Combined microRNAome and transcriptome analysis of follicular phase and luteal phase in porcine ovaries

The aim of this study was to explore the expression difference of miRNAs and mRNAs between the follicular phase (FP) and luteal phase (LP) in porcine ovaries and provide a theoretical basis for the research on mammalian reproductive regulation. RNA‐Seq and miRNA‐Seq were used to identify differentially expressed genes (DEGs) and miRNAs (DEMs) between the FP and LP in ovaries of six sows (3‐year‐old Yorkshire pigs with similar weights and same parities). Bioinformatic analysis was used to screen potential genes and miRNAs related to porcine ovarian function. Real‐time qualitative PCR was used to validate the sequencing results. RNA‐Seq results showed that 3,078 genes were up‐regulated, and 1,444 genes were down‐regulated in the LP compared with the FP, and DEGs were significantly enriched in 242 Gene Ontology (GO) terms and 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. miRNA‐Seq identified 112 DEMs, of which 25 were up‐regulated and 87 were down‐regulated in the LP compared with the FP. We obtained 186 intersection genes (IGs) between the 4,522 DEGs and 2,444 target genes predicted from the 112 DEMs. After constructing a miRNA‐gene‐pathway network, we identified key miRNAs and genes including miR‐17‐3p, miR‐214, miR‐221‐5p, miR‐125b, FGF1, YWHAG, YWHAZ, FDFT1 and DHCR24, which are enriched in Hippo and PI3K‐Akt signalling pathways, and various metabolic pathways. These results indicate that these key genes and miRNAs may play important roles in the developmental transition from FP to LP in porcine ovaries and represent candidate targets for further study.     

miRNA and piRNA expression profiles of breeder cock testes detected by next‐generation sequencing

miRNAs are small non‐coding regulatory RNAs that play key roles in diverse biological processes. In this study, we used the Solexa sequencing technique to profile miRNAs in breeder cock testes to illustrate their functions. A total of 663 co‐expressed miRNAs and 3,180 co‐expressed piRNAs were detected in three libraries. Based on Mir‐X^? miRNA qRT‐PCR, three miRNAs representing low, medium and high expression levels according to the sequencing results were selected randomly to validate the miRNAs' expression profiles. Results suggested that the miRNA expression profiles data could represent actual miRNA expression levels. Moreover, target genes prediction of the co‐expressed miRNAs and further Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed, which revealed that some candidate miRNAs were involved in the regulation of the spermatogenesis process, spermatozoa function and testicular metabolism. In conclusion, we provided a useful resource for further elucidation of the miRNAs' regulatory role in spermatogenesis, contributing to a preliminary database for functional and molecular mechanistic studies in testicular metabolism, spermatogenesis and other testes functions.     

Expression of Connexin 43 in the Porcine Foetal Gonads During Development

This study was designed to reveal connexin 43 (Cx43) mRNA and protein expression in porcine foetal gonads using RT‐PCR, immunohistochemistry and Western blot analysis. Expression of Cx43 was investigated in porcine foetal ovaries and testes on days 50, 70 and 90 post coitum (p.c.). RT‐PCR results indicated that Cx43 mRNA was expressed in both foetal ovaries and testes at all gestational ages examined. Cx43 protein was found in the foetal ovary but its distribution varied across ovarian compartments and changed during development. In foetal ovaries, Cx43 was localized between the interstitial cells surrounding egg nests on all investigated days of prenatal period. Moreover, Cx43 expression was observed between germ cells on day 50 p.c. as well as between pre‐granulosa and granulosa cells of primordial and primary follicles on days 70 and 90 p.c. In the foetal testes, Cx43 protein was detected between neighbouring Leydig cells on all examined days of prenatal period and between adjacent Sertoli cells exclusively on day 90 p.c. The presence of Cx43 protein in all investigated foetal gonads was confirmed by Western blot analysis. Cx43 protein detection between pre‐granulosa cells of primordial follicles suggests its role in regulation of the initial stages of follicle development. The Cx43 immunoexpression between neighbouring Leydig and between Sertoli cells indicates its involvement in controlling their functions. We propose that Cx43‐mediated gap junctional communication is involved in the regulation of porcine foetal gonadal development.     

