circ-0081343 mediates nuclear translocation of RBM8A
To identify the protein that circ-0081343 interacted with, we performed RNA pull-down using biotinylated circ-0081343 probes and NC probes and applied western blotting to isolate and identify proteins directly bound to circ-0081343 (Fig. S1A). Proteins were analyzed using LC-MS, and a total of 619 proteins were identified (Fig. S1B). 17 circ-0081343 interacted proteins were predicted using catRAPID. After RNA pull down, protein levels of RBM8A, SRSF3, and TARDBP were detected in circ-0081343 probe group but not in NC group by Western blot, indicating circ-0081343 can bind to these proteins in HTR-8/Svneo cells (Fig. S1C). The binding propensity of protein-RNA pairs for RBM8A, SRSF3, and TARDBP were estimated by catRAPID (Table. 1). To examine whether circ-0081343 regulated the expression of RBM8A, SRSF3, and TARDBP, HTR-8/Svneo cells were transfected with ov-circ-0081343 and si-circ-0081343, respectively. The circ-0081343 was significantly induced in HTR-8/Svneo cells transfected with ov-circ-0081343 and reduced in si-circ-0081343 (Fig. S2 A and B). However, qRT-PCR and Western blot results revealed that overexpression and knockout of circ-0081343 had no effect on the mRNA and protein levels of RBM8A, SRSF3 and TARDBP in HTR-8/Svneo cells (Fig. S2 C-D).
We previously found that circ_0081343 was localized in the cytoplasm, while SRSF3 and TARDBP were mainly expressed in the nucleus [15, 16]. RBM8A is widely expressed in both cytoplasm and nucleus [17]. To verify the interaction of RBM8A protein with circ-0081343, RIP experiments were performed on extracts from HTR-8/Svneo cells using an antibody against RBM8A. Circ_0081343 enrichment was observed in the input group, indicating that RBM8A protein could bind circ-0081343 (Fig. 1A). This indicates that RBM8A can directly bind with circ-0081343 in the form of RNA-binding protein (RBP). In HTR-8/SVneo cells, we found overexpression of circ-0081343 induced cytoplasmic RBM8A and reduced nuclear RBM8A, while knockout of circ-0081343 had an opposite effect on RBM8A (Fig. 1B and C), suggesting that circ-0081343 regulated the nuclear translocation of RBM8A through binding to it in the cytoplasm.
Circ-0081343 Mediates Nuclear Translocation Of Rbm8a Via Ipo3
RT-PCR and Western blot results showed that overexpression of circ-0081343 down-regulated the mRNA and protein expression of IPO13, and inhibition of circ-0081343 up-regulated the mRNA and protein expression of IPO13 (Fig. 2A and B), indicating that circ-0081343 inhibited IPO13 mRNA and protein expression. We detected RBM8A and IPO13 protein expression in IP assay using IPO13 or RBM8A antibodies, indicating that there was an interaction between RBM8A and IPO13 protein (Fig. 2C).
To further examine whether circ-0081343 regulates nuclear transport of RBM8A via IPO13, IPO13 was silenced or overexpressed in HTR-8/SVneo cells treated with si-circ-0081343 using si-IPO13 and ov-IPO13 transfection, respectively. Immunofluorescent results showed that silence of IPO13 decreased the nuclear RBM8A expression and overexpression of IPO13 increased the nuclear RBM8A, indicating that circ-0081343 restrained nuclear transport of RBM8A via down-regulation of IPO13 (Fig. 2D).
The current study suggested that IPO13 mainly transports target proteins into the nucleus in an NLS-dependent manner [18, 19], therefore, we used NLS software to identify the NLS sequence and amino acid sites of RBM8A (Fig. S3A). The RBM8A-NLS wild-type plasmid and RBM8A-NLS mutant plasmid were constructed using a vector with HA tag and the NLS amino acid sequence LKEKAKKRKGR was mutated to CEQQPEQWQCG. Immunofluorescent images showed that RBM8A was expressed in both cytoplasm and nucleus in RBM8A-NLS wild-type transfected group, while it was mainly located in the cytoplasm in the RBM8A-NLS mutant transfected group (Fig. S3B). These results suggested that IPO13 transported RBM8A into the nucleus in an NLS-dependent manner.
