EMBO/SourceData huggingface dataset:
Figure legend: "siPool mediated LINC00941 knockdown (B) in calcium-induced keratinocyte differentiation (n = 3 biological replicates/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"LINC00941: 100287314"
Figure legend: "siPool mediated LINC00941 knockdown in calcium-induced keratinocyte differentiation, results in increased abundance of early and late differentiation marker transcripts on day 3 of differentiation (C) (n = 3 biological replicates/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"LINC00941: 100287314"
Figure legend: "LINC00941 knockdown in day 3 (D3) organotypic epidermal tissue cultures (D) (n = 3-4 tissue cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"LINC00941: 100287314"
Figure legend: "LINC00941 knockdown in day 3 (D3) organotypic epidermal tissue cultures results in increased expression of key differentiation genes (E) (n = 3-4 tissue cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"LINC00941: 100287314"
Figure legend: "B LINC00941 knockdown efficiency (siLINC00941) in epidermal tissue on day 3 of differentiation as obtained by qRT-PCR measurements (n = 4-5 epidermal tissue cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"LINC00941: 100287314"
Figure legend: "C Heatmap of differentially expressed genes (padj &lt; 0.05 and -1 &gt; log2FC &gt; 1) upon LINC00941 depletion on day 3 in organotypic epidermal tissue with marked keratinocyte differentiation genes (n = 4-5 epidermal tissue cultures/knockdown group)."
NCBI gene IDs:
"LINC00941: 100287314"
Figure legend: "A Differentially expressed genes in day 3 LINC00941 depleted epidermal tissue cluster within the epidermal differentiation complex (EDC) (n = 4-5 biological replicates/knockdown group)."
NCBI gene IDs:
"LINC00941: 100287314"
Figure legend: "B LINC00941 knockdown on day 3 in calcium-induced keratinocyte differentiation cultures results in increased expression of SPRR5 (FC = fold change) (n = 3 biological replicates/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"LINC00941: 100287314
SPRR5: 110806278"
Figure legend: "C Detected fragments per million (FPM) for SPRR5 in control (siCtrl) as well as LINC00941 deficient (siLINC00941) epidermal tissue for all biological replicates on day 3 (D3) of differentiation as obtained by DeSeq2 (FC = fold change) (n = 4‑5 epidermal tissue cultures/knockdown group)."
NCBI gene IDs:
"LINC00941: 100287314
SPRR5: 110806278"
Figure legend: "SPRR5 induction during the course of keratinocyte (KC) differentiation is shown by northern blot (D) for four different primary keratinocyte isolates and compared to undifferentiated keratinocytes (n = 8 biological replicates). Data is presented as mean ± SD."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "SPRR5 induction during the course of keratinocyte (KC) differentiation is shown by qRT-PCR analysis (E) for four different primary keratinocyte isolates and compared to undifferentiated keratinocytes (n = 8 biological replicates). Data is presented as mean ± SD."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "F p63 knockdown on day 3 of keratinocyte differentiation leads to decreased SPRR5 transcript levels (FC = fold change) (n = 3-4 biological replicates /knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"SPRR5: 110806278
p63: 8626"
Figure legend: "siPool-mediated SPRR5 knockdown on day 4 to 6 (D4-D6) of calcium-induced keratinocyte differentiation (A) (n = 3-5 cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "siPool-mediated SPRR5 knockdown on day 4 to 6 (D4-D6) of calcium-induced keratinocyte differentiation leads to decreased expression of key differentiation markers as shown by qRT-PCR (B) (FC = fold change) (n = 3-5 cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "siPool-mediated SPRR5 knockdown on day 4 to 6 (D4-D6) of calcium-induced keratinocyte differentiation leads to decreased expression of key differentiation markers as shown western blot analysis (C) (n = 3-5 cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "D SPRR5 knockdown efficiency in day 3 (D3) organotypic epidermal tissue (n = 4 epidermal tissue cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "E SPRR5 depletion in regenerated organotypic epidermal tissue results in drastically reduced expression of differentiation proteins as shown by immunofluorescence analysis. Collagen VII (Col VII, green) stain indicates the basement membrane, nuclei are shown in blue and the differentiation proteins filaggrin and loricrin are shown in red (n = 4 tissue cultures/knockdown group; one exemplary picture for each group is depicted). Scale bar: 50 µm."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "F SPRR5 knockdown in regenerated epidermal tissue results in reduced transcript levels of key differentiation genes as obtained by qRT-PCR (n = 4 epidermal tissue cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "B Overview of SPRR5 levels in control (siCtrl) and SPRR5 deficient (siSPRR5) epidermal tissue on day 3 and day 4 as obtained by qRT-PCR analysis (n = 3-5 epidermal tissue cultures/knockdown group). Data is presented as mean ± SD. Statistical significance was tested by an unpaired t-test and corrected for multiple testing after Bonferroni (* = adj. p-value &lt; 0.05, ** = adj. p-value &lt; 0.01, *** = adj. p‑value &lt; 0.001, and n.s. = not significant)."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "Heatmaps of differentially expressed genes (padj &lt; 0.05 and -0.5 &gt; log2FC &gt; 0.5) upon SPRR5 depletion on day 3 (C) in organotypic epidermal tissue (n = 3-5 epidermal tissue cultures/knockdown group)."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "Heatmaps of differentially expressed genes (padj &lt; 0.05 and -0.5 &gt; log2FC &gt; 0.5) upon SPRR5 depletion on day 4 (D) in organotypic epidermal tissue (n = 3-5 epidermal tissue cultures/knockdown group)."
