| Literature DB >> 27666820 |
Qian Gao1, Hanxiao Ren1, Mingkun Chen1, Ziguang Niu1, Haibo Tao1, Yin Jia1, Jianrong Zhang1, Wenjie Li1.
Abstract
β-crystallin B2 (CRYBB2) knockout mice exhibit morphological and functional abnormalities in the ovary. Long non‑coding RNAs (lncRNAs) regulate gene transcription and translation, and epigenetic modification of genomic DNA. The present study investigated the role of lncRNAs in mediating the effects of CRYBB2 in the regulation of ovary development in mice. In the current study, ovary tissues from wild‑type (WT) and CRYBB2 knockout mice were subjected to lncRNA and mRNA microarray profiling. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to group the differentially expressed lncRNAs into regulated gene pathways and functions. The correlation matrix method was used to establish a network of lncRNA and mRNA co‑expression. Quantitative reverse transcription-polymerase chain reaction (RT‑qPCR) was used to verify expression of a number of these differentially expressed lncRNAs and mRNAs. There were 157 differentially expressed lncRNAs and 1,085 differentially expressed mRNAs between ovary tissues from WT and CRYBB2 knockout mice. The GO and KEGG analyses indicated that these differentially expressed lncRNAs and mRNAs were important in Ca2+ signaling and ligand and receptor interactions. The correlation matrix method established an lncRNA and mRNA co‑expression network, consisting of 53 lncRNAs and 45 mRNAs with 98 nodes and 75 connections. RT‑qPCR confirmed downregulation of lncRNA A‑30‑P01019163 expression, which further downregulated its downstream gene purinergic receptor P2X, ligand‑gated ion channel, 7 (P2rx7) expression in ovary tissues from CRYBB2 knockout mice. In conclusion, CRYBB2 regulates expression of different lncRNAs to influence ovary development. lncRNA A‑30‑P01019163 may affect ovarian cell cycle and proliferation by regulating P2rx7 expression in the ovary.Entities:
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Year: 2016 PMID: 27666820 PMCID: PMC5101957 DOI: 10.3892/mmr.2016.5761
Source DB: PubMed Journal: Mol Med Rep ISSN: 1791-2997 Impact factor: 2.952
Figure 1.Cluster analysis of differentially expressed lncRNAs and mRNAs in ovary tissues from WT and β-crystallin B2 knockout mice. The horizontal axis represents the sample group and the vertical axis represents the differentially expressed mRNAs or lncRNAs. Upregulated genes are red and downregulated genes are green. Included are 157 lncRNAs (42 downregulated vs. 115 upregulated) and 1,085 mRNAs (570 downregulated vs. 515 upregulated) KO, knockout; WT, wild-type; lncRNA, long non-coding RNA.
Differentially expressed long non-coding RNAs in ovary tissues from β-crystallin B2 knockout mice.
| Probe name | P-value | FC (abs) | Regulation |
|---|---|---|---|
| A_30_P01032506 | 0.001900622 | 2.244835 | Down |
| A_30_P01029732 | 0.026376737 | 2.3413253 | Down |
| A_30_P01020038 | 0.020382054 | 2.3550973 | Down |
| A_30_P01019163 | 0.008867065 | 2.3823233 | Down |
| A_30_P01017808 | 0.003141625 | 2.3902857 | Down |
| A_30_P01028465 | 0.026580842 | 2.3909771 | Down |
| A_30_P01024278 | 0.010205811 | 2.4727218 | Down |
| A_30_P01031572 | 0.036648612 | 2.5956807 | Down |
| A_30_P01027590 | 0.034441914 | 2.6343288 | Down |
