EMBO/soda-nel huggingface dataset:
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver (2020)
Figure 2

Figure 2. Acute ERS compromises LIVER-TF expression and activities of their densely co-bound hepatic CRMs.

(A) Comparison of transcriptomics (data from 3 independent experiments) and H3K27ac ChIP-seq (data from 3 independent experiments) from MPH. Genes were assigned to H3K27ac regions as described in Material and Methods. The number of ERS DOWN genes is indicated relative to the number of ERS UP genes for the 3 categories of H3K27ac regions. Fisher's exact test with BH correction for multiple testing was used to assess statistical significance, *P < 0.05, #P < 0.05.

(B) Similar analyses to (A). The number of LIVER-ID and UBQ genes is indicated relative to the number of other genes for the 3 categories of H3K27ac regions. The H3K27ac ChIP-seq data were obtained from 3 independent MPH experiments. Chi-square test with BH correction for multiple testing was used to assess statistical significance, #P < 0.05.

(C) Multidimensional scaling (MDS) was performed as described in Materials and Methods and transcriptional regulator co-recruitment was depicted using density plots for regions with increased (a), decreased (b) or unchanged (c) H3K27ac levels in MPH upon acute ERS. The boxed area (d) represents a subset of transcriptional regulators (TR) with a high degree of co-binding in H3K27ac DOWN regions. LIVER-ID TFs are depicted in red.

(D) Heatmaps showing the percentage of enhancers overlapping H3K27ac down regions. Enhancers were first split into those bound or not by a given LIVER-ID TF (right) and then based on co-binding of additional LIVER-ID TFs (defining 3 subgroups with 0-2, 3-5 or 6-8 co-bound additional LIVER-ID TFs).

(E) Enrichment plots from GSEA performed using LIVER-ID TFs as the gene set and transcriptomic changes induced by acute ERS in MPH (upper panel) or mouse liver (lower panel) as the ranked gene list.

(F) RT-qPCR analyses of selected LIVER-ID TFs monitoring expression changes induced by acute ERS in MPH (4 to 7 independent experiments). The bar graph shows means ± SD (standard deviations). One-sample t-test with BH correction for multiple testing was used to determine if the mean Log2 FC ERS/Control is statistically different from 0, *P < 0.05. This graph is also displayed in Appendix Fig.S6E.

(G) RT-qPCR analyses of selected ERS UP and LIVER-ID TF genes monitoring expression changes induced by 4h ERS in MPH pre-treated or not for 30min with 5mM PBA (3 independent experiments). Mean Log2 FC ERS/Control are shown. The bar graph shows means ± SD (standard deviations). Two-way ANOVA with Bonferroni's post-hoc test was used to assess statistical significance, *P < 0.05.

(H-I) Nuclear extracts (H) and chromatin fractions (I) from MPH were subjected to Western blot with antibodies against HNF4A, NR1H4/FXR, FOXA2/HNF3B or DDIT3/CHOP. LMNA or histone H3 were used as loading controls. Results obtained from 3 independent biological replicates are shown. See Appendix Fig.S6H and Ploton et al. (Ploton et al., 2018) for antibody validation.
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver (2020)
Figure 3

Figure 3. Induction of NFIL3 by acute ERS contributes to repression of genes involved in xenobiotic metabolism.

(A) RT-qPCR analyses of Hlf, Tef, Dbp and Nfil3 expression monitoring changes induced by acute ERS in MPH (3 to 5 independent experiments) (left panel) or mouse liver (5 mice per group) (right panel). The bar graphs show means ± SD (standard deviations). One-sample t-test with BH correction for multiple testing was used to determine if the mean Log2 FC ERS/Control is statistically different from 0, *P < 0.05.

(B) Total protein extracts from MPH (left panel) or mouse liver (right panel) were subjected to Western blot with an antibody against NFIL3. ACTB was used as loading control. See Appendix Fig.S7B for antibody validation.

