A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans
- Department of Biological Sciences, University of Southern California, United States
- Department of Biology, Colorado State University, United States
- Cell and Molecular Biology Program, Colorado State University, United States
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Germany
- International PhD Programme on Gene Regulation, Epigenetics, and Genome Stability, Germany
Figures
Figure 1 with 1 supplement
SIMR-1 is a perinuclear-localized Tudor domain protein.
(A) Proteins identified by IP-mass spec of MUT-16::GFP::3xFLAG but not wild-type animals. The percent coverage and total number of peptides captured are indicated for each MUT-16-associated protein. …
Figure 1—figure supplement 1
Identification and localization of MUT-16-associated proteins.
(A) Proteins identified by IP-mass spec of MUT-16::GFP::3xFLAG that are enriched at least four-fold in MUT-16 immunoprecipitations relative to control immunoprecipitations. See Supplementary file 2 …
Figure 2 with 1 supplement
Small RNA-related phenotypes associated with deletions in MUT-16-associated proteins.
(A) Animals carrying deletions for each previously-uncharacterized gene identified in the MUT-16 IP-mass spec experiment were assayed for their ability to respond to somatic (nhr-23 or lin-29) or …
Figure 2—figure supplement 1
Mutator-class small RNAs are reduced in simr-1 but not hpo-40 mutants.
(A) Box plot displaying total small RNAs levels targeting mutator-target genes in the indicated mutant strains relative to wild-type animals. (B) Scatter plots display small RNA reads per million …
Figure 3 with 1 supplement
simr-1 mutants have a transgenerational fertility defect at elevated temperature.
(A) Brood size was scored for a single generation at 20°C, followed by 11 generations at 25°C, demonstrating that simr-1 mutants become progressively sterile at 25°C. 10 broods were scored for each …
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Figure 3—source data 1
Data used to generate Figure 3A and Figure 3—figure supplement 1.
- https://cdn.elifesciences.org/articles/56731/elife-56731-fig3-data1-v2.xlsx
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Figure 3—source data 2
Data used to generate Figure 3B.
- https://cdn.elifesciences.org/articles/56731/elife-56731-fig3-data2-v2.xlsx
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Figure 3—source data 3
Data used to generate Figure 3C.
- https://cdn.elifesciences.org/articles/56731/elife-56731-fig3-data3-v2.xlsx
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Figure 3—source data 4
Data used to generate Figure 3D.
- https://cdn.elifesciences.org/articles/56731/elife-56731-fig3-data4-v2.xlsx
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Figure 3—source data 5
Data used to generate Figure 3E.
- https://cdn.elifesciences.org/articles/56731/elife-56731-fig3-data5-v2.xlsx
Figure 3—figure supplement 1
hpo-40 does not contribute to the progressive sterility of simr-1 mutants.
Brood sizes of wild-type, hpo-40 single mutants, and simr-1; hpo-40 double mutants were scored for a single generation at 20°C, followed by 11 generations at 25°C, demonstrating that hpo-40 does not …
Figure 4 with 1 supplement
simr-1 mutants have piRNA-related defects.
(A) Images of adult animals, in which the henn-1 mutation weakly desilences the piRNA sensor (top). simr-1[A11V] (middle) and simr-1[R159C] (bottom) mutants, obtained from an EMS mutagenesis screen …
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Figure 4—source data 1
Data used to generate Figure 4B.
- https://cdn.elifesciences.org/articles/56731/elife-56731-fig4-data1-v2.xlsx
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Figure 4—source data 2
Data used to generate Figure 4D.
- https://cdn.elifesciences.org/articles/56731/elife-56731-fig4-data2-v2.xlsx
Figure 4—figure supplement 1
simr-1 mutants do not display defects associated with mutants in the mutator or ERGO-1 26G-siRNA pathways.
(A) Images of adult animals carrying the piRNA sensor in a wild-type (top), simr-1 mutant (middle), or mut-16 mutant (bottom) background. The piRNA sensor was maintained in a wild-type background …
Figure 5 with 1 supplement
simr-1 mutants display reduced small RNAs mapping to mutator and piRNA-target genes.