| A_30_P01022135 | 0.04770927 | 3.120179 | Down |
| A_30_P01031631 | 0.001265911 | 3.135137 | Down |
| A_30_P01032372 | 0.009654216 | 3.4001627 | Down |
| A_30_P01032133 | 0.012271924 | 3.434039 | Down |
| A_30_P01024342 | 2.97×10−4 | 3.7296832 | Down |
| A_30_P01024108 | 0.004697592 | 3.8198798 | Down |
| A_30_P01022445 | 2.66×10−5 | 3.8623033 | Down |
| A_30_P01022656 | 2.08×10−4 | 4.069888 | Down |
| A_30_P01023636 | 0.02164327 | 4.4273615 | Down |
| A_30_P01022538 | 9.77×10−4 | 5.492365 | Down |
| A_30_P01033546 | 0.004913332 | 5.9940124 | Down |
| A_30_P01019023 | 0.024659809 | 3.7894382 | Up |
| A_30_P01024108 | 0.004697592 | 3.8198798 | Up |
| A_30_P01017880 | 0.034943227 | 3.8256395 | Up |
| A_30_P01022445 | 2.66×10−5 | 3.8623033 | Up |
| A_30_P01026472 | 0.022304738 | 3.8728366 | Up |
| A_30_P01030900 | 0.023211088 | 3.9997435 | Up |
| A_30_P01022656 | 2.08×10−4 | 4.069888 | Up |
| A_30_P01018745 | 1.84×10−5 | 4.266393 | Up |
| A_30_P01033353 | 0.03583063 | 4.398616 | Up |
| A_30_P01021636 | 0.01934708 | 4.4207296 | Up |
| A_30_P01023636 | 0.02164327 | 4.4273615 | Up |
| A_30_P01022538 | 9.77×10−4 | 5.492365 | Up |
| A_30_P01019825 | 0.006051722 | 5.5902176 | Up |
| A_30_P01033546 | 0.004913332 | 5.9940124 | Up |
| A_30_P01024788 | 1.11×10−5 | 7.118162 | Up |
| A_30_P01024270 | 6.38×10−5 | 8.226261 | Up |
| A_30_P01027087 | 0.003292078 | 8.981714 | Up |
| A_30_P01031162 | 0.011685452 | 9.579193 | Up |
| A_30_P01021698 | 1.31×10−5 | 10.52238 | Up |
| A_30_P01020936 | 4.52×10−4 | 22.788074 | Up |
FC, fold change.
Differentially expressed mRNAs in ovary tissues from β-crystallin B2 knockout mice.
| Gene | P-value | FC (abs) | Regulation |
|---|---|---|---|
| Prkar2b | 0.040216 | 2.1857524 | Down |
| Lrp11 | 0.006975 | 2.9040618 | Down |
| P2rx7 | 4.11×10−4 | 4.6213336 | Down |
| Calml3 | 0.011701 | 5.126569 | Down |
| Dclre1c | 3.39×10−4 | 5.1453366 | Down |
| Lpcat2 | 0.002695 | 5.828531 | Down |
| Stk32a | 0.001242 | 5.833555 | Down |
| Cyp19a1 | 0.034041 | 6.1799 | Down |
| Megf10 | 0.045621 | 6.1827664 | Down |
| Plcxd1 | 1.04×10−4 | 6.82413 | Down |
| Gm5103 | 0.005622 | 8.389297 | Down |
| Fermt1 | 0.001363 | 8.656997 | Down |
| Mlxip | 3.10×10−4 | 8.746344 | Down |
| Slc6a2 | 0.046581 | 8.750824 | Down |
| Gm7969 | 0.012795 | 9.970471 | Down |
| Ces2a | 0.028129 | 10.472376 | Down |
| Dclre1c | 1.23×10−4 | 10.645219 | Down |
| Ostn | 9.07×10−6 | 11.019576 | Down |
| Jph4 | 0.001674 | 12.722166 | Down |
| Onecut2 | 0.048542 | 13.894124 | Down |
| Ces2a | 0.028128909 | 10.472376 | Up |
| Dclre1c | 1.23×10−4 | 10.645219 | Up |
| Jph4 | 0.001673621 | 12.722166 | Up |
| Onecut2 | 0.04854157 | 13.894124 | Up |
| Itln1 | 5.97×10−5 | 14.339393 | Up |
| Arsk | 7.13×10−5 | 16.06716 | Up |
| Sfrp4 | 0.023781205 | 17.065975 | Up |
| Plekhg4 | 0.047409292 | 17.067673 | Up |
| Nuf2 | 6.05×10−5 | 17.872303 | Up |
| Adh7 | 0.0064019 | 18.950857 | Up |
| Itln1 | 4.63×10−5 | 19.05549 | Up |
| Ptgfr | 0.032550577 | 20.059986 | Up |
| Pou6f1 | 1.71×10−4 | 23.766891 | Up |
| Saa2 | 0.023944996 | 25.063555 | Up |
| Wnt10b | 0.02046059 | 27.648937 | Up |
| Ifi202b | 0.001051159 | 28.72067 | Up |
| Dcpp1 | 0.014649089 | 40.37458 | Up |
| Cd5l | 4.12×10−4 | 42.74245 | Up |
| Dcpp2 | 0.012848383 | 45.13117 | Up |
FC, fold change.