miRNA在哺乳动物性腺发育中的功能

MicroRNA(miRNA)作为一种内源性的非编码RNA,以影响靶基因表达的方式来调节机体功能。miRNA能调控哺乳动物性腺(睾丸和卵巢)的发育,促进精子与卵母细胞的分化成熟,影响受精卵的发育过程,并可能作为诊断生殖疾病卵巢癌的重要指标。本文对miRNA的生物合成过程,miRNA在哺乳动物性腺发育以及卵巢癌变过程中的调控功能进行了综述,提出该领域主要发展方向是miRNA在哺乳动物性腺发育中的体内功能研究,希望以分子生物学和生物信息学手段,从分子、系统等不同角度阐明单一某种miRNA在哺乳动物性腺发育及卵巢癌变过程中的具体调节机制和信号通路情况。这为研究哺乳动物生殖疾病,选育畜牧生产中优质品种提供了新的思路和途径。     

调控香猪繁殖候选miRNA筛选

研究旨在从香猪卵巢small RNA测序数据中挖掘调控香猪繁殖的microRNA （miRNA）,解析miRNA调控香猪卵巢功能及繁殖性状的分子机制,对于猪的遗传选育具有重要意义。研究选取发情期和间情期的香猪各4头,屠宰后取其卵巢组织,提取总RNA进行small RNA测序,利用生物信息学方法检测miRNA表达谱,筛选差异表达的miRNA,预测差异表达miRNA靶基因,并对靶基因进行GO功能富集和KEGG通路富集分析。结果显示,香猪卵巢组织中miRNA在染色体上呈不均匀分布,主要分布于1号染色体和X染色体上。香猪卵巢中共有627个已知猪miRNAs表达,其中有34个差异表达miRNAs,表达量前五的分别是miR-23、let-7i-5p、miR-103、miR-30e-5p和miR-1271-5p。GO功能分析结果显示,靶基因主要参与的生物学过程是细胞过程（cellular process）,主要分布于细胞（cell）,主要分子功能是结合（binding）;KEGG显著富集通路中,促性腺激素释放激素受体通路（gonadotropin-releasing hormone receptor pathway）、胰岛素样生长因子通路（IGF pathway）和表皮生长因子受体信号通路（EGF receptor signaling pathway）与卵母细胞的发育成熟相关,因此推测miR-23b、let-7i-5p、miR-103、miR-30e-5p和miR-1271-5p可能参与了香猪繁殖调控。本研究初步筛选出5个可能调控香猪繁殖性能的miRNAs,可为从分子水平提高香猪产仔数提供理论基础。     

Integrated analysis of miRNA–mRNA interaction in ovaries of Turpan Black Sheep during follicular and luteal phases

To investigate the regulatory mechanism of the follicular–luteal phase transition in Turpan black sheep (Ovis aries), the genome-wide expression patterns of microRNAs (miRNAs) and genes were investigated in ovaries of six sheep (3 years and single lamb with 3 consecutive births) during follicular and luteal phases of the oestrous cycle. Bioinformatic analysis was used to screen potential miRNAs and genes related to Turpan black sheep ovarian function. RT-qPCR was used to validate the sequencing results. In total, we identified 139 known and 71 novel miRNAs in the two phases with miRNA-seq, and a total of 19 miRNAs were significantly differentially expressed, of which 7 were up-regulated and 12 were down-regulated in the follicular phase compared with luteal phase. A total of 150 genes were significantly differentially expressed, including 63 up-regulated and 87 down-regulated in the follicular phase compared with the luteal phase by RNA-seq data analysis. Those DEGs were significantly enriched in 103 GO terms and several KEGG pathways, including metabolic pathway, ovarian steroidogenesis, steroid hormone biosynthesis and oestrogen signalling pathway. In addition, we created a miRNA–mRNA regulatory network to further elucidate the mechanism of follicular–luteal transition. Finally, we identified key miRNAs and genes including miR-143, miR-99a, miR-150, miR-27a, miR-125b, STAR, STAT1, which might play crucial roles in reproductive hormone biosynthesis and follicular development. The miRNA–mRNA interactive network clearly illustrates molecular basis involving in follicular–luteal transition.     