Integrating of RNA-seq and ChIP-seq data to unravel the potential pathways regulated by circ-0081343-mediated RBM8A nuclear translocation.
We performed RNA-seq of HTR-8/SVneo cells transfected with si-circ-0081343 and Chip-seq of HTR-8/SVneo cells transfected with si-circ-0081343 using RBM8A antibody and integrated these data to explore the potential target pathways regulated by circ-0081343-mediated RBM8A nuclear translocation. The ChIP-seq signal intensity (RPM) in promoter regions of differentially and non-differentially expressed genes from RNA-seq data was shown as a box plot for both differentially and non-differentially expressed genes (Fig. 3A). The heatmaps displayed the log10 (FPKM) of RNA-seq and log10 (RPM) values of ChIP-seq (Fig. 3B). The ChIP-seq signal changes and the gene expression changes were shown as heatmaps based on ChIP-seq data and RNA-seq analysis (Fig. 3C). Scatter plot depicted ChIP-seq log2 versus RNA-seq FPKM for all peak-associated genes (Fig. 3D). After integrating RNA-seq and ChIP-seq data, a total of 1335 genes were identified that could be affected by nuclear translocation of RBM8A (Fig. 3E). GO BP analysis and KEGG signaling pathway analysis of DEGs were performed using clusterProfiler (3.8.1) and clusterProfile (3.8.1), respectively (Fig. 3F and g, Table 2).
Table 1
The binding propensity of protein-RNA pairs
Protein | Sequence Position | Motif | K-mer | Z-score | P-value |
RBM8A | 126 | rygcgb | gcccgu | 2.473 | 0.0067 |
| 133 | rygcgb | gcgugg | 2.743 | 0.00304 |
| 135 | rygcgb | gugcgu | 2.743 | 0.00304 |
SRSF3 | 103 | wcwwc | ucauc | 2.431 | 0.00753 |
| 179 | cuckuy | cucucu | 2.22 | 0.0132 |
| 181 | cuckuy | cucguu | 2.58 | 0.00494 |
| 197 | cuckucy | cuguuau | 2.22 | 0.0132 |
TARDBP | 60 | ugugug | uacgug | 1.789 | 0.0368 |
| 62 | ugugug | cgugug | 2.183 | 0.0145 |
| 64 | ugugug | ugugga | 1.789 | 0.0368 |
| 132 | ugugug | ugcgug | 2.009 | 0.0368 |
| 160 | ugugug | aguuug | 2.156 | 0.0155 |
| 165 | ugugug | gcugug | 2.147 | 0.0159 |
| 167 | ugugug | uguggg | 2.716 | 0.0033 |
| 183 | ugugug | cgugug | 2.752 | 0.00296 |
| 185 | ugugug | ugugau | 2.183 | 0.0145 |
| 196 | ugugug | ucuguu | 1.908 | 0.0282 |
Table 2
GO pathway enrichment list
Term | Database | ID | Input number | Background number | P-Value |
Cytokine-cytokine receptor interaction | KEGG Pathway | Has0 4060 | 31 | 265 | 1.10751164253e-09 |
Metabolic pathways | KEGG Pathway | Has0 1100 | 79 | 1243 | 2.13429811159e-09 |
PI3K-Akt signaling pathway | KEGG Pathway | Has0 4151 | 31 | 342 | 2.37355493534e-07 |
p53 signaling pathway | KEGG Pathway | Has0 4115 | 13 | 69 | 7.32523767693e-07 |
NOD-like receptor signaling pathway | KEGG Pathway | Has0 4621 | 11 | 57 | 4.23485239998e-06 |
Nuclear Translocation Of Rbm8a Inhibits Autophagy Via P13k/akt Pathway