NCBI gene IDs:
"SPRR5: 110806278"
Figure legend: "(c) UVRAG binds Beclin1 through its CCD. After transfection with Beclin1-V5, together with full-length or fragments of Flag-UVRAG, 293T whole cell lysates (WCLs) were used for immunoprecipitation (IP) with anti-Flag followed by immunoblotting (IB) with anti-V5."
NCBI gene IDs:
"Beclin1: 8678
UVRAG: 7405"
Figure legend: "(e) UVRAGCCD is required for Beclin1 interaction. After transfection with Beclin1-V5 (lanes 2 and 4) together with Flag-UVRAGΔCCD (lanes 1 and 2) or Flag-UVRAGΔC2 (lanes 3 and 4), WCLs were used for immunoprecipitation with anti-Flag followed by immunoblotting with anti-V5."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(f) Beclin1 binds UVRAG through its CCD. After transfection with Flag-UVRAG together with full-length or fragments of Beclin1-V5, WCLs were used for immunoprecipitation with anti-V5 followed by immunoblotting with anti-Flag."
NCBI gene IDs:
"Beclin1: 8678"
Figure legend: "(a) The Bcl-2 binding domain of Beclin1 is sufficient to bind vBcl-2. At 48 h posttransfection with wild-type and mutant Beclin1-V5, together with HA-vBcl-2, WCLs of 293T cells were used for immunoprecipitation with anti-V5 followed by immunoblotting with anti-HA."
NCBI gene IDs:
"Beclin1: 8678"
Figure legend: "(b) The loss of Beclin1 interaction of vBcl-2AAA mutant. At 48 h posttransfection with wild-type HA-vBcl-2 or vBcl-2AAA mutant, together with Beclin1-V5, WCLs of 293T cells were used for immunoprecipitation with anti-V5, followed by immunoblotting with anti-HA."
NCBI gene IDs:
"Bcl-2: 596"
Figure legend: "(c) vBcl-2 interaction with wild-type UVRAG in the presence of Beclin1. At 48 h posttransfection with Flag-UVRAG together with Beclin1-V5 and HA-vBcl-2 or vBcl-2AAA mutant, WCLs of 293T cells were used for immunoprecipitation with anti-HA followed by immunoblotting with anti-Flag."
NCBI gene IDs:
"Bcl-2: 596"
Figure legend: "(e) PI(3)KC3 N-terminal C2 domain binds Beclin1. At 48 h posttransfection with Beclin1-V5 together with full-length or fragments of Flag-PI(3)KC3, WCLs of 293T cells were used for immunoprecipitation with anti-Flag followed by immunoblotting with anti-V5. CAT, catalytic domain."
NCBI gene IDs:
"PI(3)KC3: 5289"
Figure legend: "(f) Beclin1CCD and Beclin1ECD are sufficient for binding PI(3)KC3. At 48 h posttransfection with Flag-PI(3)KC3 together with full-length or fragments of Beclin1-V5, WCLs of 293T cells were used for immunoprecipitation with anti-V5 followed by immunoblotting with anti-Flag. CT, C terminus (aa 337-448)."
