Literature DB >> 27666820

Long non-coding RNAs regulate effects of β-crystallin B2 on mouse ovary development.

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.

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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


Introduction

β-crystallin B2 (CRYBB2) expression was initially reported in the eye lens where it functions to maintain lens transparency and refractive index. CRYBB2 deficiency was demonstrated to result in the generation of age-associated cataracts (1). However, a number of previous studies demonstrated that CRYBB2 is also expressed in the retina, brain, testis, and ovary (2–5). Our previous study observed that CRYBB2 was expressed in human and mouse ovaries, particularly in ovarian granulosa cells (6). CRYBB2 knockout mice exhibited morphological and functional abnormalities in the ovary, including reduced ovarian index (ratio of ovary weight to total body weight) with increased follicle atresia, reduced mature follicles and dysregulated estrous cycle (7). Our data from a previous study also indicated a high level of estrogen in the diestrus and metestrus, but a low level of progesterone in the metestrus compared with wild-type (WT) mice (6). At the genetic level, expression of cell cycle and apoptosis-associated proteins, including B-cell lymphoma 2, cyclin-dependent kinase 4, and cyclin D2, were markedly lower in the CRYBB2 knockout mice compared with WT mice (6). These data suggest that CRYBB2 may be important in ovary development, however, the underlying molecular mechanism by which CRYBB2 regulates ovarian development remains to be elucidated. To identify and assess the role of CRYBB2 in ovary development, differentially expressed long non-coding RNAs (lncRNAs) were profiled in CRYBB2 knockout mice. lncRNAs are a class of non-coding RNAs with nucleotides >200 bp and transcribed by RNA polymerase II. Functionally, lncRNAs may regulate gene transcription, protein translation, and epigenetic modification of genomic DNA. Altered expression and regulation of lncRNAs has been associated with human diseases and aging (8–12). For example, previous studies have suggested that overexpression of lncRNA HOX transcript antisense RNA associated with the recurrence of hepatocellular carcinoma, poor prognosis in colorectal cancer, and malignant behaviors of gastrointestinal stromal tumors (13–15). lncRNAs modulate cell functions by regulating expression of targeted downstream genes (16), which may in turn affect embryo development (17), inactivate the X chromosome, and regulate genomic imprinting (18). Thus, the current study assessed whether these lncRNAs mediate the functions of CRYBB2 in ovary development and investigated the underlying mechanisms. Microarray profiling between ovarian tissues from CRYBB2 knockout and WT mice was conducted and bioinformatic analysis of differentially expressed lncRNAs and mRNAs was performed. A number of these differentially expressed lncRNAs and mRNAs were verified using quantitative reverse transcription-polymerase chain reaction (RT-qPCR).

Materials and methods

Animals

Male and female C57BL/6 mice were obtained from the Experimental Animal Center of the Second Military Medical University (Shanghai, China). CRYBB2 knockout mice were generated by the Ingenious Targeting Laboratory (Ronkonkoma, NY, USA), as described previously (19). All mice were maintained on a 12 h light/dark cycle with a temperature of 21±1°C and humidity of 50~70% in a pathogen-free facility with access to food and water ad libitum. Bedding material and a plastic house or tube was placed in the cage for environmental enrichment. Daily examinations were performed on all animals throughout the experimental period. Humane euthanasia of mice was performed under isoflurane anesthesia using intracardiac injection of pentobarbitone (150 mg/kg). The present study was conducted in accordance with institutional guidelines and approved by the Animal Care and Use Committee of Changhai Hospital (Shanghai, China). A total of three 8-9-week-old (weight, 18.0±2.0 g) female CRYBB2 knockout mice and three age-matched WT female mice were obtained. Ovary tissues were collected from mice following a 10-day experimental period.

