EMBO/sd-character-level-ner huggingface dataset:
Figure 5(A) Percentage of [V/I]X[V/I] tripeptides among (top) the total number of all tripeptides (% tripeptides) or (middle) the total number of [V/I]X[V/I] tripeptides in the structured (black) or disordered regions (red) ([V/I]X[V/I] %) shown as a function of the X residue type. (Bottom) The difference between [V/I]X[V/I] % for disordered and structured regions shows the enrichment (positive) or depletion (negative) of specific [V/I]X[V/I] motifs in disordered regions. The grey bars indicate the [V/I]L[V/I] and [V/I]P[V/I] motifs studied in this work, i.e. ILV and IPV. (B) Volcano plot representing the interactors that are enriched for the P182L mutant versus GFP as a negative control, obtained with affinity-enrichment mass spectrometry. Proteins that co-immunoprecipitated significantly more (p<0.05) with the P182L variant are shown in the upper right quadrant. Interactors with one or more [I/V]-x-[I/V] motifs are displayed in red while other significantly enriched interactors are displayed in black. (C-D) Co-immunoprecipitation from HeLa cells stably overexpressing V5-epitope-tagged HSP27 (WT or P182L mutant) using anti-V5 beads. Co-immunoprecipitation was quantified and presented as a percentage relative to the P182L variant (n=3). The mean ± one standard deviation (n=3) is shown. Right: the location of Pro182 (red) in the crystal structure of peptide-bound cHSP27 (PDB: 4mjh) and in silico creation of the P182L mutation (blue). The peptide is shown in white sticks. P182L specifically weakens binding of the HSP27 IxI/V motif. (E) Co-immunoprecipitation from HeLa cells stably overexpressing V5-epitope-tagged HSP27 (WT or P182L mutant) and transiently transfected with BAG3-eGFP (WT or IPV-mutant) using anti-GFP beads. Western blots for anti-GFP (BAG3), V5 (HSPB1), and α-tubulin. NS indicates a non-specific band. Note that detection of BAG3 (anti-GFP) and HSP27 (anti-V5) occurs with different antibodies. The locations of the IPV-to-GPG mutations in BAG3 are depicted below. (F) Co-immunoprecipitation from HeLa cells transiently transfected with V5-epitope-tagged HSP27 (P182L or S155Q/P182L mutant) using anti-V5 beads (n=2). Right: the location of Ser155 (red) in the crystal structure of peptide-bound cHSP27 (PDB: 4mjh) and in silico creation of the S155Q mutation (purple) showing a clash with the bound peptide. The peptide is shown in white sticks.S155Q disrupts binding of all IxI/V motifs.
Figure 5A, B. The relative YTHDF1-RIP enrichment ratio of the indicated genes in C666 cells (A) and CNE2EBV cells with induced EBV reactivation (24 h post TPA/NaB treatment) (B). The EEF1A1 mRNA known to contain m6A sites and RPL30 mRNA containing no m6A modification were used as positive and negative controls, respectively. BALF1 and BCRF1 containing no m6A modification, identified in this study, were used as viral negative controls. The fold enrichment was determined by calculating the 2-ΔCt of the RIP sample relative to the input sample. The mean of the fold enrichment by IgG was normalized to 1. C. The relative Myc-RIP enrichment ratios of wild-type and mutant BZLF11-262nt mRNA in CNE2EBV cells. CNE2EBV cells were co-transfected with wild-type or mutant BZLF11-262nt and myc-YTHDF1 or vector control for 24 h. The fold Myc-RIP enrichment was determined by calculating the 2-ΔCt of the RIP sample relative to the input sample. The mean of the fold Myc-RIP enrichment level on WT-BZLF1 