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. 2015 Jun 4;16(6):669-83.
doi: 10.1016/j.stem.2015.04.002. Epub 2015 Apr 30.

An Apela RNA-Containing Negative Feedback Loop Regulates p53-Mediated Apoptosis in Embryonic Stem Cells

Mangmang Li  1 , Hongfeng Gou  1 , Brajendra K Tripathi  2 , Jing Huang  3 , Shunlin Jiang  1 , Wendy Dubois  1 , Tim Waybright  4 , Ming Lei  3 , Jianxin Shi  5 , Ming Zhou  4 , Jing Huang  6
Affiliations

An Apela RNA-Containing Negative Feedback Loop Regulates p53-Mediated Apoptosis in Embryonic Stem Cells

Mangmang Li et al. Cell Stem Cell. .

Abstract

Maintaining genomic integrity is of paramount importance to embryonic stem cells (ESCs), as mutations are readily propagated to daughter cells. ESCs display hypersensitivity to DNA damage-induced apoptosis (DIA) to prevent such propagation, although the molecular mechanisms underlying this apoptotic response are unclear. Here, we report that the regulatory RNA Apela positively regulates p53-mediated DIA. Apela is highly expressed in mouse ESCs and is repressed by p53 activation, and Apela depletion compromises p53-dependent DIA. Although Apela contains a coding region, this coding ability is dispensable for Apela's role in p53-mediated DIA. Instead, Apela functions as a regulatory RNA and interacts with hnRNPL, which prevents the mitochondrial localization and activation of p53. Together, these results describe a tri-element negative feedback loop composed of p53, Apela, and hnRNPL that regulates p53-mediated DIA, and they further demonstrate that regulatory RNAs add a layer of complexity to the apoptotic response of ESCs after DNA damage.

