EMBO/soda-nel huggingface dataset:
Changing POU dimerization preferences converts Oct6 into a pluripotency inducer (2016)
Figure 5

Figure 5. Cells reprogrammed using the synthetic Oct6 molecule show pluripotency in vitro and in vivo.

A. In vitro differentiation of O6SKM iPSC lines into cells of all three germ layers as shown by immunochemistry: endoderm (α-fetoprotein, AFP), mesoderm (α-smooth muscle actin, SMA), and ectoderm (β-tubulin, TUJ1). Nuclei (DNA) were stained by Hoechst (blue). Scale bars: 200 μm.

B. F1 offspring of chimera male mice with contribution from O6SKM iPSCs and CD1 female mice.

C. Pictures demonstrating germline transmission; endogenous Oct4-GFP signal was detected in the gonads of F1 pups. Scale bars: 200 μm.
Apolipoprotein E promotes subretinal mononuclear phagocyte survival and chronic inflammation in age-related macular degeneration. (2015)
Figure 1

Subretinal MPs accumulate on the retinal pigment epithelium in AMD

Confocal microscopy of IBA-1 (green staining) immunohistochemistry of RPE flatmounts (RPE autofluorescence visible as orange due to its autofluorescence in the red and green channel) from a healthy donor (A), a geographic atrophy lesion (B), and large drusen (C and D). (A, B, D): orthogonal Z-stack projection; (C): oblique Z-stack projection and dissecting microscope appearance of postmortem large drusen after removal of the overlaying retina (inset).

Double-labeling on the subretinal side of the retina (to avoid masking by RPE autofluorescence) of IBA-1+ (E, green fluorescence) and CD18 (F, red fluorescence; G, merge).

Orthogonal and lateral Z-stack of a subretinal IBA-1+ (green fluorescence) MPs adjacent to the RPE (orange autofluorescence) in the vicinity of a large drusen.

Data information: Controls omitting the primary antibody showed no staining apart from the autofluorescence. AZ: atrophic zone; LD: large drusen. Scale bar: 50 μm (A–D); 10 μm (E–H).
Apolipoprotein E promotes subretinal mononuclear phagocyte survival and chronic inflammation in age-related macular degeneration. (2015)
Figure 2

Subretinal MPs express APOE

APOE (A) and IBA-1 (B, merge in C) double-labeling on paraffin sections of surgical specimens of human tonsils.

APOE (D) and IBA-1 (E, merge in F) double-labeling on the subretinal aspect of a large drusen overlaying retina (to avoid specific signal masking by the RPE orange autofluorescence).

APOE (red staining) immunohistochemistry of control donor tissue (G) and adjacent to GA lesion (H).

IBA-1 (green staining, RPE far-red autofluorescence) double-labeling of the GA lesion shown in (H). Representative images from five donor eyes with large drusen, five donor eyes with GA, and three healthy donors between 70 and 89 years old.

Data information: Controls omitting the primary antibody showed no staining apart from the autofluorescence (H inset). ONL: outer nuclear layer; INL: inner nuclear layer; Ch: choroid. Scale bar: 10 μm.
Apolipoprotein E promotes subretinal mononuclear phagocyte survival and chronic inflammation in age-related macular degeneration. (2015)
Figure 3

APOE promotes subretinal MP accumulation in Cx3cr1GFP/GFP mice

Immunohistochemistry of APOE (red) and IBA-1 (green) on a section (A, blue Hoechst) and the subretinal side of a retinal flatmount (B and C) from a 12-month-old Cx3cr1GFP/GFP mouse (representative of 3 independent experiments, experiments omitting the primary antibody immunostaining served as negative controls). ONL: outer nuclear layer; RPE: retinal pigment epithelium.

Quantitative RT–PCR of ApoEmRNA normalized with S26mRNA of C57BL/6J and Cx3cr1GFP/GFP monocytes cultured for 24 h in contact with POS of an overlaying retinal explant (n = 4/group per experiment; Mann–Whitney U-test, *P = 0.0286, the experiment was repeated twice with similar results).

Quantitative RT–PCR of ApoEmRNA normalized with S26mRNA of C57BL/6J and Cx3cr1GFP/GFP FACS-sorted microglial cells, freshly extracted from adult brain (n = 4–5/group; Mann–Whitney U-test, C57BL/6J versus Cx3cr1GFP/GFP *P = 0.0159).