Based on GO enrichment analysis, we examined the regulation of circ-0018343 on P13K/AKT pathway. Western blot results showed p-PI3K and p-AKT protein levels were significantly reduced after overexpression of circ-0081343; but increased after silence of circ-008134 in HTR-8/Svneo cells (Fig. 4A). Western blot analysis revealed that circ-0081343 overexpression increased LC3II/I radio while decreasing p62 protein expression in HTR-8/Svneo cells, indicating that overexpression of circ-0081343 induced autophagy; and autophagy inhibitor (3-MA) inhibited the active autophagy induced by circ-0081343 overexpression (Fig. 4B). Furthermore, TEM images showed the number of autophagosomes was significantly increased after overexpression of circ-0081343, and was significantly reduced by 3-MA (Fig. 4D). Silence of circ-0081343 showed an opposite effect on LC3II/I radio and p62 protein expression, suggesting that blockade of circ-0081343 resulted in insufficient autophagy. The autophagy activator (Rapamycin) induced autophagy that restrained by circ-0081343 overexpression (Fig. 4C) and restored the insufficient autophagosomes caused by silence of circ-0081343 after overexpression of circ-0081343 (Fig. 4D).
We next examined whether the circ-0018343-mediated autophagy was dependent on RBM8A. Western blot analysis revealed that p-PI3K and p-AKT protein levels were significantly increased after RBM8A overexpression, but decreased after RBM8A inhibition (Fig. 5A), suggesting that the circ-0018343 inactivated PI3K/AKT pathway via restraint the nuclear translation of RBM8A in HTR-8/Svneo cells. RBM8A overexpression down-regulated LC3II/I radio while up-regulated p62 protein expression, indicating that RBM8A inhibited autophagy (Fig. 5B); and TEM images showed that Rapamycin restored the insufficient autophagosomes caused by RBM8A overexpression (Fig. 5D). Western blot results showed that silence of RBM8A induced LC3II/I expression but decreased p62 expression and 3-MA inhibited autophagy caused by RBM8A inhibition (Fig. 5C). The increased autophagosomes by silencing RBM8A were reduced after 3-MA treatment (Fig. 5D).
Transfection of the ov-circ-0081343 plasmid alone inactivated P13K/AKT pathway, increased the LC3II/I radio, decreased the expression of p62, and increased autophagosome formation (Fig. 6A and B). Overexpression of RBM8A was able to reverse these changes to normal (Fig. 6A and B). Taken together, reduction of nucleus RBM8A expression that caused by cicr-0081343 overexpression inactivated PI3K/AKT pathway, and induced autophagy.
Nuclear RBM8A interacted with PI3K3C3 promoter and downregulated PI3K3C3.
To elucidate the mechanism coordinating nuclear RBM8A mediated autophagy, ChIP-qPCR was employed to analyze PIK3C3, ULK2, and RPTOR, which were the top 3 upregulated genes in HTR-8/SVneo cells after silencing circ-0081343 according to ChIP-seq data. The percentage of input analysis represents the amount of DNA pulled down in si-circ-0081343 group using RBM8A antibody in the ChIP reaction, comparing to the amount of DNA pulled down in the NC group. We observed that three regions of PIK3C3, one region of ULK2, and one region of RPTOR were significantly enriched in HTR-8/SVneo cells after silencing circ-0081343 (Fig. 7A). Western blot results showed protein level of PI3K3C3 was significantly reduced in HTR-8/SVneo cells after silence of circ-0081343 or overexpression of RBM8A (Fig. 7B and C), suggesting that nuclear RBM8A downregulated PI3K3C3 protein expression through protein-DNA interaction.