(C) Chromatin fractions from MPH (upper panel) or mouse liver (lower panel) were subjected to Western blot with an antibody against NFIL3. Histone H3 was used as loading control.

(D) Enrichment scores from GSEA performed using LIVER-ID genes repressed by acute ERS in MPH (MPH ERS DOWN) as the gene set and liver transcriptomic changes induced by acute ERS and/or deletion of Nfil3 (NFIL3 KO) as the ranked gene lists were integrated and corrected for multiple testing using the BubbleGUM tool. For the NFIL3 KO ERS vs WT ERS comparison, the Core Enrichment genes (i.e. the subset of genes that contributes most to the enrichment result) were subjected to functional enrichment analyses using the ToppGene Suite. The top ranked KEGG Pathway with its Bonferroni-corrected p-value is shown.

(E) Box plots showing mRNA expression for 5 genes from the Core Enrichment from D involved in xenobiotic metabolism issued from the transcriptomic analyses. Shown are Log2 FC relative to the mean normalized expression in the WT Control group (5 mice per group). Box plots are composed of a box from the 25th to the 75th percentile with the median as a line and min to max as whiskers. Two-way ANOVA with Bonferroni's post-hoc test was used to assess statistical significance, *P < 0.05.

(F) The Integrated Genome Browser (IGB) was used to visualize ChIP-seq profiles for NFIL3 (green) and several LIVER-ID TFs (red) in the mouse liver at the Gsta3 gene locus. Levels of H3K27ac in MPH and cells from the non-parenchymal fraction (NPC) are shown in blue. The grey bar indicates the position of a BRD4 SE.
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver (2020)
Figure 4

Figure 4. Acute ERS triggers hepatic SE decommissioning through impaired recruitment of the cell identity maintenance cofactor BRD4.

(A) BRD4 occupancy (left panels) and H3K27ac levels (right panels) at regulatory regions associated with ERS UP or LIVER-ID genes (8 regions at ERS gene loci and 10 regions at LIVER-ID gene loci, depicted in Appendix Fig.S10B and listed in Table EV5) were assessed by ChIP-qPCR in MPH (10 independent experiments) or mouse liver (10 mice per group) to define changes induced by acute ERS. Box plots are composed of a box from the 25th to the 75th percentile with the median as a line and min to max as whiskers. One-sample t-test with BH correction for multiple testing was used to determine if the mean Log2 FC ERS/Control is statistically different from 0, *P < 0.05.

(B) Left panel, BRD4 mRNA (4 independent experiments) or protein expression levels (5 independent experiments; densitometric quantification of Fig.4B and Appendix Fig.S10C) in MPH subjected to acute ERS. The bar graphs show means ± SD (standard deviations). Student's t-test was used to assess statistical significance. Right panel, Total protein extracts from MPH pre-treated for 3h with 0.01µM MZ1 followed by addition of 1µM thapsigargin (ERS) for 4h were subjected to Western blot with an antibody against BRD4. LMNA was used as loading control.

(C) Heatmaps showing Log2 FC (relative to the DMSO/Control condition) for 5 ERS UP and LIVER-ID genes issued from RT-qPCR analyses (Appendix Fig.S11) of MPH pre-treated with 500nM JQ1 (left) or 0.01µM MZ1 (right) followed by addition of 1µM thapsigargin (ERS) for 4h (3 to 6 independent experiments). Two-way ANOVA with Bonferroni's post-hoc test was used to assess statistical significance.

(D) Heatmaps showing average H3K27ac ChIP-seq signals in MPH at LIVER-ID domains overlapping (+) or not (-) with BRD4 SE. The arrow indicates the position of gene transcriptional start sites.

(E) Box plots showing Log2 FC ERS/Control in MPH (3 independent experiments) (left panel) or mouse liver (3 mice per group) (right panel) for genes associated with LIVER-ID + BRD4 SE or LIVER-ID - BRD4 SE, which are listed in Table EV1. Box plots are composed of a box from the 25th to the 75th percentile with the median as a line and min to max as whiskers. Student's t-test was used to assess statistical significance, *P < 0.05.
Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis (2022)
Figure 1

Figure 1: Overview and validation of the transcriptional analyses.