Quantitative RT–PCR of ApoEmRNA normalized with S26mRNA of C57BL/6J and Cx3cr1GFP/GFP peritoneal macrophages cultured for 24 h with CX3CL1. (n = 4/group per experiment; Mann–Whitney U-test, *P = 0.0286. The experiment was repeated twice with similar results).

APOE Western blot analysis of equivalent amounts of supernatant protein from CX3CL1-exposed C57BL/6J and Cx3cr1GFP/GFP peritoneal macrophages at 24 h. Soluble Mer receptor tyrosine kinase that is released constitutively from cultured macrophages served as a loading control. The experiment was repeated twice with similar results.

12-month-old IBA-1 stained RPE flatmounts of Cx3cr1GFP/GFP (H) and Cx3cr1GFP/GFPApoE−/− (I) mice.

Quantification of subretinal IBA-1+ mononuclear phagocytes in 2-month-old (left) and 12-month-old (right) mice of the indicated strains (n = 9–20/group ANOVA/Dunnett test at 12 months: Cx3cr1GFP/GFP versus any other group *P < 0.0001; Mann–Whitney U-test at 12 months of Cx3cr1GFP/GFP versus Cx3cr1GFP/GFPApoE−/− *P < 0.0001).

Quantification of subretinal IBA-1+ mononuclear phagocytes after 4 days of light challenge of 2-month-old mice of the indicated strains (n = 10–25/group ANOVA/Dunnett test: Cx3cr1GFP/GFP versus any other group *P < 0.0001; Mann–Whitney U-test of Cx3cr1GFP/GFP versus Cx3cr1GFP/GFPApoE−/− *P < 0.0001).

IBA-1- (green) and CD102- (red) stained RPE flatmounts 7 days after laser injury of 2-month-old Cx3cr1GFP/GFP (E) and Cx3cr1GFP/GFPApoE−/− (F) mice.

Quantification of subretinal IBA-1+ mononuclear phagocytes on the RPE counted on the RPE at a distance of 0–500 μm to CD102+ CNV 7 days after the laser injury of 2-month-old mice of the indicated strains (n = 8–10 eyes/group ANOVA/Dunnett test: Cx3cr1GFP/GFP versus any other group *P < 0.0001; Mann–Whitney U-test of Cx3cr1GFP/GFP versus Cx3cr1GFP/GFPApoE−/− *P < 0.0001).

Data information: +R: cultured with an overlying retinal explant. Scale bars, 50 μm.
Apolipoprotein E promotes subretinal mononuclear phagocyte survival and chronic inflammation in age-related macular degeneration. (2015)
Figure 4

APOE inhibits subretinal MP clearance

Representative image of a RPE flatmount 12 h after the subretinal injection (red marking) of 4 μl PBS with 12,000 CFSE-stained thioglycollate-elicited peritoneal cells that contain 70% macrophages (inset close-up view).

Quantifications of CFSE+F4/80+ macrophages at different time points after subretinal injections of C57BL/6J and Cx3cr1GFP/GFP CFSE+ macrophages (n = 5/per group (12 h) and n = 6/per group thereafter; Mann–Whitney U-test, C57BL/6J versus Cx3cr1GFP/GFP: 1 day n = 20/group *P < 0.0001; 2 day n = 6/group *P = 0.0317).

Representative image of TUNEL/Hoechst double-staining 12 h after subretinal injection of C57BL/6J CFSE+ macrophages (experiment repeated three times, inset close-up view).

Representative cytometry images of SSC-A/CFSE and CD11b/F4/80 gated analysis of eye cell suspensions prepared 24 h after the injection of Cx3cr1GFP/GFP CFSE+ macrophages and cytometric quantification of eye cell suspensions at 24 h after the injection of C57BL/6J and Cx3cr1GFP/GFP macrophages into C57BL/6J (n = 16–20/group; Mann–Whitney U-test, *P = 0.0024).

Quantification of subretinal CFSE+ cells on RPE and retinal flatmounts 24 h after subretinal injections of CFSE+ magnetic-bead-sorted bone marrow-derived monocytes (Mo) from C57BL/6J and Cx3cr1GFP/GFP mice into C57BL/6J mice (n = 8–12/group; Mann–Whitney U-test, *P = 0.0006).

Quantification of subretinal CFSE+ cells on RPE and retinal flatmounts 24 h after subretinal injections of CFSE+CD11b FACS-sorted brain microglial cells from C57BL/6J and Cx3cr1GFP/GFP mice into C57BL/6J mice (n = 9–12/group; Mann–Whitney U-test, *P = 0.0087).