PI3K is Class IA PI3K, and PI3K3C3 is Class III PI3K [20, 21]. Here, we used the PI3K inhibitor, LY294002 to explore the effect of PI3K on autophagy in HTR-8/SVneo cells. We observed that the downregulated PI3K3C3 by silence of circ-0081343 or overexpression of RBM8A was significantly increased by LY294002 (Fig. 7C and D), indicating that PI3K had an adverse effect on PI3K3C3 in HTR-8/SVneo cells. Furthermore, consistence with the above results, silence of circ-0081343 or overexpression of RBM8A reduced protein expression of LC3 in HTR-8/SVneo cells, while PI3K inhibitor restrained the adverse effect of silence of circ-0081343 or overexpression of RBM8A on LC3, significantly induced the LC3 expression (Fig. 7E and F), suggesting that inactivation of autophagy by silence of circ-0081343 or overexpression of RBM8A can be induced via inhibition of PI3K.
Circ-0081343 Improves Pregnancy Outcome In Fgr Mouse Model Via Restoring The Impaired Autophagy
circ-0081343 improves pregnancy outcome in FGR mouse model via restoring the impaired autophagy
The EMBOSS Needle comparison tool found no homologous sequences between the human and rat circ-0081343 sequences. A comparison of circ-0081343 sequences from human and mouse placentas revealed 91.50% sequence homology. Mice were undergoing bilateral uterine vein ligation to establish FGR mouse model. We constructed the ad-mmu-circ-0081343 adenovirus and injected it into FGR mouse model. RT-PCR analysis showed that placental circ-0081343 expression was significantly reduced in FGR and FGR + Ad-null groups, which mimicked in vivo placental tissues with low expression of circ-0081343. The ad-mmu-circ-0081343 injection significantly induced circ-0081343 expression in FGR placenta (Fig. 8A). The total number of pups and the average number of pups per litter did not significantly differ between the four groups, but the alive pup’s rate was significantly lower in the FGR, FGR + Ad-null, and FGR + Ad-mmu-circ-0081343 groups (Table 3). FGR pups were defined as pups with body weight less than 1.25g. The incidence of FGR in 4 groups was as follows: control group (8.86%), FGR group (47.30%), FGR + Ad-null group (43.47%) and FGR + Ad-mmu-circ-0081343 group (25.26%) (Table 3). The incident rate of FGR was significantly reduced in FGF mouse injected with Ad-mmu-circ-0081343. The body and size and weight of the pups in the FGR and FGR + Ad-null groups were significantly lower than those in the control and FGR + Ad-mmu-circ-0081343 groups (Fig. 8B and C). The placental weight in FGR + Ad-mmu-circ-0081343 group was significantly higher than in FGR and FGR + Ad-null groups, but it was still lower than in control group (Fig. 8D).
Table 3
The general condition of pregnant mice and fetus
Group(S) | Control | FGR | FGR + CAd | FGR + mmu-circ-0081343 |
Dams (Pregnant mice) (n) | 7 | 7 | 7 | 8 |
Maternal GD19 weight (g) | 54.02 ± 1.52 | 52.94 ± 1.07 | 52.71 ± 2.06 | 53.84 ± 0.94 |
Implants examined, No | 81 | 84 | 79 | 93 |
Live fetuses, No (%) | 78(96.2) | 68(80.95) **/## | 69(82.22) **/## | 85(91.40) ** |
Resorbed fetuses, No (%) | 1(1.23) | 4(3.57)** | 3(3.80)** | 4(4.30)** |
Death fetuses, No (%) | 2(2.47) | 10(11.90)**/## | 7(8.86)**/## | 4(4.30)** |
FGR per litter (%) | 7.59 | 37.83**/## | 40.57**/## | 27.50** |
The layers of placenta were labeled as: decidua zone (DZ), junctional zone (JZ) and labyrinth zone (LZ) [22]. In control, the DZ, JZ, and LZ structures were clearly defined, and the LZ was densely distributed with abundant blood flow (Fig. 8E). In FGR and FGR + Ad-null groups, the proportions of DZ and JZ were significantly higher, while LZ was significantly lower. Furthermore, the majority of decidual cells had hyaline degeneration and lysis necrosis, resulting in vacuole-like changes, and the sizes of trophoblast cell in the LZ were various, with scattered apoptotic cells. We also observed the interstitial edema in the vascular zone (Fig. 8E). The placental pathology in FGR + Ad-mmu-circ-0081343 group was comparable to the control group (Fig. 8E).