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Figures

Figure 1
Figure 1. Apela Is Repressed by p53 and Enriched in mESCs
(A) Left, Annexin V staining to measure the percentage of apoptotic cells. Right, the percentage of survived cells treated with different concentrations of ADR for 24 hours. Error bars are SEM; n=3. (B) Western blot (W.B.) of mESCs treated with 0.5 µM ADR for various time (upper panels) and with various concentrations of ADR for 24 hours (lower panels). (C) Identifying mESC-enriched p53 direct targets upon DNA damage. (D) Real-time PCR to measure the levels of Apela and Nanog (control). Ctr, untreated; Adr, treated with 0.5 µM ADR for 8 hours. A.U., arbitrary unit. Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01. (E) Upper, Northern blot with total RNA; lower, real-time PCR. (F) RNA-seq and ChIP-seq on the Apela locus. Black bars underneath the p53 (Adr) view are identified p53 peaks; R1-3, Region 1-3. Promoter and enhancer are annotated using histone modifications, Med1 and Pol II. See also Figure S1, Table S1 and S2.
Figure 2
Figure 2. Apela Is Involved in p53-mediated DIA of mESCs
(A) Real-time PCR showing Apela knockdown. Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01. (B) Histograms of the Annexin V staining of mESCs in the presence (shApela_1 and shApela_2) or absence (shLuc) of Apela knockdown. Ctr, untreated; Adr, treated with 0.5 uM ADR for 24 hours. (C) Quantification of (B). (D) W.B. of cleaved caspase-3, p53, and β-actin. Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01. (E) W.B. showing the effect of Apela knockdown on the sub-cellular localization of p53. Each lane of cytoplasmic and nuclear fractions was loaded with proteins from same number of cells. GAPDH, a cytoplasmic marker; H3, a nuclear marker. (F) W.B. showing the effect of Apela knockdown on the sub-cellular localization of p53. TFP1, a mitochondrial marker; α-tubulin, a cytosolic marker; Lamin A/C, a nuclear marker. Each lane of mitochondrial and cytosolic fractions contains same amount of protein. See also Figure S2 and Table S3.
Figure 3
Figure 3. The Coding Ability of Apela Is Dispensable for its Function in p53-Mediated DIA of mESCs
(A) RNA-seq and ChIP-seq of histone modifications and RNA Pol II on the Aplnr locus. Real-time PCR measuring the expression of Aplnr (B) and Apela (C) during EB formation. 0 day, the mESC stage; non-RT, no reverse transcriptase. Error bars are SEM; n=3. (D) Schematics showing modifications of the coding region of Apela: Apela_WT, wild type Apela; Apela_nonATG, Apela with the first start codon ATG changed to GGG; Apela_2noATG, Apela with both start codons changed to GGG; Apela_Δcoding, Apela without the coding region. (E) Real-time PCR measuring the relative RNA level of Apela in the rescue experiments: empty vector and vectors expressing modified Apela were stably transduced into mESCs containing shLuc, shApela_1, and shApela_2 using a PiggyBac system. Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01. (F) Rescue experiment: Annexin V staining of mESCs (shLuc, shApela_1, and shApela_2) transduced with the empty vector or a vector expressing an Apela variant (Apela_noATG, Apela_2noATG, or Apela_Δcoding). Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01. (G) Effect of Apela peptide (1–1000 ng/ml) on DIA of mESCs. Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01; n.s., not significant. See also Figure S3.
Figure 4
Figure 4. Apela Binds to hnRNPL Independent of p53 Status and DNA Damage
(A) Silver staining of RPA. Right, representative peptides identified by mass spectrometry. (B) W.B. showing RPA from (A) with hnRNPL antibody (Ab), hnRNPK Ab (control), and Lin28 Ab (control). Ab1, 1st Ab for hnRNPL. (C) W.B. showing RPA using Apela and two other RNA controls, NR_045496 and Snhg1. Ab2, another Ab for hnRNPL. (D) RIP-seq showing average-normalized, log2-transformed FPKM of hnRNPL-RIP and Input. The two red lines are the arbitrary cutoffs of 8-fold enrichment. (E) RIP-seq showing the enrichment of Apela in RIP with hnRNPL Ab. Nanog mRNA, a negative control; green, untreated; red, 0.5 µM ADR for 8 hours. Input and hnRNPL-RIP were scaled to the same level. (F) RIP with hnRNPL Ab followed by real-time PCR. Percentage of input was calculated to measure the relative interaction between hnRNPL and RNAs. Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01; n.s., not significant. (G) Upper, schematics of hnRNPL variants; lower, RPA using Apela (antisense and sense) and Flag-tagged hnRNPL fragments. See also Figure S4 and Table S4.
Figure 5
Figure 5. hnRNPL Binds to the CA Tracts within the 3’ UTR of Apela
(A) RPA using different fragments of Apela to map the interacting domain in Apela with hnRNPL. Numbers are the nucleotide positions from 5’ and 3’ end. Error bars are SEM; n=3. (B) Mapping the region within Apela that binds hnRNPL. (C) RPA using wild type Apela (Apela_WT) and the 3’UTR of Apela (Apela_3UTR). (D) Representative histograms of Annexin V staining of mESCs in the rescue experiment using vector only, Apela_WT and Apela_3UTR in the absence (Ctr) or presence of ADR treatment (Adr, 24 hours). (E) Quantification of (D). Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01. (F) Sequences of wild type (WT) Apela and mutants (M1, 1st CA tract disrupted; M2, 2nd CA tract disrupted; M12, both CA tracts disrupted). (G) RPA using WT and mutant Apela. (H) Representative histograms of Annexin V staining of mESCs in the rescue experiment in the absence (Ctr) or presence of ADR treatment (Adr, 24hours). (I) Quantification of (H). Error bars are SEM; n≥3. T-test; *, p<0.05; **, p<0.01; n.s., not significant. See also Figure S5.
Figure 6
Figure 6. hnRNPL Inhibits p53 Activation and p53-dependent Apoptosis of mESCs
(A) Real-time PCR measuring hnRNPL mRNA levels. Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01. (B) W.B. showing the effect of hnRNPL knockdown on p53. (C) Immunoprecipitation (IP) followed by W.B. showing the effect of hnRNPL knockdown on p53 K379ac and S18P. Total p53 amount in each lane was adjusted to the same level for comparing K379ac and S18P levels. (D) W.B. showing the effect of hnRNPL knockdown on p53 degradation; 3D view showing the band intensity of p53; lower panel, quantification of p53 levels. (E) W.B. showing the effect of hnRNPL knockdown on the mitochondrial localization of p53. (F) Representative histograms of Annexin V staining of mESCs without (shLuc) and with hnRNPL knockdown in the absence (Ctr) or presence of ADR treatment (Adr, 24 hours). (G) Quantification of (F). Error bars are SEM; n=3. T-test; *, p<0.05; **, p<0.01; n.s., not significant. See also Figure S6.
Figure 7
Figure 7. Apela Inhibits hnRNPL/p53 Interaction
(A) Immunostaining showing the co-localization of hnRNPL and p53 in mESCs untreated or treated with 0.5 µM ADR for 8 hours. (B) Co-IP using p53 Ab followed by W.B. with hnRNPL Ab. (C) Co-IP using recombinant hnRNPL and recombinant p53. (D) Pulldown using purified GST-tagged p53 fragments and mESC lysate. (E) Co-IP using purified GST-tagged FL p53 and Flag-tagged hnRNPL fragments followed by W.B. with Flag Ab. (F) Domain structures of p53 and hnRNPL. The dashed black lines indicate the interacting domains within p53 and hnRNPL. (G) Co-IP showing the effect of Apela knockdown on the interaction between p53 and hnRNPL: co-IP in mESCs (shLuc, shApela_1, and shApela_2) using p53 Ab followed by W.B. with hnRNPL, p53 and β-actin Abs. (H) Left, a model of a tri-element negative feedback loop formed by p53, Apela, and hnRNPL; Right, the well-established negative feedback loop involving p53 and Mdm2 was shown as a comparison. See also Figure S7.
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