Quantification of subretinal CFSE+F4/80+ macrophages on RPE and retinal flatmounts 24 h after subretinal injections of CFSE+ macrophages from C57BL/6J, Cx3cr1GFP/GFP, Cx3cr1GFP/GFPApoE−/−, and ApoE−/− mice into C57BL/6J mice (n = 8–12/group; one-way ANOVA/Dunnett test of Cx3cr1GFP/GFP versus any other group *P ≤ 0.0001; Mann–Whitney U-test, Cx3cr1GFP/GFP versus Cx3cr1GFP/GFPApoE−/− *P = 0.0006).

Quantification of subretinal CFSE+F4/80+ macrophages on RPE and retinal flatmounts 24 h after subretinal injections of C57BL/6J CFSE+ macrophages into C57BL/6J and with exogenously added APOE3 at 1, 10, or 100 μg/ml calculated intraocular concentrations (n = 6–7/group; one-way ANOVA/Dunnett test: C57BL/6J versus 10 μg *P = 0.0488; C57BL/6J versus 100 μg ‡P = 0.006. Mann–Whitney U-test: C57BL/6J versus 10 μg *P = 0.0012; C57BL/6J versus 100 μg ‡P = 0.0013).

Data information: All primary cells were prepared from male mice; all recipient C57BL/6J mice were male. Mo: monocytes; MC: microglial cells; Mϕ: macrophages; SCC-A: side scatter detector A. Scale bars: 1 mm (A); 50 μm (C).
Apolipoprotein E promotes subretinal mononuclear phagocyte survival and chronic inflammation in age-related macular degeneration. (2015)
Figure 5

FAS-FASL signaling mediates subretinal MP clearance

Quantitative RT–PCR of FasLmRNA normalized with β-actinmRNA of 2-month-, 12-month-, and 2-month-old mice after 4 days of light challenge of C57BL/6 and Cx3cr1GFP/GFP mouse RPE/choroid plexus (aging: n = 5–6/group; Mann–Whitney U-test: 12 months *P = 0.0129; 4 days light challenge: n = 7–8/group; *P = 0.029).

Immunohistochemistry of FASL (red) and IBA-1 (green) of a RPE flatmounts and sections (insets, Hoechst staining blue) from a 12-month-old WT (B) and Cx3cr1GFP/GFP(C) mouse (representative of three independent experiments, immunostainings omitting the primary antibody served as negative controls).

Quantitative RT–PCR of FasLmRNA normalized with β-actinmRNA of 12-month-old C57BL/6 RPE/choroid plexus extracts 3 h after subretinal injection of C57BL/6J macrophages or Cx3cr1GFP/GFP macrophages (n = 6 per group), Mann–Whitney U-test, *P = 0.0087.

IBA-1-stained RPE flatmounts of 2-month-old C57BL/6J, Faslgld/gld, and Faslpr/lpr mice after 4 days of light challenge.

Quantification of subretinal IBA-1+ mononuclear phagocytes in control (left) and 4-day light-challenged (right) 2-month-old mice of the indicated strains (n = 6–10/group ANOVA/Dunnett test at 4-day light challenge: C57BL/6J versus FasLgld/gld and C57BL/6J versus Faslpr/lpr both *P < 0.0001; Mann–Whitney U-test at 4-day light challenge: C57BL/6J versus FasLgld/gld *P < 0.0001; C57BL/6J versus Faslpr/lpr *P < 0.0001).

Quantification of subretinal CFSE+F4/80+ macrophages on RPE and retinal flatmounts 24 h after subretinal injection of C57BL/6J CFSE+ macrophages into C57BL/6J and FasLgld/gld mice and Faslpr/lpr macrophages into C57BL/6J mice (n = 10–15/group, one-way ANOVA/Dunnett test: C57BL/6J macrophages inj. into C57BL/6J mice versus C57BL/6J macrophages inj. into Fasgld/gld mice *P = 0.0002; C57BL/6J macrophages inj. into C57BL/6J mice versus Faslpr/lpr macrophages inj. into C57BL/6J mice *P < 0.0001. Mann–Whitney U-test: C57BL/6J macrophages inj. into C57BL/6J mice versus C57BL/6J macrophages inj. into FasLgld/gld mice *P < 0.0001; C57BL/6J macrophages inj. into C57BL/6J mice versus Faslpr/lpr macrophages inj. into C57BL/6J mice *P < 0.0001).