Western blot results showed that PI3K3C3 and Beclin1 protein levels were significantly reduced and p62 protein level was significantly increased in FGR and FGR + Ad-null groups compared to control, and Ad-mmu-circ-0081343 injection restored protein levels of PI3K3C3 and Beclin1, while decreased p62 expression (Fig. 9A and B). Furthermore, P13/AKT pathway was active in FGR and FGR + Ad-null groups, and inactive in Ad-mmu-circ-0081343 injection groups (Fig. 9C). These results suggested that circ-0081343 improves pregnancy outcome in FGR mouse model via P13/AKT mediated autophagy.
Rbm8a Downregulates Circ-0081343 Expression
Based on JASPAR and PROMO database, 6 transcription factors that bind to the circ-0081343 promoter region were identified (Table 4). qRT-PCR and Western blot results showed that mRNA and protein expression were significantly increased after overexpression of PAX5, YY1, FOXP3, SRY, Hoxd9 and SP1 (Fig. S4 A and B); and they were significantly reduced after transfection with shRNA of PAX5, YY1, FOXP3, SRY, Hoxd9 and SP1 (Fig. S4 C and D). However, overexpression or knockdown of PAX5, YY1, FOXP3, SRY, Hoxd9 and SP1 had no effect on the expression of circ-0081343, suggesting that circ-0081343 was not regulated by these transcription factors (Fig. S4 E and F).
Table 4
Prediction of transcription factors binding to the promoter region of circ-0081343.
Model ID | Model name | Score | Relative score | Start | End | Strand | predicted site sequence |
MA0850.1 | FOXP3 | 5.632 | 0.858740454384751 | 288 | 294 | -1 | gtaaatg |
MA0850.1 | FOXP3 | 5.375 | 0.852274408290388 | 449 | 455 | 1 | gtaaagg |
MA0850.1 | FOXP3 | 5.501 | 0.855444532056496 | 688 | 694 | 1 | gaaaaga |
MA0850.1 | FOXP3 | 5.501 | 0.855444532056496 | 984 | 990 | -1 | gaaaaga |
MA0850.1 | FOXP3 | 9.305 | 0.951152078138043 | 1016 | 1022 | -1 | gcaaaca |
MA0850.1 | FOXP3 | 8.371 | 0.927652906728957 | 1088 | 1094 | 1 | ataagca |
MA0850.1 | FOXP3 | 5.482 | 0.854966497520337 | 1105 | 1111 | 1 | gtaaaaa |
MA0850.1 | FOXP3 | 7.284 | 0.900304299318167 | 1113 | 1119 | -1 | gcaagca |
MA0850.1 | FOXP3 | 7.226 | 0.898845035997261 | 1399 | 1405 | 1 | aaaaaca |
MA0850.1 | FOXP3 | 5.870 | 0.864728465942955 | 1403 | 1409 | 1 | acaaaga |
MA0850.1 | FOXP3 | 5.482 | 0.854966497520337 | 1510 | 1516 | 1 | gtcaaca |
MA0850.1 | FOXP3 | 5.482 | 0.854966497520337 | 1729 | 1735 | 1 | gtacaca |
MA0913.1 | Hoxd9 | 6.829 | 0.856716206310909 | 252 | 261 | 1 | ccaagaaaaa |
MA0913.1 | Hoxd9 | 6.614 | 0.851746266066696 | 1102 | 1111 | 1 | tcagtaaaaa |
MA0913.1 | Hoxd9 | 13.027 | 0.999989181351063 | 1394 | 1403 | 1 | gcaataaaaa |
MA0079.3 | SP1 | 5.828 | 0.854463593375058 | 107 | 117 | -1 | cctcagccccc |
MA0079.3 | SP1 | 12.677 | 0.940631854380767 | 139 | 149 | -1 | cctccgcctcc |
MA0079.3 | SP1 | 6.881 | 0.867711538891048 | 308 | 318 | -1 | tcctctccccc |
MA0079.3 | SP1 | 6.193 | 0.859055711241474 | 313 | 323 | -1 | tcccttcctct |
MA0079.3 | SP1 | 13.766 | 0.954332721110978 | 337 | 347 | -1 | gcccctcccca |