mRNA was normalized to 1. D. The relative enrichment of the BZLF1 and BRLF1 mRNA in CNE2EBV cells with transfected with siYTHDF2, siYTHDF3 or siNC siRNA following EBV reactivation. After 24 h of siRNA transfection, CNE2EBV cells were treated with TPA (30 ng/ml) and NaB (2 mM) for 24 h. The RIP assays were performed using YTHDF1-specific antibody or IgG control in these cells. Fold enrichment was determined by calculating the 2-ΔCt of the RIP sample relative to the input sample. E, F. The relative m6A and YTHDF1 enrichment of the BZLF1 (E) or BRLF1 (F) mRNAs measured in CNE2EBV cells transfected with the METTL14-specific siRNAs (siM14) or siNC control following EBV reactivation. After 24 h of siRNA transfection, CNE2EBV cells were treated with TPA (30 ng/ml) and NaB (2 mM) for 24 h, followed by MeRIP and RIP assays. The fold enrichment was determined by calculating the 2-ΔCt of the RIP sample relative to the input sample. G. Residual mRNA levels of BZLF1 and BRLF1 after termination of transcription via ActD treatment in C666 cells transfected with YTHDF1-specific siRNAs or the siNC control. After 24 h of siRNA transfection, the C666 cells were treated with ActD and the mRNA levels analyzed by qRT-PCR. The relative mRNA level at 0 h after the ActD treatment was normalized to 1. H. Residual mRNA levels of BZLF1 and BRLF1 after termination of transcription via ActD treatment in CNE2EBV cells transfected with YTHDF1-specific siRNAs or the siNC control following EBV reactivation. After 24 h of siRNA transfection, CNE2EBV cells were induced with NaB (2 mM) for 24 h, treated with ActD and analyzed by qRT-PCR. The relative mRNA level at 0 h after the ActD treatment was normalized to 1.
Figure 6Western blotting showing that the phosphorylation of transfected N-terminal MYRF (pMYRF) was promoted by treatment with the PKG activator of 8-Br-cGMP (10 or 100 μM) for 1 hr or co-transfected 150Q-HTT for 24 hr, which was blocked by treatment of the PKG inhibitors of RKRARKE (50 μM) or KT5823 (5 μM) for 12 hr. trans-nMYRF: transfected N-terminal MYRF. Adeno-associated virus vector expressing full-length PRKG2 under the control of the CMV promoter. Western blotting of N2a cell line that was transfected with AAV-PRKG2 for 48 hr. The blots were probed with anti-Ser259 (pMYRF) antibody. Note that overexpression of PRKG2 increased phosphorylation of N-terminal MYRF (nMYRF) in a dose-dependent manner. Stereotaxic injection of AAV-GFP virus into the corpus callosum (CC, indicated between two dotted lines) in the mouse brain. Ctx: cortex, Str: striatum. Scale bar: 100 μm..   Immunohistochemical staining with anti-Ser259 (pMYRF) showing that AAV-PRKG2, but not AAV-GFP, promotes MYRF phosphorylation in the corpus callosum. Scale bar: 40 μm.   Quantitative analysis of the pMYRF- or total MYRF-positive cells in each filed (40X). Twenty random fields in each section were examined, n=3 mice in each group. One-way ANNOVA with Tukey's test; ***P=8.79x10-5. Data are mean ±SEM. Double immunofluorescent staining with antibodies to PRKG2 and Ser259 showing that AAV-PRKG2, but not AAV-GFP (green), promotes MYRF phosphorylation (red) in the injected corpus callosum. Scale bar: 40 μm. Western blotting analysis of the mouse corpus callosum tissues using anti-Ser259 (pMYRF), phosphor-PRKG2 (pPRKG2) or phosphor-VASP (pVASP). Note that overexpression of mouse PRKG2 leads to the phosphorylation of MYRF and VASP. fMYRF: full-length MYRF, nMYRF: N-terminal MYRF.
