Deciphering the genetic interactions between Pou4f3, Gfi1, and Rbm24 in maintaining mouse cochlear hair cell survival
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, China
- University of Chinese Academy of Sciences, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, China
Figures
Figure 1 with 2 supplements
RBM24 expression is repressed in cochlear hair cells (HCs) in the absence of POU4F3.
(A) Simple illustration of how Pou4f3-/- strain was generated. (B) One example gel image of tail-DNA PCR used to distinguish WT (Pou4f3+/+), heterozygous (Pou4f3+/-), and homozygous (Pou4f3-/-) mice. (C–F’’’) Triple staining of RBM24, POU4F3, and BCL11B in WT (C, E–E’’’) and Pou4f3-/- (D, F–F’’’) mice (n = 3 for each) at E16.5; only the RBM24 (green) channel (together with nuclear staining) is shown in (C, D) at low magnification. (E–E’’’) and (F–F’’’): High-magnification images of basal turn in WT and Pou4f3-/- mice, respectively. In the absence of POU4F3, RBM24 expression completely disappeared, although nascent BCL11B+ outer hair cells (OHCs) were present. IHC: inner hair cell. Scale bars: 100 μm (D), 20 μm (F’’’).
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Figure 1—source data 1
The original agarose gel image in Figure 1B (Pou4f3+/+, Pou4f3+/-, and Pou4f3-/-).
- https://cdn.elifesciences.org/articles/90025/elife-90025-fig1-data1-v1.zip
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Figure 1—source data 2
File containing Figure 1B and the original agarose gel analysis with highlighted bands and sample labels.
- https://cdn.elifesciences.org/articles/90025/elife-90025-fig1-data2-v1.zip
Figure 1—figure supplement 1
RBM24 expression is repressed in cochlear hair cells (HCs) at E16.5 when POU4F3 is inactivated.
(A) Illustration of how Pou4f3-/- mice (Founder 0, F0) were rapidly generated using CRISPR-stop. (B–, C) Sanger sequencing chromatograms of WT (B) and F0 Pou4f3-/- (C) samples. The base ‘C’ (black arrow in B) was completely converted to ‘T’ (red arrow in C), resulting in pre-emergence of a protein translation stop codon. The Pou4f3-/- mutants (F0 mice) were immediately ready for phenotypic analysis. (D–E’’’) Triple staining of pan-HC marker POU4F3, RBM24, and outer hair cell (OHC) marker INSM1 in whole-mount cochlear samples (basal turns) of WT (D–D’’’, n = 3) and Pou4f3-/- (E–E’’’, n = 9) mice at E16.5. Relative to WT HCs, Pou4f3-/- HCs showed no expression of POU4F3 or RBM24, but expressed INSM1 normally. Orange arrows in (E–E’’’): one INSM1+ OHC that lost POU4F3 and RBM24 expression. IHC: inner hair cell. Scale bar: 20 μm (E’’’).
Figure 1—figure supplement 2
Severe degeneration of Pou4f3-/- hair cells (HCs) occurs by perinatal ages.
(A–C’’) Dual staining of POU4F3 and MYO7A in middle-turn regions of cochleae from WT mice (A–A’’) at P1 and Pou4f3-/- mice at P0 (B–B’’) and P1 (C–C’’). The Pou4f3-/- mice were from a germline-stable strain produced through CRISPR/Cas9-mediated large DNA fragment deletion (Figure 1A). Arrows in (B–C’’): surviving HCs in the absence of POU4F3 expression. (D) Percentages of remaining HCs in basal, middle, and apical turns in Pou4f3-/- mice at P0 (n = 4) or P1 (n = 3), relative to WT mice at P1 (n = 4). Data are presented as means ± SD. Student’s t-test; **p<0.01; ****p<0.0001; n.s., no significant difference. HC degeneration in middle and basal turns was more severe at P1 than at P0, but this difference was not significant in the apical turn (D). (E–F’’) Dual staining of RBM24 and MYO7A in WT (E–E’’, n = 3) and Pou4f3-/- (F–F’’, n = 3) mice at P1. White arrow in (F–F’’): one remaining Pou4f3-/- HC that lost RBM24 expression. OHC: outer hair cell; IHC: inner hair cell. Scale bars: 20 μm (C’’, F’’).