(A) Overview of the biological system with experimental paradigm, illustrating NSCs, BPs and NBNs were isolated at each day during development from E10.5 to PN.

(B) Notch signaling effector Hes5 is expressed high in NSCs while Eomes (Tbr2) and Btg2 are expressed high in both NSCs and BPs at the mRNA level. Each dot defines the mean and lines define the Standard Deviation (SD). 3-4 biological replicates were collected for each time point.

(C) Heatmap validating the known cell-type specific marker gene expression from RNA sequencing data.

(D) Principal Component Analysis (PCA) projection of all samples of NSCs, BPs and NBNs throughout development onto the first two principal components (PCs) covering maximum variance reveals that PC1 sorts samples by cell type and PC2 sorts samples by developmental stage.

(E) Heatmap illustrating the novel marker genes identified from the RNA sequencing data, as signature genes for NSCs, BPs and NBNs. NSCs- Neural stem cells, BPs-Basal progenitors, NBNs-Newborn neurons, E-Embryonic day, PN-Post natal, VZ-Ventricular zone, SVZ- Subventricular zone, IZ-Intermediate Zone. Expression values on the heatmaps are log2 (transcripts per million).
Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis (2022)
Figure 6

Figure 6: Dynamic expression of neuronal specification factors in NSCs, BPs and NBNs.

(A) Illustration of distinct projection neurons born sequentially during neurogenesis.

(B) Heatmap illustrating the dynamics of expression of cortical layering markers in NSCs at population level.

(C) Examples of expression dynamics of deep layer markers Tbr1, Ctip2 and upper layer markers Satb2, Cux2 in NSCs, BPs and NBNs, profiles at population level (left) and single cell level (right). Each dot defines the mean and lines define the SD. 3-4 biological replicates were collected for each time point.

(D) Experimental validation of NSCs isolated at E13.5 using Hes5::GFP transgenic embryos, showing no detectable protein for Tbr1, Ctip2 and Satb2. NSCs do express Brn2 (Pou3f2) in vitro and in vivo at protein level. Scale bar = 20μm.

(E) Heatmap illustrating the dynamics of expression of cortical layering markers in BPs at population level.

(F) Experimental validation of BPs isolated at E16.5 using Tbr2::GFP transgenic embryos, showing no detectable protein for Tbr1, Ctip2 and Satb2. Scale bar = 20μm.

(G) Heatmap illustrating the dynamics of expression of cortical layering markers in NBNs at population level.

(H) Experimental validation of NBNs isolated at E16.5 using Tbr2::GFP transgenic embryos, showing protein expression for Tbr1, Ctip2, Satb2 and Brn2(Pou3f2). Scale bar = 20μm .

In B, E and F, heatmaps are based on z-score of log2(TPM) expression values.
Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis (2022)
Figure 8

Figure 8: Dynamic and heterogenic expression profile of bHLH factors during forebrain development.

(A) Heatmaps representing the expression profile of bHLH factors. Three main groups are observed based on k-means clustering of z-scored log2(TPM) of expression value: stem cell maintenance (high expression in the NSCs at early embryonic times and low in BPs and NBNs), neurogenic (high expression in the NSCs during neurogenesis and high expression in BPs and NBNs) and gliogenic (high expression in the NSCs at late embryonic times and low in BPs and NBNs). Expression profiles are represented by their z-score.

(B) Expression profile of selected stem cell maintenance markers Hes1, Hey1 and Id4. Each dot defines the mean and lines define the SD. 3-4 biological replicates were collected for each time point.

(C) Expression profile of selected neurogenic markers Neurog2, Neurod2, and Neurod6. Each dot defines the mean and lines define the SD. 3-4 biological replicates were collected for each time point.