Figure 6A. Heat map showing log2 fold expression changes of differentially expressed genes in AC tissues overexpressing Foxb1, Foxb1-Eomes, Eomes, Irx3, Irx3-Otx2, Otx2 and Lhx8. B. Correlation heat map of overexpression RNA-seq samples and single cell clusters. C. Fold enrichment of genes with zygotically defined (ZyD) H3K4me3 at their promoter in AC with transcription factor overexpression. Asterisk indicates hypergeometric p-value <= 0.01.
uORFs act repressively in vertebrate developmentMost uORFs are not conserved at the peptide sequence level - Pie charts depict coding potential (phyloCSF score) of (A) all potential uORFs and (B) translated uORFs.Figure 2Most uORFs are not conserved at the peptide sequence level - Pie charts depict coding potential (phyloCSF score) of (A) all potential uORFs and (B) translated uORFs. uORFs with a phyloCSF score ≥ 50 were considered conserved, uORFs were considered weakly conserved if their phyloCSF score was positive but less than the conservation threshold of 50. (C) Translated uORFs are enriched in conserved peptides - Enrichment plot indicates log-odds ratio of conserved uORFs in the set of translated uORFs versus all uORFs. (D) uORFs repress translation in an additive manner at 5hpf - Cumulative distribution of translation efficiency in expressed (>0.5RPKM) uORF-containing transcripts versus transcripts lacking uORFs. Transcripts containing oORFs are excluded from this plot. Control transcripts (0 uORFs) have a coding CDS (Global ORFScore > 6.044) but no uORF in their 5' TL. Two-sided Wilcoxon p-values are provided for each uORF set compared to the control. (E) oORFs are strong repressors of translation - Cumulative distribution of translation efficiency at 5hpf in expressed (>0.5RPKM) oORF-containing transcripts versus transcripts lacking oORFs. Transcripts containing uORFs are excluded from this set. Control transcripts (0 oORFs) have a coding CDS (Global ORFScore > 6.044) but no uORF in their TLS. Two-sided Wilcoxon p-value is provided for the oORF set compared to the control. (F) miR-430 is a widespread developmental translation repressor - Cumulative distribution of translation efficiency at 5hpf in expressed (>0.5RPKM) miR-430 site-containing transcripts (single or multiple 7/8-mers) versus transcripts which lack a miR-430 site in their 3' UTR. Two-sided Wilcoxon p-value is provided for the miR-430 set compared to the control. (G) uORFs are associated with lower RNA levels - Cumulative distribution of translation efficiency at 5hpf in expressed (>0.5RPKM) uORF-containing transcripts versus transcripts lacking uORFs. Transcripts containing oORFs are excluded from this plot. Control transcripts (0 uORFs) have a coding CDS (Global ORFScore > 6.044) but no uORF in their 5' UTR. Two-sided Wilcoxon p-values are provided for each uORF set compared to the control. (H) oORFs are associated with lower RNA levels - Cumulative distribution of translation efficiency at 5hpf in expressed (>0.5RPKM) oORF-containing transcripts versus transcripts lacking oORFs. Transcripts containing uORFs are excluded from this set. Control transcripts (0 oORFs) have a coding CDS (Global ORFScore > 6.044) but no uORF in their 5' UTR. Two-sided Wilcoxon p-value is provided for the oORF set compared to the control. (I) miR-430 targets RNAs for degradation by 5hpf - Cumulative distribution of translation efficiency at 5hpf in expressed (>0.5RPKM) miR-430 site-containing transcripts (single or multiple 7/8-mers) versus transcripts which lack a miR-430 site in their 3' UTR. Two-sided Wilcoxon p-value is provided for the miR-430 set compared to the control.
