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15 pages, 1992 KiB

Open AccessEditor’s ChoiceArticle

miR-302d Targeting of CDKN1A Regulates DNA Damage and Steroid Hormone Secretion in Bovine Cumulus Cells

by Jianbo Liu, Jiabao Zhang, Yi Zheng, Guokun Zhao, Hao Jiang and Bao Yuan

Genes 2023, 14(12), 2195; https://doi.org/10.3390/genes14122195 - 10 Dec 2023

Cited by 2 | Viewed by 1678

Abstract

(1) Background: DNA damage in cumulus cells hinders oocyte maturation and affects steroid hormone secretion. It is crucial to identify the key factors that regulate cellular DNA damage and steroid hormone secretion. (2) Methods: Treatment of bovine cumulus cells with bleomycin to induce [...] Read more.

(1) Background: DNA damage in cumulus cells hinders oocyte maturation and affects steroid hormone secretion. It is crucial to identify the key factors that regulate cellular DNA damage and steroid hormone secretion. (2) Methods: Treatment of bovine cumulus cells with bleomycin to induce DNA damage. The effects of DNA damage on cell biology were determined by detecting changes in DNA damage degree, cell cycle, viability, apoptosis, and steroid hormones. It was verified that mir-302d targeted regulation of CDKN1A expression, and then affected DNA damage and steroid hormone secretion in cumulus cells. (3) Results: Bleomycin induced increased DNA damage, decreased G1-phase cells, increased S-phase cells, inhibited proliferation, promoted apoptosis, affected E₂ and P₄ secretion, increased CDKN1A expression, and decreased miR-302d expression. Knockdown of CDKN1A reduced DNA damage, increased G1-phase cells, decreased G2-phase cells, promoted proliferation, inhibited apoptosis, increased E₂ and P₄ secretion, and increased the expression of BRCA1, MRE11, ATM, CDK1, CDK2, CCNE2, STAR, CYP11A1, and HSD3B1. The expression of RAD51, CCND1, p53, and FAS was decreased. Overexpression of CDKN1A resulted in the opposite results. miR-302d targets CDKN1A expression to regulate DNA damage and then affects the cell cycle, proliferation, apoptosis, steroid hormone secretion, and the expression of related genes. (4) Conclusions: miR-302d and CDKN1A were candidate molecular markers for the diagnosis of DNA damage in bovine cumulus cells. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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17 pages, 3310 KiB

Open AccessArticle

A Redesigned Method for CNP-Synchronized In Vitro Maturation Inhibits Oxidative Stress and Apoptosis in Cumulus-Oocyte Complexes and Improves the Developmental Potential of Porcine Oocytes

by Jinlun Lu, Min Guo, Xiaodong Wang, Rui Wang, Guangyin Xi, Lei An, Jianhui Tian and Meiqiang Chu

Genes 2023, 14(10), 1885; https://doi.org/10.3390/genes14101885 - 28 Sep 2023

Cited by 1 | Viewed by 2069

Abstract

In vitro embryo production depends on high-quality oocytes. Compared with in vivo matured oocytes, in vitro oocytes undergo precocious meiotic resumption, thus compromising oocyte quality. C-type natriuretic peptide (CNP) is a follicular factor maintaining meiotic arrest. Thus, CNP-pretreatment has been widely used to [...] Read more.

In vitro embryo production depends on high-quality oocytes. Compared with in vivo matured oocytes, in vitro oocytes undergo precocious meiotic resumption, thus compromising oocyte quality. C-type natriuretic peptide (CNP) is a follicular factor maintaining meiotic arrest. Thus, CNP-pretreatment has been widely used to improve the in vitro maturation (IVM) of oocytes in many species. However, the efficacy of this strategy has remained unsatisfactory in porcine oocytes. Here, by determining the functional concentration and dynamics of CNP in inhibiting spontaneous meiotic resumption, we improved the current IVM system of porcine oocytes. Our results indicate that although the beneficial effect of the CNP pre-IVM strategy is common among species, the detailed method may be largely divergent among them and needs to be redesigned specifically for each one. Focusing on the overlooked role of cumulus cells surrounding the oocytes, we also explore the mechanisms relevant to their beneficial effect. In addition to oocytes per se, the enhanced anti-apoptotic and anti-oxidative gene expression in cumulus cells may contribute considerably to improved oocyte quality. These findings not only emphasize the importance of screening the technical parameters of the CNP pre-IVM strategy for specific species, but also highlight the critical supporting role of cumulus cells in this promising strategy. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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15 pages, 2989 KiB