RNA isolation, cDNA synthesis and labeling, and hybridization

Ovarian tissues were homogenized on ice and total cellular RNA was isolated using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA) according to the manufacturer's protocol and then quantified using NanoDrop ND-1000 (Thermo Fisher Scientific, Inc., Wilmington, DE, USA) and agarose gel electrophoresis. RNA samples were further purified using an RNeasy Mini kit (Qiagen, Inc., Valencia, CA, USA) and reverse transcribed into cDNA with fluorescent labeling for microarray hybridization using using the AffinityScript QPCR cDNA Synthesis kit (Agilent Technologies, Inc., Santa Clara, CA, USA). These labeled cDNA probes were then hybridized to Agilent mouse expression profiling (8×60K) microarray using the Gene Expression Hybridization kit (Agilent Technologies, Inc.) according to the manufacturer's protocol. The arrays were scanned into a file and analyzed using Feature Extraction software, version v10.7.3.1 (Agilent Technologies, Inc.). The arrays were scanned at 5 µm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices, LLC, Sunnyvale, CA, USA) piloted by GenePix Pro 6.0 software (Molecular Devices, LLC) and then imported into NimbleScan software (version 2.5; Roche NimbleGen, Inc., Madison, WI, USA) for grid alignment and expression data analysis. Expression data were normalized using quantile normalization and the Robust Multichip Average algorithm included in the NimbleScan software. The probe level files and mRNA level files were generated following normalization. All mRNA level files were imported into Agilent GeneSpringGX software (version 11.0; Agilent Technologies, Inc.) for further analysis. Differentially expressed lncRNAs and mRNAs were identified via fold change filtering.

Functional analysis of microarray data

Gene Ontology (GO; www.geneontology.org) was performed to group differentially expressed lncRNAs and their targeted genes into biological processes, cellular components, and molecular features of the biological functions. Kyoto Encyclopedia of Genes and Genomes (KEGG; www.genome.jp/kegg) analysis was performed to identify roles of the target genes and group them into gene pathways. The correlation matrix method was used to establish a diagram of lncRNA and mRNA co-expression regulatory networks. Prior to functional analyses, the predicted potential lncRNA targets were integrated with the differentially expressed mRNAs using a cut-off value of ≥2.0 fold change or P<0.05.

RT-qPCR

Total RNA was isolated from granulosa cells from the ovaries of WT and CRYBB2 knockout mice using TRIzol reagent and reverse transcribed into cDNA using the PrimeScript RT Reagent Kit (Takara Biotechnology, Co., Ltd., Dalian, China) according to the manufacturer's protocols. These cDNA samples were then subjected to qPCR analysis using a Applied Biosystems 7300 Real-Time PCR system (Applied Biosystems; Thermo Fisher Scientific, Inc.) with the SYBR Green PCR Master Mix kit (Takara Biotechnology, Co., Ltd.). qPCR amplification was conducted at 95°C for 2 min, followed by 40 cycles of 95°C for 15 sec, and 60°C for 30 sec. The relative expression of each target gene compared to β-actin was calculated using the 2−ΔΔCq method (20). Specific primers used were as follows: Forward, 5′-AGCCATGTACGTAGCCATCC-3′ and reverse, 5′-CTCTCAGCTGTGGTGGTGAA-3′ for β-actin; forward, 5′-CGAGTTGGTGCCAGTGTGGA-3′ and reverse, 5′-CCTGCTGTTGGTGGCCTCTT-3′ for P2rx7; and forward, 5′-TCCACTCAGGAAGAGCTGGT-3′ and reverse, 5′-TAGCACCCTCGGGATATCTG-3′ for lncRNAA-30-P01019163.

Statistical analysis

All data were presented as the mean ± standard deviation. The data were Log2-transformed and median centered by genes using Cluster software, version 3.0 (http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm). Statistical analyses were performed using SPSS 17.0 (SPSS, Inc., Chicago, IL, USA). The data were statistically analyzed using an unpaired Student's t-test or by one-way analysis of variance followed by Tukey's test. P<0.05 was considered to indicate a statistically significant difference.