a) Rhod-2 fluorescence in control or overexpressing TbMCU (TbMCU-OE) PCF.f6(a) Rhod-2 fluorescence in control or overexpressing TbMCU (TbMCU-OE) PCF. Scale bar, 10 μm. (b,c) Rhod-2 (mitochondrial) (b) and Fluo-4 (cytosolic) (c) fluorescence in control (−Tet) and overexpressing TbMCU (+Tet) PCF (means±s.d., n=3, **P0.05, Student's t-test); NS, not significant. (d) Ca2+ uptake by digitonin-permeabilized PCF overexpressing TbMCU. Trypanosomes were incubated as in Fig. 2c. Multiple pulses of CaCl2 (arrowheads) were added to a final concentration of 8 μM. (e) Ca2+ uptake in TbMCU-OE PCF (+Tet) 200 s after addition of Ca2+, as compared with uninduced trypanosomes considered as 1 (−Tet) (means±s.d., n=3, **P0.01, Student's t-test). (f) Mitochondrial membrane potential of digitonin-permeabilized control (−Tet) and TbMCU-OE (+Tet) PCF. The reactions were incubated as in Fig. 3a. (g) Changes in safranine fluorescence after addition of ADP, Ca2+ or FCCP to -Tet and +Tet PCF trypanosomes (means±s.d., n=3, **P0.001, Student's t-test). (h) Mitochondrial oxidative stress as measured with MitoSOX Red in control (C) and TbMCU-overexpressing (OE) PCF permeabilized with 50 μM digitonin in the presence of 0.4 mM Ca2+. Controls were treated with 2 μM antimycin A (C+AA), or were trypanosomes exposed to 0.4 mM Ca2+ in the absence of digitonin (−DIG+Ca2+), and trypanosomes permeabilized with digitonin in the absence of Ca2+ (C, yellow line). (i) Quantification of change at 900 s. Results are expressed as mean fluorescence±s.d. (n=3, **P0.001, Student's t-test). (j) Growth of trypanosomes in the absence (control, black lines) or presence (TbMCU-OE, red lines) of 1 μg ml−1 tetracycline (means±s.d., n=3). (k) Dead cells in representative fields of control (−Tet) and TbMCU-OE (+Tet) PCF are indicated (white arrows). Scale bar, 10 μm. (l) Cell viability on apoptotic challenge of control (−Tet) or TbMCU-OE (+Tet) PCF trypanosomes with H2O2 and C2-ceramide. The percentage of cell death was obtained from means±s.d. by analysing >60 fields (including >400 cells) (n=3). **P0.01, Student's t-test.
Figure 6(A) The association SNP rs1432689 genotypes are correlated to differential SPINK6 mRNA expression in over 1000 human lung tissues from three centers. The box denotes interquartile range; the thick line and diamond within the box are the median and mean respectively; whiskers are the minimum and maximum and open dots are outliers. Linear regression was used for eQTL data analysis. Data of three cohorts were applied to meta-analysis and resulted in the P-value of the association SNP. (B) rs1432689 genotypes are correlated to SPINK6 expression in human lung tissues and esophagus mucosa from GTEx database. Sample sizes for each genotype are shown in the x-axis. The y-axis shows the normalized expression of SPINK6 (Norm. expression) in the indicated trusses. Median and interquartile range are represented by a white line and dark box respectively. Data distribution is colored with light blue; a wider section of the violin plot indicates the data on the section have a higher frequency. Linear regression was used for data analysis.
Figure 9Succinate triggers a unique succinylation modification of K87 in the NP of IAV which further alters the electrostatic environment of the vRNA binding site. As a result, the formation of vRNPs particles is impaired. This further contributes to an inhibition of viral multiplication as well as viral-induced inflammatory response. In vivo, IAV-infected mice treated intranasally with succinate are more resistant to the development of acute pneumonia.
Figure 2a, Distributions of cell cycle phase durations for RPE, U2OS, and H9 cells using single-cell measurements of phase duration Black curves represent fits to Erlang distribution. b, Erlang model of cell cycle progression. Each phase consists of a distinct number of steps, k. Each step is a Poisson process with rate parameter, λ. After fitting each phase to the Erlang distribution, we were able to accurately simulate all phase durations except for M phase (2-sided Kilmogorov-Smirnov test for difference between measured and simulated distributions c, Fitted shape parameter, k, representing the number of steps for each phase. Error bars represent std from 1000 bootstraps. d, Normalized shape parameter, k, for G1, S, and G2 phases in RPE, U2OS, and H9 cells. Bar height represents the fraction of total cell cycle steps spent in each phase. Error bars represent std from 1000 bootstraps. e, Fitted rate parameter, λ, representing the progression rate of each step within a cell cycle phase. Error bars represent std from 1000 bootstraps. f, Rate parameter λ for each phase, shown by cell type.
