Cell and molecular transitions during efficient dedifferentiation
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, United Kingdom
- Ludwig-Maximilians-University Munich, Germany
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, United Kingdom
Figures
Figure 1
Comparing the gene expression trajectories of dedifferentiation and development.
(A) Schematics of different dedifferentiation scenarios. Top: dedifferentiation is a simple reverse of forward development. Bottom: dedifferentiation visits distinct cell states during reversal. (B) …
Figure 2 with 9 supplements
Overlapping and distinct transitions during dedifferentiation and development.
(A) Simplified PCA: RNAseq timecourse data from forward development and dedifferentiation in liquid medium and bacteria. (B) Summary of gene expression transitions during dedifferentiation showing …
Figure 2—figure supplement 1
Genes induced during dedifferentiation and repressed during development.
(A) Overlay of genes used for GO analysis onto the PCA plot of population RNAseq data from Figure 2A. The genes selected were the top positively contributing genes to PC1 variance (594 genes). …
Figure 2—figure supplement 2
Genes repressed during dedifferentiation and induced during development.
(A) Overlay of genes used for GO analysis onto the PCA plot of population RNAseq data from Figure 2A. The genes selected were the top negatively contributing genes to PC1 variance (924 genes). …
Figure 2—figure supplement 3
Genes specific to development, not dedifferentiation.
(A) Overlay of genes used for GO analysis onto the PCA plot of population RNAseq data from Figure 2A. The genes selected were the top positively contributing genes to PC2 variance (547 genes). …
Figure 2—figure supplement 4
Genes specific to dedifferentiation, not development.
(A) Overlay of genes used for GO analysis onto the PCA plot of population RNAseq data from Figure 2A. The genes selected were the top negatively contributing genes to PC2 variance (673 genes). …
Figure 2—figure supplement 5
Different classes of gene expression profile during dedifferentiation.
Two-way hierarchical clustering of gene expression changes during dedifferentiation on bacteria. The horizontal axis represents time during dedifferentiation and the vertical axis represents genes, …
Figure 2—figure supplement 6
Functional enrichment analysis of genes repressed during dedifferentiation.
Left panels show enlarged segments of Figure 2—figure supplement 5 showing (A) ‘early off’ (412 genes) and (B) ‘late off’ (1774) clusters. The accompanying GO tables are shown on the right, with …
Figure 2—figure supplement 7
Functional enrichment analysis of genes transiently induced during dedifferentiation.
Left panels show enlarged segments of Figure 2—figure supplement 5 showing (A) ‘transient 1’ (188 genes), (B) ‘transient 2’ (218) and (C) ‘transient 4’ (867) clusters. The accompanying GO tables are …
Figure 2—figure supplement 8
Functional enrichment analysis of genes induced during dedifferentiation.
Left panels show enlarged segment of Figure 2—figure supplement 5 showing the ‘on’ cluster (990 genes). The accompanying GO table is shown on the right, with the genes enriched for translation …
Figure 2—figure supplement 9
Functional enrichment analysis of genes transiently repressed during dedifferentiation.
Left panels show enlarged segments of Figure 2—figure supplement 5 showing (A) ‘transient off 1’ (313 genes) and (B) ‘transient off 2’ (349) clusters. The accompanying GO tables are shown on the …
Figure 3 with 1 supplement
Molecular regulation of dedifferentiation.
(A) Testing the importance of transcription factors expressed early in dedifferentiation. Expression of bzpS and mybD during dedifferentiation in liquid medium alongside their developmental profiles …
Figure 3—figure supplement 1
Analysis of candidate regulators of dedifferentiation.
(A) DhkA mRNA expression is strongly repressed during dedifferentiation. Expression of dhkA during dedifferentiation in bacteria and liquid medium alongside its developmental profile. (B) Schematic …
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Figure 3—figure supplement 1—source data 1
Fluid uptake and clonal recovery data.
Related to Figure 3D and Figure 3—figure supplement 1D,E.
- https://cdn.elifesciences.org/articles/55435/elife-55435-fig3-figsupp1-data1-v2.xlsx
Figure 4 with 1 supplement
Single cell analysis of the coupling between events of dedifferentiation.
(A) Example time lapse showing dedifferentiating amoebae expressing Act8 and PCNA reporters. Arrow indicates dividing cell. Scale bar = 10 μm. Time is hr:min. (B) Act8 reporter expression is induced …
Figure 4—figure supplement 1
Timing of gene expression changes and cell division during dedifferentiation in single cells.