(D) Expression profile of selected gliogenic markers Olig1, Olig2 and Id1. Each dot defines the mean and lines define the SD. 3-4 biological replicates were collected for each time point.

(E) Expression of stem cell markers (Hes1, Hey1 and Id4), neurogenic markers (Neurog2, Neurod2, and Neurod6) and gliogenic markers (Olig1,2 and Id1) in NSCs during different embryonic time points in the single-cell levels. Each point represents the expression value of one single cell in log2(TPM).

Extended View Figure Legends
RanGTP and importin β regulate meiosis I spindle assembly and function in mouse oocytes (2019)
Figure 1

Figure 1. Quantitative FLIM/FRET imaging reveals pleiotropic effects of RanT24N on chromosomal gradients and importin β - cargo binding

(A) Schematics of Rango-3 sensor.

(B) Representative images of importin β cargo gradients detected by Rango-3 FLIM/FRET imaging. Scale bars, 20µm.

(C) Line scans of Rango-3 FRET efficiency (E) in 10 µm-wide areas centered at the dashed lines in (B).

(D-F) Quantification of the Rango-3 E gradients (top panels) and average cellular Rango-3 E (bottom) in involving untreated oocytes (controls) or oocytes injected with RanT24N mRNA, importin β(71-876) protein or treated with 20 µM IPZ. Data for each panel are from at least 2 separate experiments. Means ± SDs, t-test, oocyte numbers indicated in brackets.

(G) Nonlinear single-exponential regression was used to fit the average of radial Rango-3 τdonor line scans in control oocyte (Fig. 1 D) with the one-phase decay model. The dashed line corresponds to the average of spindle pole distance from chromosomes in the same cell.

(H) Immunoblotting in biochemical pull-downs with recombinant Ran proteins added to human DL D1 cell lysates. A representative of at least 5 repeats.
RanGTP and importin β regulate meiosis I spindle assembly and function in mouse oocytes (2019)
Figure 2

Figure 2. The RanT24N, T42A double mutant disrupts chromosomal cargo gradients without perturbing importin β-cargo binding in oocytes.

(A) Quantification of chromosomal cargo gradients (top) and average Rango-3 E in oocytes injected with increasing concentrations of Ran mutant mRNA concentrations. Data from oocytes imaged side-by-side within one experiment. Means ± SDs, one-side ANOVA, Tukey's test. Numbers of analyzed oocytes are indicated in the brackets in the top panel and are identical for both panels. Additional analyses of the same data are in Appendix Figure S2.

(B) Representative images of importin β cargo gradients detected by Rango-3 FLIM/FRET imaging. Scale bars, 20µm.

(C) Linescans of the estimated Rango-3 FRET efficiency (E) in 10 µm-wide areas centered at the dashed lines in (A).

(D) Quantification of the Rango-3 E gradients (top panels) and average cellular Rango-3 E (bottom) oocytes that were treated side-by-side by the injection of mRNA for Rango-3, alongside with buffer (controls) or 2000ng/µl mRNA for RanT24N or RanT24N, T42A. Means ± SDs, one-side ANOVA, Tukey's test, oocyte numbers indicated in brackets.
RanGTP and importin β regulate meiosis I spindle assembly and function in mouse oocytes (2019)
Figure 3

Figure 3. IPZ perturbs the RanGTP gradients through interfering with RCC1 binding to chromatin

(A) Schematics of RBP-3 sensor function.

(B) Chromosomal gradients detected by RBP3 FLIM/FRET imaging. Scale bars, 20µm.

(C) Line scans of the estimated RBP-3 in 10 µm-wide areas centered at the dashed lines in (B).

(D-F) Quantification of the RBP-3 gradients (top panels) and average cellular RBP-3 E (bottom) in separate experiments involving untreated oocytes (controls) or oocytes injected with RanT24N mRNA, importin β(71-876) protein or treated with 20µM IPZ. Means ± SDs, t-test, oocyte numbers indicated in brackets.