NCBI gene IDs:
"Beclin1: 8678"
Figure legend: "(g) PI(3)KC3 interaction with UVRAG in the presence of Beclin1. At 48 h posttransfection with Flag-UVRAGΔCCD or UVRAGCCD together with HA- PI(3)KC3 and Beclin1-V5, WCLs of 293T cells were used for immunoprecipitation with anti-Flag followed by immunoblotting with anti-HA."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(a) UVRAG expression and LC3 process in HCT116 cells. The same protein amounts of 293T, NIH3T3, HCT116 and MCF7 cells were used for immunoblotting with anti-UVRAG and anti-tubulin. WCLs of 293T cells transfected with Flag-tagged UVRAG were included as controls. WCLs of HCT116.vector and HCT116.UVRAG were incubated with or without starvation conditions and used for immunoblotting with anti-LC3 and anti-tubulin. The raw data for this experiment is presented in the Supplementary information, Fig. S5."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(b) Electron microscopy of autophagy in HCT116 cells. HCT116.vector and HCT116.UVRAG cells were incubated under normal or starvation conditions for 4 h and subjected to scanning electron microscopy. Scale bars (from left to right panels) represent 2 nm, 0.5 nm, 0.2 nm and 0.2 nm. The arrows indicate autophagosome or autolysosome."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(c) UVRAG induces autophagosome formation in HCT116 cells. After transfection with GFP-LC3 vector, HCT116.vector and HCT116.UVRAG cells were maintained under normal conditions or starved for 3 h. GFP-LC3 was detected using an inverted fluorescence microscope. Arrows indicate autophagosomes. The scale bars represent 10 μm."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(d) After transfection with GFP-LC3 vector, HCT116.vector and HCT116.UVRAG cells were maintained under normal conditions, starved for 3 h in the absence or presence of 10 mM 3-methyladenine or treated with or without 2 μM rapamycin or rapamycin + 10 mM 3-methyladenine. Autophagome was quantified as the mean ± s.d. of combined results from three independent experiments."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(a) HCT116.vector and HCT116.UVRAG cells were labelled with LysoTracker and subjected to flow cytometry analysis. HCT116.vector, HCT116.UVRAG, and HCT116.UVRAG ΔCCD cells were treated with or without wortmannin (1 μM) for 2 h and their lysates were used to measure the lysosomal acid phosphatase enzymatic activity. Data represents mean ± s.d. of three experiments."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(b) UVRAG induces autophagosome formation in NIH3T3 cells. After transfection with GFP-LC3 vector, NIH3T3.vector and NIH3T3.UVRAG cells were maintained under normal conditions, starved for 3 h in the absence or presence of 10 mM 3-methyladenine or treated with or without 2 μM rapamycin or rapamycin + 10 mM 3-methyladenine. Data represents mean ± s.d. of three experiments."
NCBI gene IDs:
"UVRAG: 78610"
Figure legend: "(a) Autophagic activity of UVRAG mutants. HCT116 cells expressing wild-type or mutant UVRAG were transfected with GFP-LC3 expression vector and incubated under normal or starvation conditions for 3 h. Autophagy was quantified as described in Fig. 3."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(b) Effect of wild-type and mutant UVRAG on Beclin1-mediated autophagy. MCF7.vector, MCF7.Beclin1 and MCF7.Beclin1ΔECD cells were cotransfected with wild-type UVRAG or its mutant expression vector together with GFP-LC3 expression vector. At 16-18 h posttransfection, cells were incubated under normal or starvation conditions for 4 h. Autophagy was quantified as described in Fig. 3. The scale bars represent 20 μm."
NCBI gene IDs:
"Beclin1: 8678
UVRAG: 7405"
Figure legend: "(c, d) Interdependence between UVRAG and Beclin1 for autophagosome induction. HCT116.vector and HCT116.UVRAG cells were transfected with control siRNA, Beclin1 siRNA or UVRAG siRNA together with GFP-LC3 expression vector as indicated. Autophagy was quantified as described in Fig. 3. WCLs of these cells were used for immunoblotting with anti-UVRAG, anti-Beclin1 or anti-tubulin. The scale bars represent 20 μm. In all figures, data represents mean ± s.d. of three experiments. The raw data for c and d are presented in the Supplementary Information, Fig S5."
NCBI gene IDs:
"Beclin1: 8678
UVRAG: 7405
UVRAG: 78610///7405"
Figure legend: "(c, d) Interdependence between UVRAG and Beclin1 for autophagosome induction.MCF7.vector, MCF7.Beclin1 and MCF7.Beclin1ΔECD cells (d) were transfected with control siRNA, Beclin1 siRNA or UVRAG siRNA together with GFP-LC3 expression vector as indicated. Autophagy was quantified as described in Fig. 3. WCLs of these cells were used for immunoblotting with anti-UVRAG, anti-Beclin1 or anti-tubulin. The scale bars represent 20 μm. In all figures, data represents mean ± s.d. of three experiments. The raw data for c and d are presented in the Supplementary Information, Fig S5."