Results

Microarray profiling of differentially expressed lncRNAs and mRNA in ovary tissues from wild type and CRYBB2 knockout mice

Microarray data on differential lncRNA and mRNA expression levels were analyzed using Cluster software, version 3.0 with the cut-off values set as ≥2-fold difference or P<0.05. The data indicated 157 differentially expressed lncRNAs (42 downregulated vs. 115 upregulated) and 1,085 differentially expressed mRNAs (570 downregulated vs. 515 upregulated; Fig. 1). The genes were selected according to a software forecast associated with the processes of ovarian development, and the lncRNAs associated with these genes were selected (Tables I and II).
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.

Table I.

Differentially expressed long non-coding RNAs in ovary tissues from β-crystallin B2 knockout mice.

Probe nameP-valueFC (abs)Regulation
A_30_P010325060.0019006222.244835Down
A_30_P010297320.0263767372.3413253Down
A_30_P010200380.0203820542.3550973Down
A_30_P010191630.0088670652.3823233Down
A_30_P010178080.0031416252.3902857Down
A_30_P010284650.0265808422.3909771Down
A_30_P010242780.0102058112.4727218Down
A_30_P010315720.0366486122.5956807Down
A_30_P010275900.0344419142.6343288Down
A_30_P010221350.047709273.120179Down
A_30_P010316310.0012659113.135137Down
A_30_P010323720.0096542163.4001627Down
A_30_P010321330.0122719243.434039Down
A_30_P010243422.97×10−43.7296832Down
A_30_P010241080.0046975923.8198798Down
A_30_P010224452.66×10−53.8623033Down
A_30_P010226562.08×10−44.069888Down
A_30_P010236360.021643274.4273615Down
A_30_P010225389.77×10−45.492365Down
A_30_P010335460.0049133325.9940124Down
A_30_P010190230.0246598093.7894382Up
A_30_P010241080.0046975923.8198798Up
A_30_P010178800.0349432273.8256395Up
A_30_P010224452.66×10−53.8623033Up
A_30_P010264720.0223047383.8728366Up
A_30_P010309000.0232110883.9997435Up
A_30_P010226562.08×10−44.069888Up
A_30_P010187451.84×10−54.266393Up
A_30_P010333530.035830634.398616Up
A_30_P010216360.019347084.4207296Up
A_30_P010236360.021643274.4273615Up
A_30_P010225389.77×10−45.492365Up
A_30_P010198250.0060517225.5902176Up
A_30_P010335460.0049133325.9940124Up
A_30_P010247881.11×10−57.118162Up
A_30_P010242706.38×10−58.226261Up
A_30_P010270870.0032920788.981714Up
A_30_P010311620.0116854529.579193Up
A_30_P010216981.31×10−510.52238Up
A_30_P010209364.52×10−422.788074Up

FC, fold change.

Table II.

Differentially expressed mRNAs in ovary tissues from β-crystallin B2 knockout mice.

GeneP-valueFC (abs)Regulation
Prkar2b0.0402162.1857524Down
Lrp110.0069752.9040618Down
P2rx74.11×10−44.6213336Down
Calml30.0117015.126569Down
Dclre1c3.39×10−45.1453366Down
Lpcat20.0026955.828531Down
Stk32a0.0012425.833555Down
Cyp19a10.0340416.1799Down
Megf100.0456216.1827664Down
Plcxd11.04×10−46.82413Down
Gm51030.0056228.389297Down
Fermt10.0013638.656997Down
Mlxip3.10×10−48.746344Down
Slc6a20.0465818.750824Down
Gm79690.0127959.970471Down
Ces2a0.02812910.472376Down
Dclre1c1.23×10−410.645219Down
Ostn9.07×10−611.019576Down
Jph40.00167412.722166Down
Onecut20.04854213.894124Down
Ces2a0.02812890910.472376Up
Dclre1c1.23×10−410.645219Up
Jph40.00167362112.722166Up
Onecut20.0485415713.894124Up
Itln15.97×10−514.339393Up
Arsk7.13×10−516.06716Up
Sfrp40.02378120517.065975Up
Plekhg40.04740929217.067673Up
Nuf26.05×10−517.872303Up
Adh70.006401918.950857Up
Itln14.63×10−519.05549Up
Ptgfr0.03255057720.059986Up
Pou6f11.71×10−423.766891Up
Saa20.02394499625.063555Up
Wnt10b0.0204605927.648937Up
Ifi202b0.00105115928.72067Up
Dcpp10.01464908940.37458Up
Cd5l4.12×10−442.74245Up
Dcpp20.01284838345.13117Up

FC, fold change.