(G) Nonlinear single-exponential regression was used to fit the average of radial RBP-3 τdonor line scans in control oocyte (D) with the one-phase decay model.

(H) Images of oocytes expressing GFP-Ran and RCC1-mCherry from injected mRNAs before FRAP assays. Scale bars, 20 µm.

(I) RCC1-mCherry half-time fluorescence recovery (right, means ± SDs, t-test.) and an immobile fraction (left, means ± SDs, Mann-Whitney-test) in control and IPZ-treated cells, oocyte numbers indicated in brackets.
RanGTP and importin β regulate meiosis I spindle assembly and function in mouse oocytes (2019)
Figure 4

Figure 4: IPZ disrupts meiosis entry, MI spindle assembly, and anaphase I onset.

(A) Dose-dependent effects of IPZ on MI spindle assembly are shown by maximum z-projection images from confocal time-lapse imaging of oocytes obtained from transgenic histone H2B-EGFP mice stained with SiR-tubulin. Dashed circles indicate oocyte edges; scale bars, 10 µm. All observed phenotype categories after IPZ treatment are shown in Appendix Figure S4 A.

(B-C) Live-cell imaging of oocytes as in (A) was used to quantify the effects of IPZ on GVBD (B) and anaphase I entry (C). Anaphase I was defined as the first time point when chromosome segregation was visible. Fisher's exact test, oocyte numbers are indicated in brackets. The full time-course of GVBD kinetics is in Appendix Figure S4 B.

(D) Frequency and severity of MI spindle disruption induced by increasing doses of IPZ, as observed by live-cell imaging in (A-C). Oocyte numbers are shown at the top of the bars.

(E) MI spindle formation in oocytes expressing CDK5RAP2-EGFP, histone H2B-mCherry and stained with SiR-tubulin matured in the presence of 15 µM IPZ. Representative still images of maximum z-projections are shown. Time in hh:mm is relative to GVBD. Scale bar, 10 µm.

(F) MT intensity at MTOCs at the time of GVBD quantified from SiR-tubulin signal that was normalized to mean cytoplasmic SiR-tubulin signal. Mean of MT intensity on MTOCs was arbitrarily centered to 1 in the control group (means ± SDs, Mann-Whitney-test). Total of 184 MTOC in 17 control oocytes and a total of 170 MTOCs in 17 IPZ-treated oocytes were analyzed.

(G) Time course of the MT intensity in the area of spindle after GVBD. Mean of MT intensity was arbitrarily centered to 1 in the control group (means ± SDs). Oocyte numbers are indicated in brackets.

(H) Oocytes expressing CDK5RAP2-EGFP, histone H2B-mCherry and stained with SiR-tubulin were treated with 15 µM IPZ after being cultured for 5h in control media. Maximum intensity z-projections from confocal live-cell imaging are shown. Time in hh:mm is relative to GVBD, DMSO or 15 uM IPZ was added at time 5:00. Scale bars, 10 µm.

(I). Spindle volume at 1h and metaphase I after IPZ addition. The metaphase time was defined as the last time point before anaphase or, in the IPZ-treated oocytes that failed anaphase entry, as the average control metaphase time. Means ± SDs, Mann-Whitney test, oocyte numbers are indicated in brackets.

(J) Time of anaphase I entry in oocytes that were treated with 15 µM IPZ after being cultured for 5h in control media. Oocyte numbers are indicated in brackets.
RanGTP and importin β regulate meiosis I spindle assembly and function in mouse oocytes (2019)
Figure 5

Figure 5: RanQ69L partially rescues the IPZ-induced MI spindle disassembly

(A) The rescue of the effects of 15 µM IPZ on MI spindles was examined in mouse oocytes expressing histone H2B-mCherry from microinjected mRNA, co-stained with SiR-tubulin and noninjected or injected with mRNAs coding for RanQ69L or hTPX2. Maximum intensity z-stack projections from confocal live-cell movies 30 min after GVBD, at metaphase I (defined as in Fig. 4 I) and anaphase I. Time in hh: mm is relative to GVBD. Scale bars, 10 µm.