NCBI gene IDs:
"Beclin1: 8678
UVRAG: 7405"
Figure legend: "(a) Increased Beclin1-PI(3)KC3 interaction by UVRAG and continued interaction of UVRAG with Beclin1 on stress conditions. HCT116.vector, HCT116.UVRAG and HCT116.UVRAGΔCCD cells were used for immunoprecipitation with anti-PI(3)KC3 followed by immunoblotting with anti-Beclin1. WCLs were used for immunoblotting with anti-Beclin1 and anti-PI(3)KC3. HCT116.UVRAG cells expressing Flag-tagged UVRAG were incubated under nutrient-rich conditions (lanes 1 and 2), starvation for 4 h (lane 3), or 2 μM rapamycin treatment for 2 h (lane 4). WCLs were then used for immunoprecipitation with anti-Beclin1 (lanes 2, 3 and 4) or preimmune antibody (lane 1) followed by immunoblotting with anti-Flag. The raw data for this experiment are presented in the Supplementary Information, Fig. S5."
NCBI gene IDs:
"UVRAG: 78610///7405"
Figure legend: "(b) Increased PI(3)KC3 activity by UVRAG. At 48 h posttransfection with Flag-tagged PI(3)KC3 with Beclin1 (lane 1), with Beclin1 + UVRAG (lane 2) or with Beclin1 + UVRAGΔCCD vector (lane 3), WCLs of 293T cells were used for immunoprecipitation with anti-Flag followed by an assay for PI(3)KC3 lipid kinase activity, as described in the Methods. At 16 h posttransfection with p40(phox) PX-EGFP fusion, HCT116.vector and HCT116.UVRAG cells were detected using an inverted fluorescence microscope. p40(phox) PX-EGFP-positive vesicles were quantified as the mean ± s.d. of combined results from three independent experiments. The scale bars represent 10 μm."
NCBI gene IDs:
"p40(phox): 5594
UVRAG: 78610///7405"
Figure legend: "(c) Suppression of autophagy by γHV68 vBcl-2. At 18 h posttransfection with GFP-LC3 vector, NIH3T3.vector, NIH3T3.vBcl-2 and NIH3T3.vBcl-2AAA, cells were incubated under normal or starvation conditions for 4 h. Subsequently, GFP-LC3 was detected using an inverted fluorescence microscope and autophagy was quantified as mean ± s.d. of combined results from three independent experiments."
NCBI gene IDs:
"Bcl-2: 12043"
Figure legend: "(a) Proliferation rates. HCT116.vector, HCT116.UVRAG, HCT116.UVRAGΔC2, HCT116.UVRAGΔCCD and HCT116.UVRAGCCD cells (1 × 105 per well) were seeded into 6-well microtitre plates. Cell numbers were counted on the days indicated. The results represent means of three independent assays."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(b) Anchorage independence. HCT116.vector, HCT116.UVRAG, HCT116.UVRAGΔC2, HCT116.UVRAGΔCCD and HCT116.UVRAGCCD cells (1 × 104) were incubated in soft agar as described in the Methods. After ten days, colonies were photographed and counted. The scale bars represent 50 μm."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(c) Tumorigenicity. HCT116.vector, HCT116.UVRAG and HCT116.UVRAGΔCCD cells (1 × 107) were subcutaneously injected into 5 nude mice, separately. At 16 days postinoculation, mice and tumours were photographed and tumour weights were measured. Arrows indicate location of tumours."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "B Typical dsDNA processing event. The dashed red line connects the minima at the end of the rewinding sections The inset shows a DNA unwinding event in the presence of nuclease-dead Dna2 E675A and RPA."
NCBI gene IDs:
"Dna2: 856569"
Figure legend: "(A) CRISPR-guided  AID∆C protein could support CSR   in  Aicda-/- CH12F3  cells. Left, CRISPR-guided AID   is schematically illustrated with each component listed. Right, CRISPR-guided AID   initiated CSR   levels to IgA. Blue arrows represent multiple CRISPR  recognition sites. The number in the parentheses indicates CRISPR  recognition sites in each S region. Three biological replicates are plotted by dots and mean with standard deviation (SD). Data information: For panels A one-way ANOVA followed by Dunnett's multiple comparisons test was used for significance assessment. For all panels, ****, p&lt;0.0001; ***, p&lt;0.001; **, p&lt;0.01; *, p&lt;0.05; ns, p&gt;0.05."