Gene ontology analysis of differentially expressed genes.
| Term | Number of genes (%) | P-value |
|---|---|---|
| Biological process | ||
| Cell cycle and proliferation | 3 (4) | 0.479979 |
| Stress response | 4 (6) | 0.205102 |
| Transport | 5 (7) | 0.563981 |
| Developmental processes | 6 (9) | 0.459856 |
| RNA metabolism | 7 (10) | 0.315857 |
| Other metabolic processes | 12 (17) | 0.007676 |
| Cell organization and biogenesis | 6 (9) | 0.193590 |
| Cell-cell signaling | 1 (1) | 0.502761 |
| Signal transduction | 11 (16) | 0.120754 |
| Protein metabolism | 6 (9) | 0.502818 |
| Death | 1 (1) | 0.827556 |
| Other biological processes | 8 (11) | 0.990425 |
| Cellular component | ||
| Cytosol | 1 (2) | 0.505969 |
| Mitochondrion | 1 (2) | 0.862146 |
| Endoplasmic reticulum/golgi | 3 (5) | 0.460760 |
| Other cytoplasmic organelle | 1 (2) | 0.604395 |
| Nucleus | 10 (18) | 0.306385 |
| Plasma membrane | 6 (1) | 0.438812 |
| Other membranes | 14 (26) | 0.661329 |
| Translational apparatus | 1 (2) | 0.330956 |
| Non-structural extracellular | 2 (4) | 0.830334 |
| Other cellular component | 15 (28) | 0.354726 |
| Molecular function | ||
| Enzyme regulator activity | 3 (5) | 0.141417 |
| Transcription regulatory activity | 4 (7) | 0.174629 |
| Transporter activity | 2 (4) | 0.623057 |
| Signal transduction activity | 11 (20) | 0.082302 |
| Nucleic acid binding activity | 7 (13) | 0.252320 |
| Kinase activity | 2 (4) | 0.503159 |
| Other molecular function | 26 (47) | 0.535279 |
KEGG pathways analysis of differentially expressed genes.
| Term | Count | P-value | Genes | Up | Down |
|---|---|---|---|---|---|
| Glutathione metabolism | 1 | 0.106032 | Gsta2 | 0 | 1 |
| Metabolism of xenobiotics by cytochrome P450 | 1 | 0.143567 | Gsta2 | 0 | 1 |
| Drug metabolism-cytochrome P450 | 1 | 0.147434 | Gsta2 | 0 | 1 |
| Ribosome | 1 | 0.172182 | Rps3a | 0 | 1 |
| PPAR signaling pathway | 1 | 0.143567 | Adipoq | 0 | 1 |
| Calcium signaling pathway | 3 | 0.00614 | P2rx7, Ptger1, Ptafr | 3 | 0 |
| Cytokine-cytokine receptor interaction | 1 | 0.45143 | Cxcl1 | 0 | 1 |
| Chemokine signaling pathway | 1 | 0.353888 | Cxcl1 | 0 | 1 |
| Neuroactive ligand-receptor interaction | 4 | 0.001745 | P2rx7, Ptger1, Ptafr, Vipr1 | 4 | 0 |
| Cell cycle | 1 | 0.226819 | Hdac1 | 0 | 1 |
| Apoptosis | 1 | 0.179664 | Prkar2b | 1 | 0 |
| Notch signaling pathway | 1 | 0.099971 | Hdac1 | 0 | 1 |
| Insulin signaling pathway | 1 | 0.268146 | Prkar2b | 1 | 0 |
| Adipocytokine signaling pathway | 1 | 0.139685 | Adipoq | 0 | 1 |
| Type II diabetes mellitus | 1 | 0.099971 | Adipoq | 0 | 1 |
| Huntington's disease | 1 | 0.334126 | Hdac1 | 0 | 1 |
| Pathways in cancer | 1 | 0.530933 | Hdac1 | 0 | 1 |
| Chronic myeloid leukemia | 1 | 0.155119 | Hdac1 | 0 | 1 |
Figure 2.lncRNA-mRNA regulatory network. Circles represent genes and triangles represent lncRNAs; lines represent the association between the two types of regulation (solid line represents a cis-regulation, the dashed line represents the trans-regulation). lncRNA, long non-coding RNA.
Figure 3.Validation of differentially expressed lncRNAs and mRNAs in ovary tissues from WT and CRYBB2 knockout mice. (A) RT-qPCR indicated lncRNA A-30-P01019163 was downregulated in ovary tissues from CRYBB2 KO mice; (B) RT-qPCR indicated P2rx7 was downregulated in ovary tissues from the CRYBB2 KO mice. *P<0.05. RT-qPCR, reverse transcription-quantitative polymerase chain reaction; KO, knock out; WT, wild-type.