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Figure 1—figure supplement 2—source data 1
File containing raw counts of the cochlear hair cells reported in the graph of Figure 1—figure supplement 2D.
- https://cdn.elifesciences.org/articles/90025/elife-90025-fig1-figsupp2-data1-v1.xlsx
Figure 2 with 3 supplements
GFI1 is dispensable for RBM24 expression.
(A) Simple cartoon depicting how Gfi1 was inactivated in one-cell-stage zygotes derived from male Gfi1HA-Cre/+ mice by using the CRISPR-stop approach. (B, C) Using sgRNA-6 as an example, Sanger sequencing chromatograms of control Gfi1HA-Cre/+ (B) and F0 Gfi1-/- (C) samples are presented. The base ‘C’ (black arrow in B) was converted to ‘T’ (red arrow in C), resulting in pre-emergence of the translation stop codon TAG. The red ‘T’ appears as a single peak, indicating that the stop codon pre-emerged in both alleles. (D–E’’) Dual staining of HA (GFI1) and RBM24 in cochleae from control Gfi1HA-Cre/+ (D–D’’, n = 3) and F0 Gfi1-/- (E–E’’) mice (n = 4) at E16.5. RBM24 expression (E’) was not altered in the absence of HA (GFI1) expression (E). OHC: outer hair cell; IHC: inner hair cell. Scale bar: 20 μm (E’’).
Figure 2—figure supplement 1
Construction of Gfi13◊HA-P2A-Cre/+ (Gfi1HA-Cre/+) mouse model in which HA expression faithfully represents GFI1 expression.
(A–C) Simple cartoon illustrating construction of Gfi1HA-Cre/+ strain. In the WT Gfi1 allele (A), a DNA fragment containing 3×HA-P2A-Cre (B) was inserted immediately before the TGA stop codon (red in A) to generate the post-targeted Gfi1HA-Cre/+ allele (C). (D) One example gel image of tail-DNA PCR used to distinguish Gfi1+/+, Gfi1HA-Cre/+, and Gfi1HA-Cre/HA-Cre mice. (E–F’’) Dual staining of HA (GFI1) and HC marker MYO7A in control Gfi1+/+ (E–E’’, n = 3) and homozygous Gfi1HA-Cre/HA-Cre mice (F–F’’, n = 3) at P1. Arrows in (F–F’’): one outer hair cell (OHC) expressing HA (GFI1) and MYO7A. (G–J’’) Fate-mapping analysis of cells expressing Gfi1 by using Gfi1HA-Cre/+; Rosa26loxp-stop-loxp-tdTomato (Ai9)/+ (Gfi1HA-Cre/+; Ai9/+) strain; confocal low-magnification and high-magnification images are presented in (G–H’’’) and (I–J’’), respectively. In Ai9/+ control mice at P2 (n = 5), no tdTomato+ cells were detected (G–G’’’, I–I’’). By contrast, in Gfi1HA-Cre/+; Ai9/+ mice (n = 5), tdTomato was detected in nonsensory cells (white arrows in H) as well as in MYO7A+ HCs, which expressed heterogeneous levels of HA (GFI1) and are indicated by different arrows in (J–J’’): white arrows (#1), one OHC with highest HA (GFI1) expression; orange arrows (#3), one OHC with lowest (or undetectable) HA (GFI1) expression; and blue arrows (#2), one OHC with intermediate HA (GFI1) expression. Scale bars: 100 μm in (H’’’), 20 μm (F’’, J’’).
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Figure 2—figure supplement 1—source data 1
The original agarose gel image in Figure 2—figure supplement 1D (Gfi1+/+, Gfi1HA-Cre/+, and Gfi1HA-Cre/ HA-Cre).
- https://cdn.elifesciences.org/articles/90025/elife-90025-fig2-figsupp1-data1-v1.zip
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Figure 2—figure supplement 1—source data 2
File containing Figure 2—figure supplement 1D and the original agarose gel analysis with highlighted bands and sample labels.
- https://cdn.elifesciences.org/articles/90025/elife-90025-fig2-figsupp1-data2-v1.zip
Figure 2—figure supplement 2
GFI1 expression is lost in Pou4f3-/- hair cells (HCs).