Quantification of subretinal CFSE+F4/80+ macrophages on RPE and retinal flatmounts 24 h after subretinal injection of Cx3cr1GFP/GFP CFSE+ macrophages into C57BL/6J with or without the Fas agonist MegaFasL (calculated intraocular concentrations 1 ng/ml; n = 7–8; Mann–Whitney U-test: *P = 0.014).

In vitro MegaFasL-induced apoptosis of monocytes and macrophages of the indicated genotypes cultured for 24 h. TUNEL+ nucleus quantification expressed as percentage of non-MegaFasL-exposed control.

Data information: All primary cells were prepared from male mice; all recipient C57BL/6J or FasLgld/gld mice were male. Mo: monocytes; MΦ: macrophages. Scale bars: 20 μm (B, C); 50 μm (E–G).
MCU controls melanoma progression through a redox-controlled phenotype switch (2022)
Figure 6

Figure 6. MCUA controls mitochondrial membrane potential and ATP production

(A-D) Resting mitochondrial membrane potential (∆Ψ), measured with TMRE in 1205Lu (A-B) and WM3734 (C-D) with and without stable MCUA_KD (1205Lu ─ shCTRL: n=81 cells from 3 biological replicates; shMCU_1: n=81 cells from 3 biological replicates; shMCU_2: n=156 cells from 3 biological replicates; WM3734 ─ shCTRL: n=108 cells from 3 biological replicates; shMCU_1: n=73 cells from 3 biological replicates; shMCU_2: n=110 cells from 3 biological replicates).

(E-F) Resting mitochondrial ATP levels, measured using the ATP-Red dye in 1205Lu (E) and WM3734 (F) with and without stable MCUA_KD (1205Lu ─ shCTRL=67 cells from at least 3 biological replicates; shMCU_1: n=80 cells from at least 3 biological replicates; shMCU_2: n=69 cells from at least 3 biological replicates; WM3734 ─ shCTRL: n=40 cells from at least 3 biological replicates; shMCU_1: n=38 cells from at least 3 biological replicates; shMCU_2: n=21 cells from at least 3 biological replicates).

(G-I) Mitochondrial ATP, measured using mito-ATEAM in 1205Lu and WM3734 with and without stable MCUA_KD. Exemplary ratiometric images (FRET/CFP) are shown for all conditions (G). Scale bar: 10 µm. Quantification of basal levels in 1205Lu (H) and WM3734 (I) (1205Lu ─ shCTRL: n=141 cells from 14 biological replicates; shMCU_1: n=143 cells from 12 biological replicates; shMCU_2: n=143 cells from 13 biological replicates; WM3734 ─ shCTRL: n=122 cells from 12 biological replicates; shMCU_1: n=103 cells from 12 biological replicates; shMCU_2: n=99 cells from 13 biological replicates).

(J) Exemplary confocal microscope images of the mitochondrial network (blue: DAPI staining of the nucleus; green: TOMM20 staining of mitochondria); scale bar: 50 µm. (K-O) Electron microscopy of mitochondria of stable MCUA_KD cell lines.

(K) Exemplary images of stable MCUA_KD cells' mitochondria. Scale bar: 500 nm.

(L-O) Quantification of mitochondrial diameter (L and N) and intercristae distance (M and O) of 1205Lu (L and M) and WM3734 (N and O) cells with and without stable MCUA_KD, presented as boxplot. The box presents the 25 %- quartile, median and 75 %-quartile, the X represents the mean and the whiskers the minimum and maximum, outliers are represented as dots (mitochondrial diameter: 1205Lu ─ shCTRL: n=47 technical replicates; shMCU_1: n=44 technical replicates; shMCU_2: n=40 technical replicates; WM3734 ─ shCTRL: n=35 technical replicates; shMCU_1: n=52 technical replicates; shMCU_2: n=38 technical replicates; intercristace distance: 1205Lu ─ shCTRL: n=330 technical replicates; shMCU_1: n=285 technical replicates; shMCU_2: n=255 technical replicates; WM3734 ─ shCTRL: n=352 technical replicates; shMCU_1: n=433 technical replicates; shMCU_2: n=357 technical replicates).

Data information: Statistical significance was determined using unpaired, two‐tailed Student's t‐test, (*) p < 0.05; (**) p < 0.01; (***) p < 0.005; no asterisk means no statistical significance (p > 0.05).
Chromosomal instability by mutations in the novel minor spliceosome component CENATAC (2021)
Figure 2

Figure 2 - CENATAC promotes error-free chromosome segregation.