Comparative Expression Analysis of Gametogenesis‐Associated Genes in Foetal and Adult Bubaline (Bubalus bubalis) Ovaries and Testes

This study was conducted to identify and analyse the expression of gametogenesis‐associated genes and proteins in foetal and adult buffalo gonads of both the sexes. Relative quantification of the genes was determined by qPCR and Western blotting. Immunohistochemistry was also performed for various gametogenesis‐associated proteins in foetal and adult gonads of both the sexes. We observed significantly (p < 0.05) increased expression of primordial germ cell‐specific, meiotic as well as genes associated with oocyte maturation and development in foetal ovaries as compared to the adult ones. However, significantly (p < 0.05) increased expression of proteins associated with oocyte maturation like GDF9 and ZP4 was found in adult ovaries, indicating temporal regulation of mRNA translation during oogenesis. Meiotic genes showed significantly (p < 0.05) increased expression in adult testes as compared to foetal testes and ovaries, indicating onset of meiosis at a later stage in spermatogenesis. In general, the expression of primordial germ cell‐associated as well as meiotic genes was higher in adult testes, indicating the increased biological activity in the organ. Immunohistochemistry revealed localized expression of gametogenesis‐associated proteins in ovarian follicles and seminiferous tubules of testes, while the surrounding somatic tissues were devoid of these proteins. The study gives an understanding of the sequential and temporal events of gene expression as well as mRNA translation during male and female gametogenesis. It could also be concluded that follicles and seminiferous tubules are the functional units of the female and male gonads, respectively, and their function could be enhanced by appropriate chemical and genetic intervention of the somatic tissue immediately surrounding them. This assumes importance in the context that buffalo attains sexual maturity at an older age of 2–3 years and have smaller ovaries with lesser number of primordial follicles in comparison with cattle, which is suggested to be the main reason of their poor breeding performance.     

香猪卵巢circ_CSPP1的鉴定及功能预测分析

研究旨在揭示香猪卵巢组织中circ_CSPP1的潜在功能。利用CIRI-full拼接circ_CSPP1的序列，circBase数据库在线blat分析circ_CSPP1的保守性，采用RT-PCR和Sanger测序技术从香猪卵巢分离和鉴定circ_CSPP1，采用miRanda、RNAhybrid和PITA软件预测和分析circ_CSPP1结合的miRNA分子及miRNA的靶基因，对靶基因进行GO和KEGG富集分析。结果显示，分离到的circ_CSPP1是保守的，由CSPP1基因的外显子8~12组成，可作为ssc-miR-324、ssc-miR-10a-5p、ssc-miR-9847-3p、ssc-miR-365-5p、ssc-miR-92b-5p、ssc-miR-885-3p、ssc-miR-7139-3p、ssc-miR-9851-3p和ssc-miR-33b-3p等14个miRNAs的分子海绵，靶向755个蛋白编码基因。GO富集分析表明，circ_CSPP1的靶基因显著富集到153个GO条目，其中细胞成熟、细胞分裂位点、细胞迁移的负调控、Wnt信号通路、细胞周期蛋白结合、子宫发育、MAPK活性的激活、黏着斑和卵裂沟等条目与卵巢功能相关。KEGG富集分析表明，circ_CSPP1的靶基因富集到260个信号通路，其中显著富集的有29个信号通路，主要富集于癌症通路、细胞周期、雌激素信号通路、PI3K-AKT信号通路、卵巢类固醇生成、催产素信号通路和细胞凋亡等信号通路。综上，circ_CSPP1可作为许多miRNA的分子海绵调控香猪卵巢颗粒细胞的增殖与凋亡、卵泡成熟、排卵过程、卵巢类固醇生成和卵巢早衰等生物学过程。     