(A) One-step generation of Pou4f3 mutants by using CRISPR-stop with zygotes derived from Gfi1HA-Cre/+ mice. (B, C) Sanger sequencing chromatograms of tail-DNA samples from control Gfi1HA-Cre/+ (B) and Gfi1HA-Cre/+; Pou4f3-/- (mosaic) (C) mice. The base ‘C’ (blue arrow in B) was converted to ‘T’ (red arrow in C), but the conversion was not complete—a double peak existed and indicated mosaic inactivation of Pou4f3 expression. (D–E’’’) Triple staining of POU4F3, RBM24, and HA (GFI1) in basal region of cochleae from Gfi1HA-Cre/+ (D–D’’’, n = 3) and Gfi1HA-Cre/+; Pou4f3-/- (mosaic, E–E’’’, n = 3) mice at E16.5. Blue arrows in (E–E’’’): one outer hair cell (OHC) that expressed POU4F3, RBM24, and HA (GFI1); orange arrows: one OHC that lost POU4F3, RBM24, and HA (GFI1) expression. This confirmed that not only does HA faithfully represent GFI1 expression, but also that HA expression depends on POU4F3 expression. Scale bar: 20 μm (E’’’).
Figure 2—figure supplement 3
RBM24 expression is normal in the absence of Gfi1.
(A) The DNA fragment between sgRNA-4 and sgRNA-9 within the Gfi1 locus was deleted using the CRISPR/Cas9 method. (B) One example gel image of tail-DNA PCR used to distinguish Gfi1+/+, Gfi1+/-, and Gfi1-/- mice. (C–D’’) Dual staining of POU4F3 and RBM24 in the middle turn of cochleae from WT (C–C’’, n = 3) and Gfi1-/- (D–D’’, n = 3) mice at P1. Severe degeneration of hair cells (HCs), particularly outer hair cells (OHCs), occurred in Gfi1-/- cochleae. Orange arrows in (D–D’’): one surviving Gfi1-/- OHC that expressed POU4F3 and RBM24. (E–F’’’) Triple staining of POU4F3, RBM24, and OHC marker BCL11B in cochleae from WT (E–E’’’, n = 3) and Gfi1-/- (F–F’’’, n = 3) mice at E16.5. POU4F3, RBM24, and BCL11B expression patterns did not differ markedly between WT and Gfi1-/- cochleae at E16.5, suggesting that Gfi1-/- HC degeneration had not yet started. Scale bars: 20 μm (D’’, F’’’).
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Figure 2—figure supplement 3—source data 1
The original agarose gel image in Figure 2—figure supplement 3B (Gfi1+/+, Gfi1+/-, and Gfi1-/-).
- https://cdn.elifesciences.org/articles/90025/elife-90025-fig2-figsupp3-data1-v1.zip
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Figure 2—figure supplement 3—source data 2
File containing Figure 2—figure supplement 3B and the original agarose gel analysis with highlighted bands and sample labels.
- https://cdn.elifesciences.org/articles/90025/elife-90025-fig2-figsupp3-data2-v1.zip
Figure 3 with 1 supplement
POU4F3 and GFI1 expressions are normal in the absence of Rbm24.
(A) Simple cartoon showing how CRISPR-stop was used to induce mosaic inactivation of RBM24 in one-cell-stage mouse zygotes harboring Gfi1HA-Cre/+. Notably, the injection was in the late one-cell stage of the zygotes, which resulted in high rates of final mosaic inactivation. (B, C) Sanger sequencing chromatograms of control Gfi1HA-Cre/+; Rbm24+/+ (B) and Gfi1HA-Cre/+; Rbm24-/- (mosaic) (C) samples. The base ‘C’ (black arrow in B) was converted to ‘T’ (red arrow in C) in a fraction of cochlear cells. Mosaic inactivation of Rbm24 is evidenced by the double peaks of ‘T’ and ‘C’ (red arrow in C). (D–E’’’) Triple staining of RBM24, HA, and POU4F3 in cochlear samples (basal turns) of control Gfi1HA-Cre/+; Rbm24+/+ (D–D’’’, n = 3) and Gfi1HA-Cre/+; Rbm24-/- (mosaic) (E–E’’’, n = 3) mice at E17. Consistent with the Sanger sequencing result (C), RBM24 expression was found to be inactivated in cochlear hair cells (HCs) in a mosaic pattern (E). Orange arrows in (E–E’’’): one outer hair cell (OHC) that lost RBM24 expression; blue arrows in (E–E’’’): one OHC that maintained RBM24 expression. Regardless of whether RBM24 expression was inactivated or not, the expression of HA (GFI1) and POU4F3 was unaltered. IHC: inner hair cell. Scale bar: 20 μm (E’’’).