A Quantification of chromosome segregation errors of patient and control lymphoblasts expressing H2B-mNeon (four biological replicates, >200 cells in total per condition).

B Representative images of H2B-mNeon-expressing HeLaEGFP-AID-CENATAC cells depleted of GAPDH (upper) or CENATAC (middle and lower) with or without re-expression of CENATAC variants as indicated. IAA, 3-indoleacetic acid. Scale bar, 10 μm.

C Quantification of mitotic defects as in (B) of H2B-mNeon-expressing HeLaEGFP-AID-CENATAC cells treated as indicated (three or five biological replicates, >85 cells in total per condition). For 2xZF the four zinc-finger cysteines were mutated to alanines; for Δ1-4 the corresponding motif was removed.

D Representative stills of HeLaEGFP-AID-CENATAC cells expressing H2B-mNeon and depleted of CENATAC. Microtubules were visualized with SiR-Tubulin. Arrowheads and arrows indicate non-congressed chromosomes and supernumerary spindle poles, respectively. Scale bar, 5 μm. Time in hours. See Figure EV2 for the control condition. See also Movies EV1 and EV2. IAA, 3-indoleacetic acid.

E Quantification of the mitotic phenotype and multipolar spindle formation in time in H2B-mNeon-expressing HeLaEGFP-AID-CENATAC cells treated as in (D) (three biological replicates, >44 cells in total per condition). See also Figure EV2.

Data information: In (A, C, E), data are presented as mean ± SEM. P-values were calculated with unpaired student's t-tests.
Chromosomal instability by mutations in the novel minor spliceosome component CENATAC (2021)
Figure 3

Figure 3 - CENATAC is a novel component of the minor spliceosome.

A Phylogenetic profiles (presences (blue) and absences (white)) of the top 15 genes co-occurring with CENATAC in 90 eukaryotic species. Top: phylogenetic tree of the eukaryotic species (see Table EV1) with colored areas for the eukaryotic supergroups. 1 for NMT1 no human ortholog was found and instead the Arabidopsis thaliana ortholog is depicted. Genes associated with the minor (U12-dependent) spliceosome are depicted in orange. See also Table EV2.

B GO term analysis of the genes co-occurring with CENATAC as in (A) with a correlation score of >0.5. Note: the amount of hits and fold enrichment score were manually changed to accomodate the recently discovered SCNM1 (Bai et al, 2021)

C Graph of fold-changes of proteins enriched (P-value < 0.05) in proteomics analysis of CENATAC vs. control co-immunoprecipitations of HeLaEGFP-CENATAC cells (three biological replicates). Splicing factors are depicted in orange. See also Appendix Figure S7.

D, E Examples (D) and quantification (E) of Northern blot analyses of minor (U6atac, U4atac, U11, and U12) and major (U2, U1, U4, U5, and U6) spliceosome snRNAs in HeLaEGFP-AID-CENATAC cells (three biological replicates, normalized to the control). See also Appendix Figure S8.

F Glycerol gradient (10-30%) analysis of HeLa S3 nuclear extracts. snRNAs were detected by Northern blot analysis, proteins (CENATAC and PRPF4) by western blot. Locations of the U6atac mono-snRNP, U4atac/U6atac di-snRNP and U4atac/U6atac.U5 tri-snRNP are indicated.

G Schematics showing key assembly stages in minor intron splicing and minor tri-snRNP assembly: intron recognition (A-complex) and the catalytic spliceosome (C-complex). For simplicity, several stages of spliceosome assembly are omitted, such as the pre-B-complex, which consists of the intron recognition complex together with the tri-snRNP before architectural changes lead to the exclusion of U11 to give rise to the B complex, after which subsequent architectural changes lead to the exclusion of U4atac to give rise to the BACT complex, which is a precursor stage for the catalytically active C complex depicted in this figure (Turunen et al, 2013b).

Data information: In (C), data are presented as fold change of the mean log 2 transformed LFQ intensity. In (E), data are presented as mean ± std. dev.
Chromosomal instability by mutations in the novel minor spliceosome component CENATAC (2021)
Figure 4

Figure 4 - Minor intron splicing defects in CENATAC mutant cells fully correlate with mitotic defects.

A RT-PCR (middle panel) and quantification (upper panel) of IPO5 minor intron 21 (U12-type) splicing on RNA extracted from HeLaEGFP-AID-CENATAC cells treated as in Figure 2C (three biological replicates, normalized to siCENATAC + IAA). The bottom panel shows RT-PCR analysis of IPO5 major intron 19 (U2-type).