(A) Distribution of times to first division (160 dividing cells pooled from four experiments). (B) Comparing cell cycle duration of dedifferentiating cells (n = 64, four replicates) with …
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Figure 4—figure supplement 1—source data 1
Act8 reporter intensity tracks, cell fate data, Act8 reporter induction measurements, and cell cycle duration measurements.
Related to Figure 4B–F and Figure 4—figure supplement 1.
- https://cdn.elifesciences.org/articles/55435/elife-55435-fig4-figsupp1-data1-v2.xlsx
Figure 5 with 1 supplement
Coupling between cell motility and rate of dedifferentiation.
(A) Regulation of cell motility during dedifferentiation. Cell speed was measured over 20 min windows, with image capture at 30 s intervals. 244–250 cells were captured for each time point, pooled …
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Figure 5—source data 1
Cell speed, persistence and division data for motility experiments.
Related to Figure 5 and Figure 5—figure supplement 1.
- https://cdn.elifesciences.org/articles/55435/elife-55435-fig5-data1-v2.xlsx
Figure 5—figure supplement 1
Heterogeneity in cell motility during dedifferentiation.
(A) Defining the number of motility clusters using silhouette criteria. Average silhouette width for different numbers of clusters in k-means clustering of cell speed profiles. Two clusters were …
Figure 6 with 1 supplement
Rapid convergence of dedifferentiation trajectories.
(A) The expression of the prestalk reporter (CryS-mNeonGreen) does not predict division probability during dedifferentiation. Reporter intensity at the beginning of dedifferentiation shows no …
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Figure 6—source data 1
CryS reporter intensity, cell division and cell speed data.
Related to Figure 6A–C.
- https://cdn.elifesciences.org/articles/55435/elife-55435-fig6-data1-v2.xlsx
Figure 6—figure supplement 1
Convergence of dedifferentiation trajectories.
Data shown are from the independent replicate of the scRNAseq experiment displayed in Figure 5. (A) Expression of different gene sets during dedifferentiation in 2415 single cells. PCA of scRNAseq …
Tables
Table 1
Gene expression in cells lacking candidate regulators of dedifferentiation.
Analysis of the gene expression phenotypes of cell lines mutated for candidate dedifferentiation regulators. Gene expression during dedifferentiation was assessed using a variety of methods, as …
| Gene | Description | Assay | Notes |
|---|---|---|---|
| bzpS | BZIP transcription factor | RNAseq | By PCA, slight delay at 2 hr. Other timepoints wild type. |
| mybD | MYB domain transcription factor | RNAseq | By PCA, slight delay at 2 hr. Other timepoints wild type. |
| nfyA | CCAAT-binding transcription factor | RNAseq | By PCA, developmental effect seen at 0 hr. Later time points wild type. |
| DDB_G0269374 | Putative DNA binding protein | RNAseq | By PCA, very slight delay at 2 hr. Other timepoints wild type. |
| DDB_G0272386 | F-box domain kelch repeat protein | RNAseq | By PCA, developmental effect seen at 0 hr. Later time points wild type. |
| DDB_G0281091 | Acidic nuclear phosphoprotein | RNAseq | By PCA, all timepoints wild type. |
| bzpI | BZIP transcription factor | Act8 reporter expression by flow cytometry | Wild type |
| eriA | Putative RNAase III | Act8 reporter expression by flow cytometry | One clone retained larger than wild type Act8 reporter uninduced population. Not replicated in independent clone. |
| fslN | Frizzled and smoothened-like protein | Act8 reporter expression by flow cytometry | Wild type |
| gbpD | cGMP binding protein, RapGEF | Act8 reporter expression by flow cytometry | Wild type |
| jcdA | Jumonji domain transcription factor | Act8 reporter expression by flow cytometry | Wild type |
| nfaA | RasGAP | Act8 reporter expression by flow cytometry | Wild type |
| ptpB | Protein tyrosine phosphatase | Act8 reporter expression by flow cytometry | Wild type |
| DDB_G0277531 | EGF-like domain protein | Act8 reporter expression by flow cytometry | Wild type |