Open AccessEditor’s ChoiceArticle

Transcriptome and Metabolome Analyses Reveal the Mechanism of Corpus Luteum Cyst Formation in Pigs

by Jiage Dai, Jiabao Cai, Taipeng Zhang, Mingyue Pang, Xiaoling Xu, Jiahua Bai, Yan Liu and Yusheng Qin

Genes 2023, 14(10), 1848; https://doi.org/10.3390/genes14101848 - 23 Sep 2023

Cited by 2 | Viewed by 2319

Abstract

Corpus luteum cysts are a serious reproductive disorder that affects the reproductive performance of sows. In this study, transcriptome and metabolome datasets of porcine normal and cyst luteal granulosa cells were generated to explore the molecular mechanism of luteal cyst formation. We obtained [...] Read more.

Corpus luteum cysts are a serious reproductive disorder that affects the reproductive performance of sows. In this study, transcriptome and metabolome datasets of porcine normal and cyst luteal granulosa cells were generated to explore the molecular mechanism of luteal cyst formation. We obtained 28.9 Gb of high−quality transcriptome data from luteum tissue samples and identified 1048 significantly differentially expressed genes between the cyst and normal corpus luteum samples. Most of the differentially expressed genes were involved in cancer and immune signaling pathways. Furthermore, 22,622 information-containing positive and negative ions were obtained through gas chromatography−mass spectrometry, and 1106 metabolites were successfully annotated. Important differentially abundant metabolites and pathways were identified, among which abnormal lipid and choline metabolism were involved in the formation of luteal cysts. The relationships between granulosa cells of luteal cysts and cancer, immune-related signaling pathways, and abnormalities of lipid and choline metabolism were elaborated, providing new entry points for studying the pathogenesis of porcine luteal cysts. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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16 pages, 8205 KiB

Open AccessArticle

Salidroside Supplementation Affects In Vitro Maturation and Preimplantation Embryonic Development by Promoting Meiotic Resumption

by Shuming Shi, Zhaojun Geng, Xianfeng Yu, Bing Hu, Liying Liu, Zhichao Chi, Linyi Qu, Mingjun Zhang and Yongxun Jin

Genes 2023, 14(9), 1729; https://doi.org/10.3390/genes14091729 - 30 Aug 2023

Cited by 6 | Viewed by 1954

Abstract

Salidroside (Sal) possesses several pharmacological activities, such as antiaging, and anti-inflammatory, antioxidant, anticancer activities, and proliferation-promoting activities, but the effects of Sal on oocytes have rarely been reported. In the present study, we evaluated the beneficial effects of Sal, which is mainly found [...] Read more.

Salidroside (Sal) possesses several pharmacological activities, such as antiaging, and anti-inflammatory, antioxidant, anticancer activities, and proliferation-promoting activities, but the effects of Sal on oocytes have rarely been reported. In the present study, we evaluated the beneficial effects of Sal, which is mainly found in the roots of Rhodiola. Porcine cumulus oocyte complexes were cultured in IVM medium supplemented (with 250 μmol/L) with Sal or not supplemented with Sal. The maturation rate in the Sal group increased from 88.34 ± 4.32% to 94.12 ± 2.29%, and the blastocyst rate in the Sal group increased from 30.35 ± 3.20% to 52.14 ± 7.32% compared with that in the control group. The experimental groups showed significant improvements in the cumulus expansion area. Sal reduced oocyte levels of reactive oxygen species (ROS) and enhanced intracellular GSH levels. Sal supplementation enhanced the mitochondrial membrane potential (MMP), ATP level, and mtDNA copy number, which shows that Sal enhances the cytoplasmic maturation of oocytes. Oocytes in the Sal group exhibited slowed apoptosis and reduced DNA breakage. Cell cycle signals and oocyte meiosis play important roles in oocyte maturation. The mRNA expressions of the MAPK pathway and MAPK phosphorylation increased significantly in the Sal group. The mRNA expression of the oocyte meiosis gene also increased significantly. These results show that Sal enhances the nuclear maturation of oocytes. Moreover, Sal increased the number of blastocyst cells, the proliferation of blastocysts, and the expressions of pluripotency genes. Sal down-regulated apoptosis-related genes and the apoptotic cell rate of blastocysts. In summary, our results demonstrate that Sal is helpful to improving the quality of porcine oocytes in vitro, and their subsequent embryonic development. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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15 pages, 1931 KiB