Figure 2Gr1-CD11b+ cells, polarized by the indicated treatment, were purified for mitochondrial respiration detection. The oxygen consumption rate (OCR) of these cells was monitored after the addition of oligomycin (OA) (1 µM), Carbonyl cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP, 1 µM), and the electron transport inhibitor rotenone and antimycin A (R/AA) (0.5 µM) at indicated time points. The basal OCR, basal extracellular acidification rate (ECAR), spare respiratory capacity, proton leak, ATP production and maximal respiration based on the OCR value were quantified. Forty µM etomoxir were added starting from day 0 of bone marrow polarization, followed by mitochondrial respiration assay by using the same amount of polarized Gr1-CD11b+ myeloid cells on day 7. The mitochondrial respiration was monitored and analyzed via XFe96 Analyzer. Exemplary plots of the proportion of CD206+ cells, the mean fluorescence intensity (MFI) of CD38 and CD73 on polarized myeloid cells was determined via flow cytometry. T cell proliferation assay was performed via co-culture with purified CD4+ T cells in the ratios of M (myeloid cells): T (T cells) = 1:30. NO production from the co-culture supernatant was quantified by Griess reaction.
Figure 4A) Consensus DNA binding sites for the TFs overexpressed in Lo-G PDACs at enhancers specific of the same cell lines were detected using FIMO (Grant et al, 2011) (p-value ≤ 2E-4). The orange dot indicates DNA binding sites over-represented relative to Hi-G-specific enhancers (as determined by Pscan using as threshold p < 1E-5, see methods). B) ChIP-seq snapshots from the low-grade CFPAC-1 cell line showing histone modifications, RNA-seq data and the recruitment of the five TFs analyzed to two representative genomic regions containing differentially expressed genes (KRT23, left and CEACAM6, right). Sequencing tracks of the high-grade PANC-1 cell line are shown at the bottom for comparison. C) Co-binding of the five TFs analyzed by ChIP-seq at the enhancers selectively acetylated in Lo-G PDACs. The matrix indicates the number of regions with the indicated combinations of bound TFs. D) TF distance from the center of acetylated regions specific of Lo-G PDACs. E) Cumulative distributions showing histone acetylation and H3K4 mono- and tri-methylation levels of the genomic regions bound by KLF5. Data are shown for in CFPAC-1 (continuous line) and PANC-1 cells at both TSS-distal (top panels) and TSS-proximal (bottom panels) regions. F) KLF5 signal intensity at genomic regions corresponding to distinct classes of enhancers. Central values represent the median.
Figure 6 Transferrin uptake was measured with serum starvation or 4 h after serum starvation as described [17]. Fluorescent transferrin was added for 45 min to the cells. Cells were analyzed after washing. The red circle around the mother centriole marker CEP164 indicates the fluorescence intensity that was determined for (B). The encircled area in MERGE is shown 2-fold enlarged on the right hand side of the figure Quantification of (A). The fluorescence intensities of transferrin within a 2 μm-radius circle surrounding the CEP164 signal were quantified. An ImageJ macro was used to measure the intensity as described in methods. Data were calculated from a total of 120 cells pooled from two independent experiments. Mean ± SD. **** P≤ 0.0001  hCDC14APD cells showed an increased localization of myosin Va containing vesicles within the 1 μm-radius of the basal body (red cicle). The encircled area in MERGE is shown 4-fold enlarged on the right hand side of the figure Quantification of C. Data was calculated from a total of 180 cells pooled from three independent experiments. Mean ± SD. * P≤ 0.05, *** P≤ 0.001, **** P≤ 0.0001  Arp2 localization in REP1 WT, hCDC14APD and DBN1 KO cells. Signal intensity was measured 30 min after serum starvation. The encircled area in MERGE is shown 4-fold enlarged on the right hand