(A) Table indicating the number of genes for which the total small RNA levels are either increased or reduced by at least two-fold for each indicated mutant. All genes also met the requirements of …
Figure 5—figure supplement 1
Small RNAs are reduced at many mutator, piRNA, and ERGO-1 target genes in simr-1 mutants at 25°C.
(A) Box plot displaying total small RNAs levels targeting genes from the indicated small RNA pathways in simr-1 mutants relative to wild-type animals raised for a single generation at 25°C. Details …
Figure 6 with 1 supplement
simr-1 mutants display reduced small RNAs mapping to piRNA-dependent transposons and increased small RNAs mapping to histone genes.
(A) Ratio of transposon-mapping small RNA reads per million total reads in simr-1 mutants and mut-16 mutants raised at 20°C or a single generation at 25°C compared to wild-type shows that small RNAs …
Figure 6—figure supplement 1
Small RNAs mapping to piRNA target transposons are reduced and small RNAs mapping to histone genes are increased in simr-1 mutants.
(A) Heat maps displaying small RNAs levels targeting mutator-dependent transposons and repeats in prg-1 and simr-1 mutants raised at 20°C, and simr-1 mutants raised at 25°C for one, two, seven, or …
Figure 7 with 1 supplement
SIMR-1 localizes to foci adjacent to P granules and Mutator foci.
(A) Immunostaining of SIMR-1 (green) with MUT-16 (red, top left), PGL-1 (red, top right), ZNFX-1 (red, bottom left), and RSD-2 (red, bottom right) demonstrates that SIMR-1 localizes to foci near Muta…
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Figure 7—source data 1
Data used to generate Figure 7B.
- https://cdn.elifesciences.org/articles/56731/elife-56731-fig7-data1-v2.xlsx
Figure 7—figure supplement 1
SIMR-1 and PRG-1 localize independently and to distinct granules.
(A) Immunostaining of SIMR-1::GFP (green) and PRG-1::mKate (red) demonstrates that SIMR-1 and PRG-1 localize near one another but their localization is not coincident. (B) Live imaging of …
Additional files
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Source code 1
Python script to calculate reads per million (RPM) over a genomic region.
- https://cdn.elifesciences.org/articles/56731/elife-56731-code1-v2.py
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Source code 2
Python script to generate WIG files for visualization of tracks in IGV.
- https://cdn.elifesciences.org/articles/56731/elife-56731-code2-v2.py
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Supplementary file 1
Known components of the L4 and adult germ granules.
- https://cdn.elifesciences.org/articles/56731/elife-56731-supp1-v2.xlsx
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Supplementary file 2
Proteins identified in MUT-16 IP.
Those examined further highlighted in blue.
- https://cdn.elifesciences.org/articles/56731/elife-56731-supp2-v2.xlsx
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Supplementary file 3
Small expression in simr-1, mut-16, and prg-1 mutant animals.
- https://cdn.elifesciences.org/articles/56731/elife-56731-supp3-v2.xlsx
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Supplementary file 4
mRNA target predictions for simr-1-depleted piRNAs.
- https://cdn.elifesciences.org/articles/56731/elife-56731-supp4-v2.xlsx
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Supplementary file 5
mRNA expression in simr-1 and mut-16 mutant animals.
- https://cdn.elifesciences.org/articles/56731/elife-56731-supp5-v2.xlsx
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Supplementary file 6
Key resources table.
- https://cdn.elifesciences.org/articles/56731/elife-56731-supp6-v2.xlsx
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Supplementary file 7
Oligonucleotides sequences used in this study.
- https://cdn.elifesciences.org/articles/56731/elife-56731-supp7-v2.xlsx
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Supplementary file 8
Statistical analysis.
- https://cdn.elifesciences.org/articles/56731/elife-56731-supp8-v2.xlsx
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Supplementary file 9
Sequencing library statistics.
- https://cdn.elifesciences.org/articles/56731/elife-56731-supp9-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/56731/elife-56731-transrepform-v2.docx