Open AccessArticle

Transcriptomic Analysis of the Developing Testis and Spermatogenesis in Qianbei Ma Goats

by Yue Zou, Xiang Chen, Xingzhou Tian, Wei Guo, Yong Ruan, Wen Tang, Kaibin Fu and Taotao Ji

Genes 2023, 14(7), 1334; https://doi.org/10.3390/genes14071334 - 25 Jun 2023

Cited by 6 | Viewed by 2167

Abstract

Reproductive competence in male mammals depends on testicular function. Testicular development and spermatogenesis in goats involve highly complex physiological processes. In this study, six testes were, respectively, obtained from each age group, immature (1 month), sexually mature (6 months) and physically mature (12 [...] Read more.

Reproductive competence in male mammals depends on testicular function. Testicular development and spermatogenesis in goats involve highly complex physiological processes. In this study, six testes were, respectively, obtained from each age group, immature (1 month), sexually mature (6 months) and physically mature (12 months old) Qianbei Ma goats. RNA-Seq was performed to assess testicular mRNA expression in Qianbei Ma goats at different developmental stages. Totally, 18 libraries were constructed to screen genes and pathways involved in testis development and spermatogenesis. Totally, 9724 upregulated and 4153 downregulated DEGs were found between immature (I) and sexually mature (S) samples; 7 upregulated and 3 downregulated DEGs were found between sexually mature (S) and physically mature (P) samples, and about 4% of the DEGs underwent alternative splicing events between I and S. Select genes were assessed by qRT-PCR, corroborating RNA-Seq findings. The detected genes have key roles in multiple developmental stages of goat testicular development and spermatogenesis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to determine differentially expressed genes (DEGs). GO analysis revealed DEGs between S and P contributed to “reproduction process”, “channel activity” and “cell periphery part” between I and S, and in “ion transport process”, “channel activity” and “transporter complex part”. KEGG analysis suggested the involvement of “glycerolipid metabolism”, “steroid hormone biosynthesis” and “MAPK signaling pathway” in testis development and spermatogenesis. Genes including IGF1, TGFB1, TGFBR1 and EGFR may control the development of the testis from immature to sexually mature, which might be important candidate genes for the development of goat testis. The current study provides novel insights into goat testicular development and spermatogenesis. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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11 pages, 4522 KiB

Open AccessCommunication

Efficient and Specific Generation of MSTN-Edited Hu Sheep Using C-CRISPR

by Rihong Guo, Huili Wang, Chunhua Meng, Hongbing Gui, Yinxia Li, Fang Chen, Chenjian Zhang, Han Zhang, Qiang Ding, Jianli Zhang, Jun Zhang, Yong Qian, Jifeng Zhong and Shaoxian Cao

Genes 2023, 14(6), 1216; https://doi.org/10.3390/genes14061216 - 2 Jun 2023

Cited by 10 | Viewed by 3799

Abstract

Hu sheep, an indigenous breed in China known for its high fecundity, are being studied to improve their growth and carcass traits. MSTN is a negative regulator of muscle development, and its inactivation results in muscularity. The C-CRISPR system, utilizing multiple neighboring sgRNAs [...] Read more.