Identification of a novel miRNA from the ovine ovary by a combinatorial approach of bioinformatics and experiments

MicroRNAs (miRNAs) are a class of short endogenous, single-stranded, non-coding small RNA molecules, about 19–25 nucleotides in length that regulate gene expression at the translation level and influence many physiological process, such apoptosis, metabolism, signal transduction, and occurrence and development of diseases. In this study, we constructed a library from the ovine luteal phase ovary by using next-generation sequencing technology (Solexa high-throughput sequencing technique) and identified 267 novel miRNAs by bioinformatics. One of the novel miRNAs (ovis_aries_ovary-m0033_3p), which expressed in the sheep ovary and testis, was confirmed by real time PCR and northern blot. Ovis_aries_ovary-m0033_3p was 21 nucleotides in length and located on chromosome 12, and it had 100% similarity to hsa-miR-214-3p, mmu-miR-214-3p, dre-miR-214and ssc-miR-214. Meanwhile, the pre-miRNA was 82 nucleotides in length and had a standard hairpin stem-loop structure. From the consistency of the sequence and structure, we speculated that ovis_aries_ovary-m0033_3p had a function similar to hsa-miR-214-3p, which is involved in the fine regulation of cell survival, embryonic development, breeding activities and resistance to ovarian cancer, so we defined it as oar-miR-214-3p. These experimental results will enrich the miRNA database for ovis aries and provide the basis for researching the regulation mechanism of miRNA in relation to breeding activities of seasonal breeding animals.     

Functional microRNA screening for dietary vitamin E regulation of abdominal fat deposition in broilers

ABSTRACT

1. Functional microRNA (miRNA) screening for abdominal fat tissue with different dietary vitamin E (VE) levels was performed to reveal miRNAs, genes and metabolic pathways involved in abdominal fat deposition in broilers.

2. A total of 240, one-day-old healthy female chicks were randomly allocated into five dietary treatments containing either 0, 20, 50, 75 or 100 IU DL-α-tocopherol acetate. The sequencing of miRNAs from abdominal fat tissues was performed. The target genes of miRNAs were predicted and enrichment analysis for these genes was performed. Diets supplemented with 50 IU VE significantly diminished abdominal fat deposition in broilers at day 35 of age.

3. A total of 29 miRNAs were differentially expressed between control and 50 IU VE treatment. Ten of the 23 target genes were enriched in four signalling pathways: tight junction, SNARE interactions in vesicular transport, regulation of autophagy and proteasome.

4. This study identified miRNA, target genes and pathways in dietary VE treatment for broilers, providing new insights into the miRNA regulation of abdominal fat deposition in broilers.     

乏情和发情初产母猪卵巢microRNA差异表达分析

为了探索卵巢microRNA （miRNA）在初产母猪生殖调控中的作用,本研究利用Illumina高通量测序技术检测了乏情和发情初产母猪卵巢miRNA的表达谱,并对表达量较高且差异显著的miRNA进行生物信息学分析。结果显示,本研究构建的两个small RNA文库共鉴定出503个miRNAs,其中已知的303个,新预测的200个。在已知的miRNA中,ssc-miR-10b在两个文库中的表达量最高,其次为ssc-miR-143-3p和ssc-miR-26a;在新预测的miRNA中,chr13_2637_mature在两个文库中的表达量最高,其次为chr8_9994_mature。与发情母猪相比,共有145个miRNAs发生显著变化（read counts>10,∣log₂（fold-change）∣>1）,上调114个,下调31个。在进一步筛选的31个表达量较高且差异显著的miRNAs（read counts>1 000,∣log₂（fold-change）∣>1）中,新预测的chr13_2585_mature上调倍数最高,且只在乏情母猪卵巢中表达。31个miRNAs共预测到7 388个靶基因,KEGG信号通路分析显示,有2 788个靶基因注释到了297个KEGG通路,前20个最富集的通路部分与生殖过程或生殖活动调控相关,表明这31个miRNAs参与了初产母猪的生殖调控。本研究结果丰富了猪miRNA数据资源,为进一步深入研究初产母猪的繁殖性能提供了理论依据。     