| ctnB | Countin | Northern blot (PCNA, csaA, hspE) | PCNA and hspE wild type. Slightly increased csaA expression. |
| gefAA | LRR protein, RasGEF | Northern blot(PCNA) | Wild type |
| gefS | RasGEF | Northern blot (PCNA, csaA, hspE) | Wild type |
| gtaN | GATA transcription factor | Northern blot (PCNA, csaA, hspE) | PCNA wild type. Weak induction in hspE. Slight delay in down-regulation of csaA. |
| krsB | STE20 family protein kinase | Northern blot (PCNA, csaA, hspE) | Weak PCNA expression in one clone, not replicated in independentclone. csaA and hspE wild type. |
| omt5 | o-methyltransferase | Northern blot (PCNA, csaA, hspE, rpl15) | Wild type |
| pakE | p21-activated kinase | Northern blot(PCNA, csaA, hspE) | Wild type |
| rasG | Ras GTPase | Northern blot (PCNA, csaA, hspE, H2Bv1, sodC) | Slight delay switching off csaA. Others wild type. |
| sigB | SrfA-induced gene | Northern blot (PCNA) | Wild type. |
| sodC | Superoxide dismutase | Northern blot (PCNA, csaA, hspE, rpl15) | Wild type |
| tagA | ABC transporter B family protein | Northern blot (PCNA) | Weak PCNA expression in one clone, not replicated in independent clone. |
| xacB | RacGEF, RacGAP | Northern blot (PCNA, csaA, hspE) | Wild type |
| zakA | Dual-specificity protein kinase | Northern blot(PCNA, csaA, hspE, rpl15) | Wild type |
| DDB_G0268696 | Putative leucine zipper transcriptional regulator | Northern blot (PCNA) | Wild type |
| DDB_G0269040 | IPT/TIG, EGF-like, C-type lectin domains | Northern blot (PCNA) | Weak PCNA expression in one clone, not replicated in independent clone. |
| DDB_G0270436 | Putative RNA binding protein | Northern blot (PCNA, csaA, hspE) | Slight delay in down-regulation of csaA. Otherwise wild type. |
| DDB_G0270480 | Northern blot (PCNA) | Wild type | |
| DDB_G0272364 | EGF-like domain-containing protein | Northern blot (PCNA) | Wild type |
| DDB_G0272434 | Notch/Crumbs orthologue | Northern blot (PCNA) | Wild type |
| DDB_G0274177 | EGF-like domains | Northern blot (PCNA) | Wild type |
| DDB_G0275621 | SET domain-containing protein | Northern blot (PCNA, rpl15) | Wild type |
| DDB_G0276549 | Putative RapGAP | Northern blot (PCNA) | Wild type |
| DDB_G0278193 | Orthologue of asparagine synthetase domain containing protein 1 | Northern blot (PCNA) | Wild type |
| DDB_G0279851 | GCN5-related N-acetyltransferase | Northern blot (PCNA, rpl15) | Weak PCNA expression in one clone, not replicated in independent clone. rpl15 wild type. |
| DDB_G0280067 | Protein phosphatase 2C-related | Northern blot (PCNA) | Wild type. Bacterial grown cells due to liquid growth defect. |
| DDB_G0283057 | Putative RapGAP | Northern blot (PCNA, rpl15) | Wild type |
| DDB_G0288203 | Ifrd1 orthologue | Northern blot(PCNA, rpl15) | Weak PCNA expression in one clone, not replicated in independent clone. rpl15 wild type. |
| DDB_G0289907 | EGF-like, C-type lectin domains | Northern blot (PCNA) | Wild type |
| DDB_G0292302 | F-box, Zn-finger protein | Northern blot (PCNA, csaA, hspE, rpl15) | Wild type |
| DDB_G0293078 | Orthologue of FAM119B | Northern blot (PCNA) | Wild type |
| DDB_G0293562 | LYAR zinc finger protein | Northern blot (PCNA, csaA, hspE, rpl15) | Wild type |
| forG | Formin | Northern blot (PCNA, hspE, rpl15), clonal recovery, RNAseq | Defect in expression of PCNA doublet upper band, observed in 3 independent clones. Slightly increased hspE at early timepoints. Defect in clonal recovery (4 replicates). Bacterial grown cells due to axenic defect. |
| rasS | Ras GTPase | Northern blot(PCNA, hspE, rpl15), clonal recovery | Defect in expression of PCNA doublet upper band (3 replicates). Slightly increased in hspE and rpl15 at early timepoints. Bacterial grown cells due to axenic defect. |
Additional files
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Supplementary file 1
Key Resources Table.
- https://cdn.elifesciences.org/articles/55435/elife-55435-supp1-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/55435/elife-55435-transrepform-v2.docx