MA0079.3 | SP1 | 9.296 | 0.898095003678431 | 413 | 423 | -1 | tccccacccta |
MA0079.3 | SP1 | 6.930 | 0.868328014988183 | 786 | 796 | -1 | ccaccacctcc |
MA0079.3 | SP1 | 9.866 | 0.905266256236943 | 802 | 812 | -1 | gcaccaccccc |
MA0079.3 | SP1 | 12.677 | 0.940631854380767 | 1322 | 1332 | -1 | cctccgcctcc |
MA0079.3 | SP1 | 12.677 | 0.940631854380767 | 1459 | 1469 | -1 | cctccgcctcc |
MA0079.3 | SP1 | 11.231 | 0.922439518942856 | 1465 | 1475 | -1 | cgcccgcctcc |
MA0079.3 | SP1 | 6.183 | 0.858929899793079 | 1788 | 1798 | -1 | cctctgcctcc |
MA0084.1 | SRY | 8.914 | 0.908001454386283 | 1399 | 1407 | 1 | aaaaacaaa |
MA0084.1 | SRY | 7.546 | 0.862201486441934 | 2030 | 2038 | -1 | ggtcacaat |
MA0095.2 | YY1 | 10.314 | 0.874521551254532 | 25 | 36 | 1 | caacatggtgaa |
MA0095.2 | YY1 | 10.314 | 0.874521551254532 | 1512 | 1523 | 1 | caacatggtgaa |
MA0095.2 | YY1 | 9.157 | 0.857734354137966 | 1559 | 1570 | 1 | catgatggcggg |
RNA binding proteins bind to circRNA flanking intron sequences and regulate the expression of circRNA [23]. Based on UCSC, the reverse complementary sequence of circ-0081343 flanking sequence was 585bp in length with 83.76% match (490/585). The specific complementation of the flanking sequences was intron 3 complementary sequence combination (upper line) and intron 4 complementary sequence combination (lower line) (Fig. S5A). CircRNAs with RNA-binding protein binding have reverse complementary sequences in their upstream and downstream introns, particularly reverse complementary Alu repeats [24]. Alu repeats are the most abundant moderately repetitive sequences in the genome and the largest family of short dispersed repeats (SINEs), with a length of approximately 300 bp and an Alu sequence occurring every 3–4 kb, accounting for approximately 10% of the genome [24]. We found that the circ-0081343 flanking intron was present with six Alu sequences, three each upstream and downstream (Fig. S5B and C).
To investigate whether the formation of circ-0081343 is related to intron or Alu sequences, we used PCDNA3.1 to construct three vectors, inserting circ-0081343 without intron sequences, circ-0081343 with complete upstream and downstream intron sequences, and circ-0081343 with Alu sequences removed, respectively (Fig. S6A). RT-PCR results showed that vectors without intron sequences were unable to express circ-0081343, while vectors containing introns, with or without Alu sequences, were able to express circ-0081343, suggesting that circ-0081343 expression was independent of the Alu sequence, but dependent on the upstream and downstream introns (Fig. S6B). RNA pull-down and Western blot results showed that the Intron3 and Intron4 of cicr-0018343 can interact with RBM8A, while the interaction of Intro3 and RBM8A was stronger, suggesting that RBM8A might regulate circ-0018343 expression (Fig. S6C and D). Expression of circ-0081343 was decreased after overexpression of RBM8A and increased after silence of RBM8A, implying that RBM8A down-regulated circ-0081343 expression (Fig. S6I and J).