Hu sheep, an indigenous breed in China known for its high fecundity, are being studied to improve their growth and carcass traits. MSTN is a negative regulator of muscle development, and its inactivation results in muscularity. The C-CRISPR system, utilizing multiple neighboring sgRNAs targeting a key exon, has been successfully used to generate genes for complete knockout (KO) monkeys and mice in one step. In this study, the C-CRISPR system was used to generate MSTN-edited Hu sheep; 70 embryos injected with Cas9 mRNA and four sgRNAs targeting exon 3 of sheep MSTN were transferred to 13 recipients. Out of 10 lambs born from five recipients after full-term pregnancies, nine had complete MSTN KO with various mutations. No off-target effects were found. These MSTN-KO Hu sheep showed a double-muscled (DM) phenotype, characterized by a higher body weight at 3 and 4 months old, prominent muscular protrusion, clearly visible intermuscular groves, and muscle hypertrophy. The molecular analysis indicated enhanced AKT and suppressed ERK1/2 signaling in the gluteus muscle of the edited Hu sheep. In conclusion, MSTN complete KO Hu sheep with a DM phenotype were efficiently and specifically generated using C-CRISPR, and the C-CRISPR method is a promising tool for farm animal breeding. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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21 pages, 9731 KiB

Open AccessFeature PaperArticle

Identification and Functional Analysis of Transcriptome Profiles, Long Non-Coding RNAs, Single-Nucleotide Polymorphisms, and Alternative Splicing from the Oocyte to the Preimplantation Stage of Sheep by Single-Cell RNA Sequencing

by Zijing Zhang, Qiaoting Shi, Xiaoting Zhu, Lei Jin, Limin Lang, Shijie Lyu, Xiaoling Xin, Yongzhen Huang, Xiang Yu, Zhiming Li, Sujuan Chen, Zhaoxue Xu, Wei Zhang and Eryao Wang

Genes 2023, 14(6), 1145; https://doi.org/10.3390/genes14061145 - 25 May 2023

Viewed by 1988

Abstract

Numerous dynamic and complicated processes characterize development from the oocyte to the embryo. However, given the importance of functional transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing during embryonic development, the effect that these features have on the blastomeres of 2-, [...] Read more.

Numerous dynamic and complicated processes characterize development from the oocyte to the embryo. However, given the importance of functional transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing during embryonic development, the effect that these features have on the blastomeres of 2-, 4-, 8-, 16-cell, and morula stages of development has not been studied. Here, we carried out experiments to identify and functionally analyze the transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms (SNPs), and alternative splicing (AS) of cells from sheep from the oocyte to the blastocyst developmental stages. We found between the oocyte and zygote groups significantly down-regulated genes and the second-largest change in gene expression occurred between the 8- and 16-cell stages. We used various methods to construct a profile to characterize cellular and molecular features and systematically analyze the related GO and KEGG profile of cells of all stages from the oocyte to the blastocyst. This large-scale, single-cell atlas provides key cellular information and will likely assist clinical studies in improving preimplantation genetic diagnosis. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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13 pages, 7351 KiB

Open AccessArticle

Melatonin Protects the Apoptosis of Sheep Granulosa Cells by Suppressing Oxidative Stress via MAP3K8 and FOS Pathway

by Bo Zhai, Xu Li, Zhongli Zhao, Yang Cao, Xinxin Liu, Zheng Liu, Huihai Ma and Wenfa Lu

Genes 2023, 14(5), 1067; https://doi.org/10.3390/genes14051067 - 11 May 2023

Cited by 7 | Viewed by 2392

Abstract

Melatonin is not only a highly effective active oxygen scavenger but also an important reproductive hormone. Melatonin has a regulatory effect on animal reproduction, especially on the ovaries. It can affect the proliferation and apoptosis of cells in follicles. However, the mechanisms of [...] Read more.