Figure 3—figure supplement 1
GATA3 is downregulated but IKZF2 is upregulated in Rbm24-deficient hair cells (HCs).
(A) Simple illustration of how mosaic Rbm24 mutant mice were generated. (B–C’’) Dual staining of RBM24 and GATA3 in cochlear tissues from control Rbm24+/+ (B–B’’) and Rbm24-/- (C–C’’) mice at P1. (D) Cartoon depicting how mosaic Rbm24 mutant mice were produced using zygotes derived by crossing female wild-type (WT) mice with male Ikzf2V5/+ mice. (E–F’’) Dual staining of RBM24 and V5 (IKZF2) in cochleae from control Ikzf2V5/+; Rbm24+/+ (E–E’’) and Ikzf2V5/+; Rbm24-/- (F–F’’) mice at P5. Scale bars: 20 μm (C’’, F’’).
Figure 4
Three Rbm24 enhancers are sufficient to drive specific EGFP expression in cochlear hair cells (HCs).
(A) Visualization of ATAC-seq (top row, orange) of P1 cochlear HCs (from our previous study, GSE181311) and POU4F3 Cut&Run assay (bottom row, blue) of E17.5 cochlear HCs (from another study, GSE150391) by using Integrative Genomics Viewer. Black arrow: Rbm24 promoter; dotted boxes: three Rbm24 enhancers (Eh1, Eh2, and Eh3). (B–G’’) Dual labeling for EGFP and MYO7A in Eh1-EGFP+ (B–C’’, n = 7), Eh2-EGFP+ (D–E’’, n = 6), and Eh3-EGFP+ (F–G’’, n = 4) mice at P1. Only the EGFP channel (plus nuclear staining) is shown for whole-mount samples (B, D, F). In cryosection cochlear samples, EGFP labeling overlapped with HC marker MYO7A. OHCs: outer hair cells; IHC: inner hair cell. Scale bars: 100 μm (F), 20 μm (G’’).
Figure 5
Forced expression of RBM24 fails to rescue outer hair cell (OHC) degeneration in Pou4f3-/-mutants.
(A) Generation of Rosa26loxp-stop-loxp-Rbm24*3×HA/+ (Rosa26Rbm24/+) mouse strain. The C-terminus of ectopic RBM24 was fused with three HA tags. (B) One example gel image of tail-DNA PCR used to distinguish WT (+/+) and knockin (Rosa26Rbm24/+) mice. (C–F’’) Dual staining of HA (RBM24) and hair cell (HC) marker MYO7A in mice featuring four distinct genotypes at P1: Pou4f3+/+ (C–C’’, n = 3), Pou4f3-/- (D–D’’, n = 3), Pou4f3+/+; Atoh1Cre/+; Rosa26Rbm24/+ (E–E’’, n = 3), and Pou4f3-/-; Atoh1Cre/+; Rosa26Rbm24/+ (F–F’’, n = 3). Ectopic HA (RBM24) was not detected in Pou4f3+/+ (C) and Pou4f3-/- (D) mice, but was detected in both Pou4f3+/+; Atoh1Cre/+; Rosa26Rbm24/+ (E) and Pou4f3-/-; Atoh1Cre/+; Rosa26Rbm24/+ (F) mice. White arrows in (E–E’’): one MYO7A+ inner hair cell (IHC) that expressed ectopic HA (RBM24). HCs appeared normal by P1, despite the induction of ectopic RBM24 expression. Orange arrows in (E–E’’): one supporting cell (SC) that expressed HA (RBM24) but not MYO7A. White arrows in (F–F’’): one remaining MYO7A+ HC that expressed ectopic RBM24. Overall, many of the Pou4f3-/- HCs degenerated even though ectopic RBM24 expression was induced. IHC: inner hair cell. Scale bar: 20 μm (F’’).
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Figure 5—source data 1
The original agarose gel image in Figure 5B (Rosa26+/+ and Rosa26Rbm24/+).
- https://cdn.elifesciences.org/articles/90025/elife-90025-fig5-data1-v1.zip
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Figure 5—source data 2
File containing Figure 5B and the original agarose gel analysis with highlighted bands and sample labels.