B RT-PCRs of IPO5, SUDS3 and ZCCHC8 minor and adjacent major introns on RNA extracted from patient lymphoblasts or HeLaEGFP-AID-CENATAC cells depleted of GAPDH or CENATAC as indicated. u, unspliced; s, spliced.

C For each condition in (A), minor intron splicing (Figure 4A) was plotted against the percentage of cells showing a mitotic phenotype (Figure 2C). R2 and p-values are provided for the linear regression trendline (dotted line).

D RT-PCRs of ZRSR2 and GAPDH (to visualize ZRSR2 knockdown efficiency, upper) and RT-PCRs of SUDS3 minor intron 7 (middle) and major intron 5 (lower) on RNA extracted from HeLaEGFP-AID-CENATAC or DLD-1 cells depleted of GAPDH or ZRSR2 as indicated.

E Quantification of mitotic defects as in Appendix Figure S6 of H2B-mNeon-expressing HeLaEGFP-AID-CENATAC or DLD-1 cells treated as in (D) (three biological replicates, >103 cells in total per condition).

Data information: In (A, E), data are presented as mean ± SEM. P-values were calculated with unpaired student's t-tests. In (C), the P- and R2-values were calculated with a Linear Regression Analysis.
Chromosomal instability by mutations in the novel minor spliceosome component CENATAC (2021)
Figure 5

Figure 5 - CENATAC promotes splicing of A-type minor introns.

A Sashimi plots showing the effect of CENATAC depletion (48hr, HeLaEGFP-AID-CENATAC cells) or ZRSR2 mutations (MDS patient cells) on AT-AC and GT-AG intron retention (left panel, Morc3), and cryptic splice site activation (right panel, Tmem231). CENATAC control represents the parental unedited HeLa cell line.

B Transcriptome-wide statistics of CENATAC depletion (48hrs) and ZRSR2 mutations on G- and A-type minor intron retention (U12 IR) and cryptic major splice site activation (U2 AS). Only introns showing at least 5 exon-exon junctions reads were included. For U12 IR, a statistical cutoff of Padj <0.05 was used. For U2 AS the probability cutoff of Pr > 0.9 was used.

C Density plots showing differences in intron retention (ΔΨ) distribution after CENATAC depletion (48 hours) or in samples with ZRSR2 mutations.

D Hierarchical clustering of A- and G-type intron retention in the unedited parental cell line treated with siGADPH for 48h (column 2), or in the HeLaEGFP-AID-CENATAC cell line treated with siGADPH for 48h (column 3) or with auxin and siCENATAC for 24 or 48 hrs (columns 4 and 5, respectively). Only introns showing a Padj< 0.05 and ΔΨ>0.1 in either the 24hr or 48hr depletion sample were included in the analysis. The A-type and G-type intron terminal dinucleotide subtypes are indicated with different colors in the first column. In case the gene contained multiple introns of the same type, the intron number is indicated in parentheses.

E RT-PCR of major (U2-type) AT-AC introns in SYCP2 (intron 5) and TAF2 (intron 1), and minor (U12-type) AT-AC intron in IPO5 (intron 21) on RNA extracted from HeLaEGFP-AID-CENATAC cells depleted of GAPDH or CENATAC. Schematic representations of unspliced/spliced PCR products are depicted on the right.

F Δ_intron_retention values for the MVA patient cell dataset (compared to the healthy sibling) using all (significant and not significant) minor A-type introns (n=179 for the depletion and n=177 for the MVA patient datasets) and minor G-type introns (n=441 for the depletion and n=446 for the MVA patient datasets). Only introns with on average at least 5 intron-mapping reads were used in the analysis. See also Appendix Figure S12.

G Venn-diagram analysis of the MVA patient cell and HeLaEGFP-AID-CENATAC CENATAC depletion datasets. A- and G-type minor introns showing statistically significant intron retention in each dataset were used. See also Dataset EV4.

Data information: In (F), data are presented as median (solid line) and mean (dashed line) inside the boxes. The boundaries of the boxes indicate 25th and 75th percentiles. Whiskers indicate the 90th and 10th percentiles. P values were calculated with two-sided Mann-Whitney Rank Sum Tests. The CENATAC depletion dataset consist of three biological replicates, the ZRSR2 mutation (MDS) dataset of eight biological replicates, and the MVA dataset of four biological replicates.