Melatonin is not only a highly effective active oxygen scavenger but also an important reproductive hormone. Melatonin has a regulatory effect on animal reproduction, especially on the ovaries. It can affect the proliferation and apoptosis of cells in follicles. However, the mechanisms of the dual antioxidation and anti-apoptosis effects of melatonin on granulosa cells are still not clear, especially in sheep. Therefore, we investigated the mechanisms of the protective effect of melatonin against oxidative damage in granulosa cells. At a concentration of 250 µmol/L, H₂O₂ promoted granulosa cell apoptosis; however, 10 ng/mL melatonin effectively alleviated the pro-apoptotic effect of H₂O₂. Furthermore, through the application of high-throughput sequencing technology, we identified 109 significantly differentially expressed genes (35 upregulated and 74 downregulated genes) involved in the protective effect of melatonin against apoptosis. The expression levels of nine related genes, i.e., ATF3, FIBIN, FOS, HSPA6, MAP3K8, FOSB, PET117, DLX2, and TRIB1, changed significantly. MAP3K8 and FOS gene overexpression impacted the protective effect of melatonin in granulosa cells; the two genes exhibited an upstream and downstream regulatory relationship. Our findings indicated that melatonin alleviated H₂O₂-induced apoptosis in sheep granulosa cells through the MAP3K8-FOS pathway. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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15 pages, 3736 KiB

Open AccessEditor’s ChoiceArticle

Intrafollicular Retinoic Acid Signaling Is Important for Luteinizing Hormone-Induced Oocyte Meiotic Resumption

by Fupeng Wang, Yawen Tang, Yijie Cai, Ran Yang, Zongyu Wang, Xiaodong Wang, Qianying Yang, Wenjing Wang, Jianhui Tian and Lei An

Genes 2023, 14(4), 946; https://doi.org/10.3390/genes14040946 - 20 Apr 2023

Cited by 4 | Viewed by 2209

Abstract

It has been clear that retinoic acid (RA), the most active vitamin A (VA) derivative, plays a central role in governing oocyte meiosis initiation. However, it has not been functionally determined if RA participates in luteinizing hormone (LH)-induced resumption from long-lasting oocyte meiotic [...] Read more.

It has been clear that retinoic acid (RA), the most active vitamin A (VA) derivative, plays a central role in governing oocyte meiosis initiation. However, it has not been functionally determined if RA participates in luteinizing hormone (LH)-induced resumption from long-lasting oocyte meiotic arrest, which is essential for haploid oocyte formation. In the present study, using well-established in vivo and in vitro models, we identified that intrafollicular RA signaling is important for normal oocyte meiotic resumption. A mechanistic study indicated that mural granulosa cells (MGCs) are the indispensable follicular compartment for RA-prompted meiotic resumption. Moreover, retinoic acid receptor (RAR) is essential for mediating RA signaling to regulate meiotic resumption. Furthermore, we found zinc finger protein 36 (ZFP36) is the transcriptional target of RAR. Both RA signaling and epidermal growth factor (EGF) signaling were activated in MGCs in response to LH surge, and two intrafollicular signalings cooperate to induce rapid Zfp36 upregulation and Nppc mRNA decrease, which is critical to LH-induced meiotic resumption. These findings extend our understanding of the role of RA in oocyte meiosis: RA not only governs meiotic initiation but also regulates LH-induced meiotic resumption. We also emphasize the importance of LH-induced metabolic changes in MGCs in this process. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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14 pages, 5072 KiB

Open AccessArticle

WNT Co-Receptor LRP6 Is Critical for Zygotic Genome Activation and Embryonic Developmental Potential by Interacting with Oviductal Paracrine Ligand WNT2

by Fusheng Yao, Jia Hao, Zhaochen Wang, Meiqiang Chu, Jingyu Zhang, Guangyin Xi, Zhenni Zhang, Lei An and Jianhui Tian

Genes 2023, 14(4), 891; https://doi.org/10.3390/genes14040891 - 10 Apr 2023

Cited by 2 | Viewed by 2042

Abstract

Mammalian preimplantation development depends on the interaction between embryonic autocrine and maternal paracrine signaling. Despite the robust independence of preimplantation embryos, oviductal factors are thought to be critical to pregnancy success. However, how oviductal factors regulate embryonic development and the underlying mechanism remain [...] Read more.