side of the figure  Quantification of E. Sub-centrosomal (1 μm-radius; red circle in E) Arp2 was measured by quantifying the intensity of Arp2 in WT, hCDC14APD and DBN1 KO cells. Both hCDC14APD and DBN1 KO cells contain significantly higher Arp2 in the pericentrosomal area (1 μm-radius) compared to WT cells after 30 min of serum starvation. Data were calculated from a total of 120 cells pooled from three independent experiments. Mean ± SD. **** P≤ 0.0001  Pericentrosomal ARP2 enrichment was comparable in the RPE1 DBN1 KO cells (Tet Control) with DBN1 KO cells expressing different DBN1 versions (WT, S142A, S142D). Data were calculated from a total of 200 cells each pooled from two independent experiments. Mean ± SD. ns: not specific  Proposed model for primary cilia length regulation by hCDC14A, CDK5 and DBN1 in RPE1 cells
Figure 3(A) Immunoprecipitation (IP) analysis of the interaction between endogenous IRGM and endogenous RIG-I, cGAS, MDA5, TLR3, TLR4, TLR7, NLRC4, and AIM2 in THP-1 cell lysates. IgG (H), IgG heavy chain. (B-D) Co-immunoprecipitation (Co-IP) analysis of the interaction between (B) GFP-IRGM and Flag-RIG-I, (C) GFP-IRGM, and Flag-cGAS, (D) GFP-IRGM and Flag-TLR3 in HEK293T cell lysates. L.E, Long exposure of input blot. IgG (L), IgG Light chain; IgG (H), IgG heavy chain. (E) GST pull-down assay of in-vitro translated and radiolabelled myc-tagged cGAS, RIG-I, and TLR3 with GST or GST-tagged IRGM. (F) Western blot analysis with the lysates of HT-29 cells stably transfected with control or Flag-IRGM plasmid and probed with the indicated antibodies. (G-I) Western blot analysis with lysates of HEK293T cells transiently expressing GFP or GFP-IRGM and (G) Flag-RIG-I or (H) Flag-cGAS or (I) or Flag-TLR3. (J-K) The qRT-PCR analysis with RNA isolated from (J) control and Flag-IRGM stable HT-29 cells (K) THP-1 cells transiently transfected with control or Flag-IRGM plasmid. Luciferase reporter assays in HEK293T cells transiently transfected with ISRE reporter plasmid and other plasmids as indicated. Luciferase reporter assays in HEK293T cells transiently transfected with ISRE reporter plasmid and other plasmids as indicated. Luciferase reporter assays in HEK293T cells transiently transfected with ISRE reporter plasmid and other plasmids as indicated. (O) Western blotting analysis with lysates of control and untreated or Bafilomycin A1 (300 nM; 4 h and 8 h) treated Flag-IRGM expressing HT29 stable cell lines. (P) Western blotting analysis with lysates of control and untreated or chloroquine (50 µM; 4 h and 8 h) treated Flag-IRGM expressing HT29 stable cell lines. (Q) The qRT-PCR analysis with RNA isolated from untreated or Bafilomycin A1 (300 nM; 4 h, 8 h, and 12 h) treated control or Flag-IRGM expressing HT-29 stable cells as indicated.
a) Pretreatment with 3-MA, but not z-VAD-fmk, significantly reduces MPP+-induced neuronal death.figf7(a) Pretreatment with 3-MA, but not z-VAD-fmk, significantly reduces MPP+-induced neuronal death. Data are means ± s.e.m.; n=6. (b) Knockdown of Atg5 expression abrogates MPP+-induced neuronal loss, whereas it reduces neuronal survival in untreated cells. Data are means ± s.e.m.; n=3. (c) Knockdown of EndoB1 or Cdk5 expression abolishes MPP+-induced neuronal death. Data are means ± s.e.m.; n=8. (d) Overexpression of EndoB1T145A inhibits MPP+-induced neuronal death. Data are means ± s.e.m.; n=5. (e) Pretreatment with 3-MA, but not z-VAD-fmk, reduces α-synucleinA53T mutant-induced neuronal death. Data are means ± s.e.m.; n=6. (f) Knockdown of Atg5 expression abolishes α-synucleinA53T mutant-induced neuronal death, whereas it reduces neuronal survival in vector-transfected cells. Data are means ± s.e.m.; n=3. (g) Knockdown of EndoB1 or Cdk5 expression abolishes α-synucleinA53T mutant-induced neuronal death. Data are means ± s.e.m.; n=4. (h) Expression of EndoB1T145A inhibits α-synucleinA53T mutant-induced neuronal death. Data are means ± s.e.m.; n=6.