In utero exposure to the anti-androgen flutamide influences connexin 43 and β-catenin expression in porcine fetal gonads

Recent reports have indicated a role of cell-to-cell interactions during gonadal development and functions. Numerous reports indicate that fetal hormonal disruption induces abnormalities in the developing reproductive system and, therefore, may interfere with reproductive functions later in adult life. Hence, this study investigated the effect of androgen deficiency during late prenatal periods on the gap junction-associated connexin 43 (Cx43) and the adherens junction-associated β-catenin expression in the fetal porcine gonads. Thus, pregnant gilts were injected with anti-androgen flutamide (for 7 d, 50 mg/kg BW per day) or corn oil (control groups) starting at 83 (GD90) or 101 (GD108) gestational day. On GD90 and GD108 the fetuses were excised and fetal gonads were obtained. To assess Cx43 and β-catenin expression real-time PCR and immunohistochemistry were performed. In fetal testes, Cx43 was localized between Leydig cells, whereas β-catenin was observed mainly within the seminiferous tubules. In fetal ovaries, Cx43 was detected between interstitial cells and between granulosa cells of forming follicles, whereas β-catenin was found within egg nests, in oocytes' membrane, and in granulosa cells of forming follicles. Immunohistochemistry showed decreased Cx43 and β-catenin expression in fetal gonads from flutamide-treated pigs compared with respective controls. However, the ovaries from animals treated with flutamide on GD108 showed increased Cx43 expression. The changes of Cx43 and β-catenin expression after prenatal flutamide treatment were confirmed at the mRNA level. These findings suggest that androgen deficiency during late gestation may lead to disturbed intercellular interactions in fetal porcine testes affecting testicular functions, as well as impaired follicular formation in fetal ovaries. Our results further signify the role of androgens in the regulation of cell-to-cell interactions within fetal porcine gonads.     

MicroRNA expression profiling of cat and dog kidneys

MicroRNAs (miRNAs) play a role in the pathogenesis of certain diseases and may serve as biomarkers. Here, we present the first analysis of miRNA expression in the kidneys of healthy cats and dogs. Kidneys were divided into renal cortex (CO) and medulla (MD), and RNA sequence analysis was performed using the mouse genome as a reference. A total of 277, 276, 295, and 297 miRNAs were detected in cat CO, cat MD, dog CO, and dog MD, respectively. By comparing the expression ratio of CO to MD, we identified highly expressed miRNAs in each tissue as follows: 41 miRNAs including miR-192-5p in cat CO; 45 miRNAs including miR-323-3p in dog CO; 78 miRNAs including miR-20a-5p in cat MD; and 11 miRNAs including miR-132-5p in dog MD. Further, the target mRNAs of these miRNAs were identified. These data provide veterinary medicine critical information regarding renal miRNA expression.     