(B-C) The frequency of GVBD (B) and anaphase I entry (C) quantified by live confocal imaging of oocytes stained and treated as in (A). Fisher's exact test, oocyte numbers are shown in brackets.

(D) Changes in spindle volume over time after GVBD. Means ± SDs, mixed-design ANOVA, oocyte numbers are shown in brackets.
RanGTP and importin β regulate meiosis I spindle assembly and function in mouse oocytes (2019)
Figure 6

Figure 6: RanT24N, T42A but not RanT24N disrupts MI spindle function in segregating anaphase I chromosomes.

(A) The effects of RanT24N, T42A, and RanT24N on MI spindle assembly observed in maximum z-projection images from confocal time-lapse imaging of oocytes expressing CDK5RAP2-EGFP, histone H2B-mCherry and stained with SiR-tubulin. Time in hh:mm is relative to GVBD. Scale bar, 10 µm.

(B, C) Live-cell imaging of oocytes as in (A) was used to quantify the effects of Ran mutant. Means ± SDs., Mann-Whitney test, oocyte numbers are indicated in brackets.

(D) MT intensity at MTOCs at the time of GVBD quantified from SiR-tubulin signal that was normalized to mean cytoplasmic SiR-tubulin signal. Mean of MT intensity on MTOCs was arbitrarily centered to 1 in the control group. Means ± SDs, Kruskal-Wallis, and Dunn's tests. 25 control oocytes with 264 MTOCs in total, 10 RanT24N-expression oocytes with 70 MTOCs in total and 19 RanT24N, T42A-expressing oocytes with 96 MTOCs in total were analyzed.

(E) Time course of the MT intensity in the area of spindle after GVBD. Mean of MT intensity was arbitrarily centered to 1 in the control group. Means ± SDs, mixed-design ANOVA, oocyte numbers are shown in brackets.

(F) Frequency and severity of MI spindle phenotypes in the oocytes expressing RanT24N or RanT24N, T42A. Oocyte numbers are shown in brackets.

(G, H) Quantification of the percentage of oocytes (G) with chromosome segregation errors in anaphase I and (H) with defective MTOC coalescence during metaphase I. Means ± SDs, oocyte numbers are shown in brackets.

(I) Detection of MTs and pericentrin-containing MTOCs by IF in control and RanT24N, T42A - expressing oocytes. Arrow indicates unaligned chromosome.

(J) Quantification of chromosomal spread area in oocytes depicted in (I), Means ± SDs, Mann-Whitney test, oocyte numbers indicated in brackets.
The Long Noncoding RNA ROCKI Regulates Inflammatory Gene Expression (2019)
Figure 2

Figure 2. Cis-Acting LncRNAs Regulate Nearby Genes and Cytokine Production in Response to Group B Streptococcus (GBS) Infection

(A) Activation and suppression of nearby genes by eight cis-acting lncRNAs. RT-qPCR analysis of THP1-derived macrophages transduced with lentiviruses expressing non-targeting control (NC) shRNA or shRNAs targeted to the indicated lncRNAs and protein-coding genes. Mean ± SD of n = 3. *p < 0.05, **p < 0.01, ***p < 0.005, ****p < 0.0001 by Student's t test.

(B-D) Silencing of cis-regulated gene pairs affects GBS-induced expression of IL-6 (B and C) and IL-1α (D). RT-qPCR analysis (B and D) or IL-6 ELISA quantification (C) of THP1-derived macrophages transduced with the indicated NC or targeting shRNAs for 72 h, infected with GBS for 1 h, and then treated with gentamicin for 30 min to terminate infection. RT-qPCR and ELISA were performed at 10 h post-infection. Mean ± SD of n = 3. *p < 0.05, **p < 0.01, ***p < 0.005, ****p < 0.0001 by Student's t test.