NCBI gene IDs:
"CRISPR: 
Aicda: 11628
AID: 11628"
Figure legend: "(B) CRISPR-guided AID  generated breaks  at the S region in Aicda-/- CH12F3  cells were quantitatively detected by  PEM-seq. Top, schematic illustration shows the bait SaCas9 site at Iγ3  region and CRISPR-guided AID  variants targeting sites at S regions. Bottom, percentages of translocation junctions between Iγ3  and Sμ  or Sα  regions are plotted as mean with SD of three biological replicates in the bar plot. Data information: For panels B, one-way ANOVA followed by Dunnett's multiple comparisons test was used for significance assessment. For all panels, ****, p&lt;0.0001; ***, p&lt;0.001; **, p&lt;0.01; *, p&lt;0.05; ns, p&gt;0.05."
NCBI gene IDs:
"Cas9: 
CRISPR: 
Aicda: 11628
AID: 11628"
Figure legend: "(C) AID-AIDE58Q dimer proteins were expressed in AID-deficient CSR-activated  B cells, AID   dimer is schematically illustrated on top and CSR  levels to IgG1  are shown. Three biological replicates are plotted by dots and mean with SD is shown. Data information: For panels C, one-way ANOVA followed by Dunnett's multiple comparisons test was used for significance assessment. For all panels, ****, p&lt;0.0001; ***, p&lt;0.001; **, p&lt;0.01; *, p&lt;0.05; ns, p&gt;0.05."
NCBI gene IDs:
"AID: 11628"
Figure legend: "(D) CSR  levels to IgA  in Aicda-/- CH12F3-miniS  cells with indicated AID  variants or CRISPR-guided AID  variants. Levels of CSR  to IgA  are plotted and mean with SD of three to six biological replicates. Data information: Unpaired two-tailed Student's t-test was performed for panel D. For all panels, ****, p&lt;0.0001; ***, p&lt;0.001; **, p&lt;0.01; *, p&lt;0.05; ns, p&gt;0.05."
NCBI gene IDs:
"CRISPR: 
Aicda: 11628
AID: 11628"
Figure legend: "(E) Mutation profiles  of miniS  region in Ung-/-Msh2-/-Aicda-/- miniS  cell lines complemented with indicated AID. Mutation frequency at each nucleotide along the 756-bp miniS region  is plotted as a bar graph with green error bars, representing mean with standard error of the mean (SEM) of three biological replicates. Positions of AID-preferred AGCT  and other RGYW  motifs are marked with orange and yellow respectively under each plot."
NCBI gene IDs:
"Aicda: 11628
AID: 11628
Msh2: 17685
Ung: 22256"
Figure legend: "(F)   Mutation profiles of  miniS region in Ung-/-Msh2-/-Aicda-/- miniS  cell lines expressing CRISPR-guided AID  variants. Mutation frequency at each nucleotide is plotted as mean with SEM of three biological replicates in the bar graph with green error bar. Plots are labeled as in (B). The sgRNA targeting position is indicated with blue lines at the bottom."
NCBI gene IDs:
"CRISPR: 
Aicda: 11628
AID: 11628
Msh2: 17685
Ung: 22256"
Figure legend: "(A) Representative images showing the localization  of AID  (green), AIDR190X (green), and endogenous IgH loci (red) in nucleofected Aicda-/- CH12F3  cells. The IgH   loci are visualized using Sμ-gRNA and indicated by white arrows. An illustration of CRISPR-Sirius IgH  locus visualization is shown on top. Scale bar, 5 µm."
NCBI gene IDs:
"CRISPR: 
Aicda: 11628
IgH: 111507"
Figure legend: "(B) OptoDroplet  formation in CH12F3  cells. Schematic illustration of light-induced optoDroplet  system is depicted on top. AID  variants were tagged to the N terminus of the optoDroplet  construct and blue light was employed to promote the formation of puncta three times followed by imaging  each time. Representative images after the third blue light activation in Aicda-/- CH12F3  cells with the indicated AID  variants are shown at the bottom. White dashed line and green line depict the shapes of nucleus  and nucleolus  based on Hoechst staining  or GFP-FBL, respectively. Scale bar, 5 µm."
NCBI gene IDs:
"Aicda: 11628
AID: 11628"
Figure legend: "(C) Representative images showing optoDroplet  formation of indicated AID  variants in HEK293T  cells. CRM1  inhibitor (CRM1i) was used for selective trapping of AID  in nuclei. Scale bar, 5 µm."
NCBI gene IDs:
"AID: 11628"