胚胎移植前供体牛与受体牛血浆外泌体miRNA差异表达分析

【目的】 探索胚胎移植前供体牛与受体牛血浆外泌体miRNA的表达差异, 以明确血浆外泌体miRNA在牛早期妊娠中的作用及其调控机制。【方法】 以3~6岁、体重480~600 kg的夏南牛作为研究对象, 选取10头供体牛进行同期发情、超数排卵和人工授精, 23头受体牛只做同期发情处理。在人工授精后第7天, 冲洗供体牛子宫以获取囊胚, 选取3头囊胚数相近的供体牛及3头与供体牛体重和年龄均相近的受体牛, 颈静脉采血, 进行血浆外泌体的分离与鉴定; 然后提取血浆外泌体miRNA, 并检测其表达量; 采用R语言中的DESeq差异算法计算P值, 并筛选出P<0.05的miRNA, 对差异表达的miRNA进行靶基因预测、GO功能富集分析和KEGG信号通路分析。【结果】 6个样本的囊泡粒径均在135 nm左右, 符合外泌体的特征。与供体牛相比, 受体牛中有9个miRNAs表达显著上调(P<0.05), 13个miRNAs显著下调(P<0.05);22个差异表达的miRNAs中, 有15个miRNAs预测出无重复的靶基因2 990个。GO功能富集分析和KEGG信号通路分析的结果表明, 这些靶基因主要富集在与生物黏附(biological adhesion)、定位(localization)、细胞连接(cell junction)功能有关的通路上, 显著富集的信号通路与黏着斑(focal adhesion)、黏着连接(adherens junction)有关, 提示血浆外泌体miRNA可能参与调控胚胎着床。【结论】 研究结果可为筛选和探究影响胚胎着床的血浆外泌体miRNA提供参考, 并为进一步阐明血浆外泌体miRNA在母牛早期妊娠调控中的作用提供依据。     

Differential expression of Wilms’ tumour 1 gene in porcine urogenital organs during development

Wilms’ tumour 1 gene (WT1) is essential for the development of mammalian urogenital system. However, the expression pattern of WT1 in the development of porcine urogenital organs is still unclear. Here, we examined the expression of WT1 mRNA and protein in porcine kidneys, ovaries and testes from embryonic days 35 and 60 (E35d, E60d, n = 3) to the newborn (0d, n = 4) and adult (210d, n = 3) stages, using real‐time PCR and immunofluorescent staining. Real‐time PCR analysis showed that porcine kidneys, ovaries and testes all expressed high level of WT1 mRNAs, especially in adult testes (p < 0.05 or 0.01 vs. kidney and ovary, respectively). Morphologically, characteristic microstructures of the kidneys, ovaries and testes were observed and discerned at all four stages. Immunofluorescently, WT1 expression was detected in a dynamic and context‐specific pattern during the development of these organs. Taken together, porcine urogenital organs express relatively high levels of WT1 mRNA. Dynamical and context‐specific expression profile of WT1 in these organs occurs during their development, implying its close association with the development and function of porcine kidney, ovary and testis.     

miR‐26a suppresses autophagy in swine Sertoli cells by targeting ULK2

A large number of microRNAs (miRNAs) have been detected from porcine testicular tissues thanks to the development of high‐throughput sequencing technology. However, the regulatory roles of most identified miRNAs in swine testicular development or spermatogenesis are poorly understood. In our previous study, ULK2 (uncoordinated‐51‐like kinase 2) was predicted as a target gene of miR‐26a. In this study, we aimed to investigate the role of miR‐26a in swine Sertoli cell autophagy. The relative expression of miR‐26a and ULK2 levels has a significant negative correlation (R² = .5964, p ≤ .01) in nine developmental stages of swine testicular tissue. Dual‐luciferase reporter assay results show that miR‐26a directly targets the 3′UTR of the ULK2 gene (position 618–624). In addition, both the mRNA and protein expression of ULK2 were downregulated by miR‐26a in swine Sertoli cells. These results indicate that miR‐26a targets the ULK2 gene and downregulates its expression in swine Sertoli cells. Based on the expression of marker genes (LC3, p62 and Beclin‐1), overexpression of miR‐26a or knock‐down of ULK2 inhibits swine Sertoli cell autophagy. Taken together, these findings demonstrate that miR‐26a suppresses autophagy in swine Sertoli cells by targeting ULK2.