Mammalian preimplantation development depends on the interaction between embryonic autocrine and maternal paracrine signaling. Despite the robust independence of preimplantation embryos, oviductal factors are thought to be critical to pregnancy success. However, how oviductal factors regulate embryonic development and the underlying mechanism remain unknown. In the present study, focusing on WNT signaling, which has been reported to be essential for developmental reprogramming after fertilization, we analyzed the receptor-ligand repertoire of preimplantation embryonic WNT signaling, and identified that the WNT co-receptor LRP6 is necessary for early cleavage and has a prolonged effect on preimplantation development. LRP6 inhibition significantly impeded zygotic genome activation and disrupted relevant epigenetic reprogramming. Focusing on the potential oviductal WNT ligands, we found WNT2 as the candidate interacting with embryonic LRP6. More importantly, we found that WNT2 supplementation in culture medium significantly promoted zygotic genome activation (ZGA) and improved blastocyst formation and quality following in vitro fertilization (IVF). In addition, WNT2 supplementation significantly improved implantation rate and pregnancy outcomes following embryo transfer. Collectively, our findings not only provide novel insight into how maternal factors regulate preimplantation development through maternal-embryonic communication, but they also propose a promising strategy for improving current IVF systems. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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21 pages, 5897 KiB

Open AccessEditor’s ChoiceArticle

Sequencing of the Pituitary Transcriptome after GnRH Treatment Uncovers the Involvement of lncRNA-m23b/miR-23b-3p/CAMK2D in FSH Synthesis and Secretion

by Tian Wang, Guokun Zhao, Song Yu, Yi Zheng, Haixiang Guo, Haoqi Wang, Peisen Zhao, Wenyin Xie, Wenzhi Ren and Bao Yuan

Genes 2023, 14(4), 846; https://doi.org/10.3390/genes14040846 - 31 Mar 2023

Cited by 2 | Viewed by 2118

Abstract

The pituitary gland is a key participant in the hypothalamic–pituitary–gonadal axis, as it secretes a variety of hormones and plays an important role in mammalian reproduction. Gonadotrophin-releasing hormone(GnRH) signaling molecules can bind to GnRH receptors on the surfaces of adenohypophysis gonadotropin cells and [...] Read more.

The pituitary gland is a key participant in the hypothalamic–pituitary–gonadal axis, as it secretes a variety of hormones and plays an important role in mammalian reproduction. Gonadotrophin-releasing hormone(GnRH) signaling molecules can bind to GnRH receptors on the surfaces of adenohypophysis gonadotropin cells and regulate the expression of follicle-stimulating hormone(FSH) and luteinizing hormone(LH) through various pathways. An increasing number of studies have shown that noncoding RNAs mediate the regulation of GnRH signaling molecules in the adenohypophysis. However, the expression changes and underlying mechanisms of genes and noncoding RNAs in the adenohypophysis under the action of GnRH remain unclear. In the present study, we performed RNA sequencing (RNA-seq) of the rat adenohypophysis before and after GnRH treatment to identify differentially expressed mRNAs, lncRNAs, and miRNAs. We found 385 mRNAs, 704 lncRNAs, and 20 miRNAs that were significantly differentially expressed in the rat adenohypophysis. Then, we used a software to predict the regulatory roles of lncRNAs as molecular sponges that compete with mRNAs to bind miRNAs, and construct a GnRH-mediated ceRNA regulatory network. Finally, we enriched the differentially expressed mRNAs, lncRNA target genes, and ceRNA regulatory networks to analyze their potential roles. Based on the sequencing results, we verified that GnRH could affect FSH synthesis and secretion by promoting the competitive binding of lncRNA-m23b to miR-23b-3p to regulate the expression of Calcium/Calmodulin Dependent Protein Kinase II Delta(CAMK2D). Our findings provide strong data to support exploration of the physiological processes in the rat adenohypophysis under the action of GnRH. Furthermore, our profile of lncRNA expression in the rat adenohypophysis provides a theoretical basis for research on the roles of lncRNAs in the adenohypophysis. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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18 pages, 4024 KiB