Bioinformatic analysis of differentially expressed lncRNAs and mRNA in ovary tissues from WT and CRYBB2 knockout mice

GO analysis was performed for functional annotation of differentially expressed lncRNAs and mRNAs and it was observed that they were predominantly involved in cell cycle regulation, cell proliferation, metabolism, and signal transduction (Table III). One particular gene, P2rx7, localized in the cytoplasm, functions to regulate cell cycle progression and proliferation, and the signal transduction process.
Table III.

Gene ontology analysis of differentially expressed genes.

TermNumber 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 processes12 (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
  Nucleus10 (18)0.306385
  Plasma membrane  6 (1)0.438812
  Other membranes14 (26)0.661329
  Translational apparatus  1 (2)0.330956
  Non-structural extracellular  2 (4)0.830334
  Other cellular component15 (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 activity11 (20)0.082302
  Nucleic acid binding activity  7 (13)0.252320
  Kinase activity  2 (4)0.503159
  Other molecular function26 (47)0.535279
Subsequently, KEGG analysis was conducted to group differentially expressed lncRNAs and mRNA into gene pathways. The data from the present study indicated that the genes predominantly formed signaling pathways associated with the regulation of Ca2+ signaling, ligand and receptor interactions, and other cell signaling pathways (Table IV). For example, P2rx7 was identified to be predominantly involved in Ca2 + signaling.
Table IV.

KEGG pathways analysis of differentially expressed genes.

TermCountP-valueGenesUpDown
Glutathione metabolism10.106032Gsta201
Metabolism of xenobiotics by cytochrome P45010.143567Gsta201
Drug metabolism-cytochrome P45010.147434Gsta201
Ribosome10.172182Rps3a01
PPAR signaling pathway10.143567Adipoq01
Calcium signaling pathway30.00614P2rx7, Ptger1, Ptafr30
Cytokine-cytokine receptor interaction10.45143Cxcl101
Chemokine signaling pathway10.353888Cxcl101
Neuroactive ligand-receptor interaction40.001745P2rx7, Ptger1, Ptafr, Vipr140
Cell cycle10.226819Hdac101
Apoptosis10.179664Prkar2b10
Notch signaling pathway10.099971Hdac101
Insulin signaling pathway10.268146Prkar2b10
Adipocytokine signaling pathway10.139685Adipoq01
Type II diabetes mellitus10.099971Adipoq01
Huntington's disease10.334126Hdac101
Pathways in cancer10.530933Hdac101
Chronic myeloid leukemia10.155119Hdac101

Building the lncRNA-mRNA regulatory network

The lncRNA target predictions were superimposed into the lncRNA-mRNA correlation network. As presented in Fig. 2, the network has a total of 98 nodes, 75 connections, 53 lncRNAs and 45 mRNAs. Expression of glutathione S-transferase α 2 (Gsta2) and DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 (Ddx43) was regulated by a total of five lncRNAs, while expression of coiled-coil domain containing 68 (Ccdc68), olfactory receptor 464 (Olfr464) and low density lipoprotein receptor-related protein 11 (Lrp11) were regulated by four lncRNAs. In addition, expression levels of protein kinase, cAMP dependent regulatory, type II β (Prkar2b), leucine-rich repeat-containing G protein-coupled receptor 6 (Lgr6) and adiponectin, C1Q and collagen domain containing (Adipoq) were regulated by a total of three lncRNAs.
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.

