Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians
- Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Germany
- Barcelona Institute of Science and Technology (BIST), Spain
- Universitat Pompeu Fabra, Spain
- University of Toronto, Canada
Figures
Figure 1 with 4 supplements
Alternative splicing is differentially regulated between planarian stem cells and differentiated cells.
(A) Planarian Stem cells ('Neoblasts'), their differentiating progeny, and differentiated cells are purified with FACS ('X1', 'X2', 'Xins', respectively). RNA-seq and computational analyses were …
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Figure 1—source data 1
Schmidtea mediterranea RNA-seq samples used in this study.
- https://doi.org/10.7554/eLife.16797.004
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Figure 1—source data 2
List of neoblast-differential AS events.
- https://doi.org/10.7554/eLife.16797.005
Figure 1—figure supplement 1
Genome annotation pipeline and summary statistics.
(A) Genome annotation pipeline used in this study. (B) Number and percentage of canonical introns (with GY-AG splice sites) in all genes, coding genes, and introns within coding regions. (C) Whole …
Figure 1—figure supplement 2
Identification and analysis of neoblast differential AS in planarians.
(A) Number of alternative splicing events identified by type. Left: number of AS events based on RNA-seq data by type. Alt3/5, Alternative acceptor /donor splice site choice; IR, intron retention; …
Figure 1—figure supplement 3
RT-PCR validation of neoblast-differential AS events.
RT-PCR validation assays for 22 and 14 representative AltEx and IR events that are predicted to be differentially regulated between neoblasts and differentiated cells by RNA-Seq analyses. Red and …
Figure 1—figure supplement 4
Gene Ontology analysis of X1-differential AS events.
(A-C) Gene Ontology analysis of neoblast-differential AS events: Gene ontology enrichment analysis for 'Biological Process', 'Molecular Function' and 'Cellular Component' terms was performed for …
Figure 2
Abundant IR in planarian neoblasts.
(A) Representative RT-PCR assays monitoring IR patterns in FACS isolated cell fractions. Red and blue introns indicate those introns with higher and lower inclusion in X1 compared to Xins fractions, …
Figure 3
The neoblast-specific AS program is extensively conserved in D. japonica.
(A) Left: representative RT-PCR assays monitoring AS patterns for five representative neoblast-differential AS events in FACS isolated cell fractions from D. japonica. Scatter plot shows …
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Figure 3—source data 1
Orthologous gene groups with neoblast/ESC-differential exons in both planarian and humans.
- https://doi.org/10.7554/eLife.16797.012
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Figure 3—source data 2
Conservation of stem cell-differential AS events.
(A) Comparison between S. mediterranea and D. japonica AS. (B) Comparison between planarian and human stem cell regulated AS (Refers to Figure 3—source data 1)
- https://doi.org/10.7554/eLife.16797.013
Figure 4 with 2 supplements
Identification of bruli and mbnl as major regulators of neoblast-specific AS.
(A) Scattered plot highlighting differential gene expression for selected tissue-specific AS factors in planarians. X-axis: differential gene expression in X1 vs Xins cell fractions for selected AS …
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Figure 4—source data 1
Annotation of RBPs in planarians.
- https://doi.org/10.7554/eLife.16797.015
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Figure 4—source data 2
Annotation of spliceosomal components in planarians.
- https://doi.org/10.7554/eLife.16797.016
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Figure 4—source data 3
Single and multiple splicing factor knockdown RNAi groups.
- https://doi.org/10.7554/eLife.16797.017
Figure 4—figure supplement 1
Identification of bruli and mbnl as major regulators of neoblast-specific AS.
(A) FACS scatter plots for bruli and control RNAi treated animals 10 days after RNAi inyection. (B) Proportion of cells in X1, X2 and Xins fractions 10 days after bruli and control RNAi treatment.
Figure 4—figure supplement 2
Enrichment of RBP binding motifs associated with neoblast-differential exons.
Motif enrichment analyses for all RNAcompete-derived motifs (Ray et al., 2013) for neoblast-differential alternatively spliced exons with increased or decreased inclusion in X1 fraction. Each …
Figure 5 with 2 supplements
Combined mbnl knockdown has stronger effects than individual knockdown.
(A) Whole worm in situ hybridization for bruli, mbnl-1 and mbnl-like1, 2 and 3. Scale bar is 0.5 mm. (B) ΔPSI in whole worm estimates by RT-PCR for two X1-inc exons (red), one X1-inc retained intron …
Figure 5—figure supplement 1
BRULI and MBNL factors domain architecture and effects on regeneration and alternative splicing.
(A-B) Amino acid sequence (A) and schematization of protein domains (B) of BRULI, MBNL-1, MBNL-LIKE-1, MBNL-LIKE-2 and MBNL-LIKE-3. RRM1 domains are depicted in green and Zinc-finger domains in …
Figure 5—figure supplement 2
bruli and mbnl factors effects on regeneration and alternative splicing.
(A) The effects of bruli and mbnl knockdown and mbnl-1 single knock down are reproducible and dependent on the level of cut. Top: Workflow of the experiment: 10 animals per experimental group and …
Figure 6 with 2 supplements
bruli and mbnl antagonistically regulate neoblast-specific AS.
(A) High negative association (p<1.4 × 10−19, one-sided binomial test) between differences in inclusion levels (ΔPSI) of X1-differential AS events in X1 versus Xins fractions, and differences in brul…
Figure 6—figure supplement 1
Examples of neoblast-differential AS events regulated by bruli and/or mbnl.
RT-PCR assays for 25 representative neoblast-differential exons and retained introns in X1, X2 and Xins fractions of worms treated with bruli, control or mbnl RNAi. Red and blue exons/introns …
Figure 6—figure supplement 2
bruli and mbnl antagonistically regulate neoblast-specific AS.
(A-B) bruli and mbnl have a minor impact on neoblast-differential AS events in Xins and X1, respectively: (A) Lack of association (p = 0.206, one-sided binomial test) between differences in …
Figure 7 with 2 supplements
bruli and mbnl antagonistically regulate neoblast biology.
(A) Schematic representation of phenotypic analysis experiments. (B) Gene expression changes estimated by RNA-Seq of several progeny markers 25 days after bruli (green) or mbnl (purple) RNAi …
Figure 7—figure supplement 1
bruli and mbnl knockdown have contrasting effect of specific gene markers.
Log2 fold change in gene expression of key markers 20, 25 and 30 days after bruli (left) or mbnl (right) treatment, measured from RNA-Seq. Red/Green intensities indicate different levels of down/up …
Figure 7—figure supplement 2
Gene Ontology analysis of genes downregulated upon bruli and mbnl knockdown.
Gene ontology enrichment analysis for 'Biological Process', 'Molecular Function' and 'Cellular Component' terms of genes downregulated upon bruli and mbnl knockdown was performed for genes that were …
Figure 8
Model for BRULI and MBNL regulation of neoblast-specific AS.
Schematic representation of BRULI and MBNL regulation of AS in different planarian cell fractions and respective RNAi mediated knockdown phenotypes.
Additional files
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Supplementary file 1
List of primers for RT-PCR AS events, RNA compete, dsRNA and probes and qPCRs.
- https://doi.org/10.7554/eLife.16797.030