Open AccessArticle

DNA Double-Strand Break-Related Competitive Endogenous RNA Network of Noncoding RNA in Bovine Cumulus Cells

by Jian-Bo Liu, Jia-Bao Zhang, Xiang-Min Yan, Peng-Gui Xie, Yao Fu, Xu-Huang Fu, Xu-Lei Sun, Dong-Xu Han, Sheng-Peng Li, Yi Zheng, Yan Gao, Nam-Hyung Kim, Bao Yuan and Hao Jiang

Genes 2023, 14(2), 290; https://doi.org/10.3390/genes14020290 - 22 Jan 2023

Cited by 2 | Viewed by 2195

Abstract

(1) Background: DNA double strand breaks (DSBs) are the most serious form of DNA damage that affects oocyte maturation and the physiological state of follicles and ovaries. Non-coding RNAs (ncRNAs) play a crucial role in DNA damage and repair. This study aims to [...] Read more.

(1) Background: DNA double strand breaks (DSBs) are the most serious form of DNA damage that affects oocyte maturation and the physiological state of follicles and ovaries. Non-coding RNAs (ncRNAs) play a crucial role in DNA damage and repair. This study aims to analyze and establish the network of ncRNAs when DSB occurs and provide new ideas for next research on the mechanism of cumulus DSB. (2) Methods: Bovine cumulus cells (CCs) were treated with bleomycin (BLM) to construct a DSB model. We detected the changes of the cell cycle, cell viability, and apoptosis to determine the effect of DSBs on cell biology, and further evaluated the relationship between the transcriptome and competitive endogenous RNA (ceRNA) network and DSBs. (3) Results: BLM increased γH2AX positivity in CCs, disrupted the G1/S phase, and decreased cell viability. Totals of 848 mRNAs, 75 long noncoding RNAs (lncRNAs), 68 circular RNAs (circRNAs), and 71 microRNAs (miRNAs) in 78 groups of lncRNA–miRNA–mRNA regulatory networks, 275 groups of circRNA–miRNA–mRNA regulatory networks, and five groups of lncRNA/circRNA–miRNA–mRNA co-expression regulatory networks were related to DSBs. Most differentially expressed ncRNAs were annotated to cell cycle, p53, PI3K-AKT, and WNT signaling pathways. (4) Conclusions: The ceRNA network helps to understand the effects of DNA DSBs activation and remission on the biological function of CCs. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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Review

Jump to: Research

16 pages, 1405 KiB

Open AccessEditor’s ChoiceReview

When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications

by Xinyue Liu, Junyuan Zheng, Jialan Ding, Jiaxin Wu, Fuyuan Zuo and Gongwei Zhang

Genes 2024, 15(2), 245; https://doi.org/10.3390/genes15020245 - 15 Feb 2024

Cited by 2 | Viewed by 2513

Abstract

Third-generation sequencing technology has found widespread application in the genomic, transcriptomic, and epigenetic research of both human and livestock genetics. This technology offers significant advantages in the sequencing of complex genomic regions, the identification of intricate structural variations, and the production of high-quality [...] Read more.

Third-generation sequencing technology has found widespread application in the genomic, transcriptomic, and epigenetic research of both human and livestock genetics. This technology offers significant advantages in the sequencing of complex genomic regions, the identification of intricate structural variations, and the production of high-quality genomes. Its attributes, including long sequencing reads, obviation of PCR amplification, and direct determination of DNA/RNA, contribute to its efficacy. This review presents a comprehensive overview of third-generation sequencing technologies, exemplified by single-molecule real-time sequencing (SMRT) and Oxford Nanopore Technology (ONT). Emphasizing the research advancements in livestock genomics, the review delves into genome assembly, structural variation detection, transcriptome sequencing, and epigenetic investigations enabled by third-generation sequencing. A comprehensive analysis is conducted on the application and potential challenges of third-generation sequencing technology for genome detection in livestock. Beyond providing valuable insights into genome structure analysis and the identification of rare genes in livestock, the review ventures into an exploration of the genetic mechanisms underpinning exemplary traits. This review not only contributes to our understanding of the genomic landscape in livestock but also provides fresh perspectives for the advancement of research in this domain. Full article

(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)

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