islet isolation and delivery. Islets are isolated from human donors and cultivated for up to 35 h until they are delivered for the generation of hPI+MVF. The entire process takes more than 8 days.

B Bright field images of hFI, hCI, hPI and hPI+MVF. Scale bar: 100 µm.

C Representative immunohistochemical stainings of insulin and CD31 in hFI, hCI, hPI and hPI+MVF. Cell nuclei are stained with Hoechst 33342 (blue). Scale bar: 100 µm.

D-G Quantitative analysis of insulin-(D), glucagon-(E), somatostatin-(F) and CD31-positive cells (G) in hFI, hCI, hPI and hPI+MVF in % of all islet or islet organoid cells (n = 20 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. hFI; #P < 0.05 vs. hCI; +P < 0.05 vs. hPI.

H Representative bright field images of angiogenic sprouting of hFI, hCI, hPI and hPI+MVF on day 3 of the sprouting assay. Scale bar: 150 µm.

I Quantitative analysis of sprouting area of hFI, hCI, hPI and hPI+MVF in % of initial size (day 0) (n = 10 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. hFI; #P < 0.05 vs. hCI; +P < 0.05 vs. hPI.

J Quantitative analysis of C-peptide secretion (pg/mL) (normalized to DNA concentration) of hFI and hPI+MVF exposed to 1.1 mM and 16.5 mM glucose (n = 3 each). Mean ± SD.

Data information: Exact P-values are specified in Appendix Table S1.
Improvement of islet transplantation by the fusion of islet cells with functional blood vessels (2020)
Figure 7

Figure 7: Cellular composition of transplanted CI, FI, PI and PI+MVF.

A Representative immunofluorescent stainings of insulin / glucagon, insulin / somatostatin and insulin / CD31 in FI, CI, PI and PI+MVF on day 14 after transplantation. Cell nuclei are stained with Hoechst 33342 (blue). Arrows mark intra-islet endothelial cells. Scale bar: 70 µm.

B-E Quantitative analysis of insulin- (B), glucagon- (C), somatostatin- (D) and intra-islet CD31-positive cells (E) within FI, CI, PI and PI+MVF on day 14 after transplantation (n = 10 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI.

Data information: Exact P-values are specified in Appendix Table S1.
Improvement of islet transplantation by the fusion of islet cells with functional blood vessels (2020)
Figure 8

Figure 8: In vivo endocrine function of CI, FI, PI and PI+MVF.

A Schematic illustration of the experimental setting: Diabetes is induced by a single injection of STZ 8 days before 250 FI or PI+MVF are transplanted under the kidney capsule of diabetic mice (n = 7 each). Blood glucose level and body weight are measured from day -8 to day 28 twice a week. On day 28, blood samples and kidney tissue are harvested for immunhistochemical stainings.

B Quantitative analysis of the body weight (g) of nondiabetic and diabetic mice transplanted with FI or PI+MVF from day -8 to day 28 (n = 7 each). Mean ± SD.

C AUC of the body weight of nondiabetic and diabetic mice transplanted with FI or PI+MVF from day 0 to day 28 (n = 7 each). Mean ± SD.

D Quantitative analysis of blood glucose level (mg/dL) of diabetic mice transplanted with FI or PI+MVF and nondiabetic controls from day -8 to day 28 (n = 7 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. PI+MVF.

E AUC of the blood glucose levels of diabetic mice transplanted with FI or PI+MVF and nondiabetic controls from day 0 to day 28 (n = 7 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. PI+MVF.

F Quantitative analysis of blood glucose level (mg/dL) according to the IPGTT of diabetic mice transplanted with FI or PI+MVF and nondiabetic controls to the indicated time points (n = 5 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI.

G AUC of IPGTT of diabetic mice transplanted with FI or PI+MVF and nondiabetic controls (n = 5 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. PI+MVF.

H Plasma insulin level (µU/mL) of diabetic mice transplanted with FI or PI+MVF and nondiabetic controls at 180 min after IPGTT (n = 4 each). Mean ± SD.

I Representative immunofluorescent stainings of insulin / CD31 in FI and PI+MVF on day 28 after islet transplantation. Scale bar: 50 µm.

J Quantitative analysis of insulin- (β-cells), glucagon- (α-cells), somatostatin- (δ-cells) and CD31-positive (endothelial) cells within transplanted FI and PI+MVF on day 28 after islet transplantation. Data are expressed in % of total islet cells (n = 25). Mean ± SD.

K Quantitative analysis of islet cells in transplanted FI and PI+MVF per HPF (n = 70 each). Mean ± SD. Unpaired Student's t-test was used for statistical analysis. *P < 0.05 vs. FI.

Data information: Exact P-values are specified in Appendix Table S1.

Expanded View Figure Legends
Activation of endogenous retroviruses during brain development causes an inflammatory response (2021)
Figure 1

Figure 1. CRISPR/Cas9 based deletion of Trim28 in NPCs results in upregulation of ERVs.

(a) A schematic of the workflow for Trim28-KO in mouse NPC cultures. Scale bars: embryo 1 mm, NPCs 20 μm.

(b) Estimation of gene editing at the Trim28 loci using NGS-sequencing of amplicons. Black bars indicate % of frameshift indels. Columns show an average of two biological replicates per guide RNA and error bars show mean ± SD.

(c) Western blot confirmed the loss of Trim28 expression upon Trim28-KO in mouse NPCs.

(d) RNA-seq analysis of the expression of TE-families using TEtranscripts

(e) The significantly upregulated TE families with a fold change larger than 0.5 upon Trim28-KO in mouse NPCs. The dashed line indicates significance.

(f) CUT&RUN analysis of H3K9me3 in mouse NPCs of all full length MMERVK10Cs (right panel) RNA-seq analysis of the Trim28-KO and control samples, visualising full length MMERVK10C elements. The location of the full length MMERVK10Cs are indicated as a thick black line under each histogram.

(g) Example of transcriptional readthrough outside the full length MMERVK10Cs into a nearby gene.