Validation of differentially expressed lncRNAs and mRNAs in ovary tissues of WT and CRYBB2 knockout mice

RT-qPCR analysis of different lncRNAs and mRNAs was performed and it was demonstrated that expression levels of lncRNA A-30-P01019163 and P2rx7 were significantly different between10 cases of ovary tissues from WT and CRYBB2 knockout mice (P<0.05; Fig. 3), whereas other lncRNAs and mRNAs did not indicate any difference between WT and CRYBB2 knockout mouse ovary tissues (data not shown).
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.

Discussion

CRYBB2 knockout mice exhibit abnormal morphological and functional mouse ovaries. The current study investigated the underlying molecular mechanisms by which CRYBB2 affects expression of lncRNAs to alter mouse ovary structure and function. Certain aberrant lncRNA expression in the regulation of other genes was assessed. A total of 157 differentially expressed lncRNAs and 1,085 mRNAs were observed. The GO database analysis indicated that these altered gene expressions and were predominantly distributed in the biological process of metabolism, immune system, and signal transduction. The KEGG database pathway analysis suggested that the predominant signaling pathways were associated with Ca2+ signaling and ligand-receptor interaction. Subsequent to establishing a correlation matrix lncRNA and mRNA co-expression network map, a total of 98 nodes, 75 connections, 53 lncRNAs, and 45 mRNAs were identified. Gsta2 and Ddx43 were regulated by five lncRNAs, Ccdc68, Olfr464 and Lrp11 by four lncRNAs, Prkar2b, Lgr6, and Adipoq by three lncRNAs. Gsta2 participates in cytochrome P450 metabolism and cytochrome P450 is important in the conversion of androgens to estrogens. P2rx7, Olfr464, Lrp11, Prkar2b, Lgr6, and Adipoq are involved in cellular signal transduction and P2rx7, Prkar2b, and Hdac1 are involved in regulation of the cell cycle and cell proliferation, while Prkar2b, Hdac1, and Dock7 are important in cell development. lncRNA A-30-P01019163 and P2rx7 were differentially expressed in ovarian tissues of CRYBB2 knockout mice. Crybb2 not only functions to maintain lens transparency and refractive index, but also affects ovary development in mice. At the gene level, Crybb2 may mediate Ca2+ signal transduction (21,22). The current study demonstrated that Crybb2 also regulates expression of lncRNAs in ovarian tissues, which may be a novel area of research on Crybb2-regulation of gene expression. Previous studies using large scale cDNA library sequencing and next generation sequencing demonstrated abundant lncRNAs in mammals, however, not all lncRNAs are functional and only a relatively small proportion have been demonstrated to be biologically relevant (11,23). For example, as of mid-2014, 197 lncRNAs have been functionally annotated in lncRNA databases (24). However, other lncRNAs may be translated into proteins (25). In addition, lncRNAs, unlike miRNAs, can down- or upregulate gene expression by targeting transcriptional activators or repressors (10), in addition to post-transcriptional regulation of protein expression. In the current study differentially expressed lncRNAs in ovary tissues of CRYBB2 knockout mice were profiled and a total of 157 differentially expressed lncRNAs were observed. Furthermore, differentially expressed mRNAs were profiled and a total of 1,085 differentially expressed mRNAs in ovary tissues of CRYBB2 knockout mice were observed. GO and KEGG pathway analyses were performed to determine associations between these lncRNAs and mRNAs, and a number of these were subsequently verified using RT-qPCR. It was observed that lncRNA A-30-P01019163 and P2rx7 were significantly differentially expressed between10 cases of ovary tissues from WT and CRYBB2 knockout mice. Thus, CRYBB2 knockout could downregulate expression of lncRNA A-30-P01019163 and, subsequently, suppress expression of the downstream gene P2rx7 and affect ovarian cell signal transduction, cell cycle, and ultimately ovarian development. The current study is a proof-of-principle study and there are certain limitations. For example, it was not confirmed how lncRNA A-30-P01019163 regulates P2rx7 expression and the mechanistic investigation into how lncRNA A-30-P01019163-regulated P2rx7 expression mediates the effects of CRYBB2 on ovary development could be expanded on. 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.
  23 in total

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