- https://cdn.elifesciences.org/articles/90025/elife-90025-fig5-data2-v1.zip
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Mus musculus) | Atoh1Cre/+ | Yang et al., 2010b | Lin Gan lab (Augusta University) | A knock-in mouse strain |
| Strain, strain background (M. musculus) | Rosa26-loxp-stop-loxp-tdTomato (Ai9) | Stock# 007905 | The Jackson Laboratory | A knock-in mouse strain |
| Strain, strain background (M. musculus) | Ikzf2V5/+ | Stock# 038463 | The Jackson Laboratory | A knock-in mouse strain |
| Strain, strain background (Mus musculus) | Pou4f3 mutant | This paper | Available upon request from Liu Lab | Constructed by CRISPR-stop |
| Strain, strain background (M. musculus) | Gfi1 mutant | This paper | Available upon request from Liu Lab | Constructed by CRISPR-stop |
| Strain, strain background (M. musculus) | Rbm24 mutant | This paper | Available upon request from Liu Lab | Constructed by CRISPR-stop |
| Strain, strain background (M. musculus) | Pou4f3 null | This paper | Available upon request from Liu Lab | Constructed by CRISPR /Cas9 |
| Strain, strain background (M. musculus) | Gfi1 null | This paper | Available upon request from Liu Lab | Constructed by CRISPR /Cas9 |
| Strain, strain background (M. musculus) | Gfi13xHA-P2A-Cre | This paper | Available upon request from Liu Lab | A knock-in mouse strain |
| Strain, strain background (M. musculus) | Eh1-EGFP+ | This paper | Available upon request from Liu Lab | A transgenic mouse line |
| Strain, strain background (M. musculus) | Eh2-EGFP+ | This paper | Available upon request from Liu Lab | A transgenic mouse line |
| Strain, strain background (M. musculus) | Eh3-EGFP+ | This paper | Available upon request from Liu Lab | A transgenic mouse line |
| Strain, strain background (M. musculus) | Rosa26CAG-lsl-Rbm24*3xHA/+ | This paper | Available upon request from Liu Lab | A knock-in mouse strain for ectopic Rbm24 expression |
| Antibody | Anti-RBM24 (rabbit polyclonal) | Proteintech | 18178-1-AP | IF (1:500) |
| Antibody | Anti-POU4F3 (mouse monoclonal) | Santa Cruz | sc-81980 | IF (1:500) |
| Antibody | Anti-POU4F3 (rabbit polyclonal) | Novus Biologicals | NBP1-88349 | IF (1:500) |
| Antibody | Anti-HA (rat monoclonal) | Roche | 11867423001 | IF (1:500) |
| Antibody | Anti-MYO7A (rabbit polyclonal) | Proteus Biosciences | 25-6790 | IF (1:500) |
| Antibody | Anti-MYO7A (mouse monoclonal) | DSHB | MYO7A 138-1 | IF (1:500) |
| Antibody | Anti-CTIP2 (rat monoclonal) | Abcam | ab18465 | IF (1:500) |
| Antibody | Anti-INSM1 (guinea pig) | Jia et al., 2015 | A kind gift from Dr. Carmen Birchmeier | IF (1:6000) |
| Antibody | Anti-GFP (chicken polyclonal) | Abcam | ab13970 | IF (1:500) |
| Antibody | Anti-GATA3 (goat polyclonal) | R&D Systems | AF2605 | IF (1:500) |
| Antibody | Anti-V5 (mouse monoclonal) | Bio-Rad | MCA1360 | IF (1:500) |
Additional files
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Supplementary file 1
List of sgRNA sequences.
- https://cdn.elifesciences.org/articles/90025/elife-90025-supp1-v1.xlsx
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Supplementary file 2
DNA sequences of ssDNA donor and Rbm24 enhancers.
- https://cdn.elifesciences.org/articles/90025/elife-90025-supp2-v1.xlsx
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Supplementary file 3
DNA sequences of genotyping primers.
- https://cdn.elifesciences.org/articles/90025/elife-90025-supp3-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/90025/elife-90025-mdarchecklist1-v1.docx
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Deciphering the genetic interactions between Pou4f3, Gfi1, and Rbm24 in maintaining mouse cochlear hair cell survival
eLife 12:RP90025.
https://doi.org/10.7554/eLife.90025.3
