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Ghafouri F, Sadeghi M, Bahrami A, Naserkheil M, Dehghanian Reyhan V, Javanmard A, Miraei-Ashtiani SR, Ghahremani S, Barkema HW, Abdollahi-Arpanahi R, Kastelic JP. Construction of a circRNA- lincRNA-lncRNA-miRNA-mRNA ceRNA regulatory network identifies genes and pathways linked to goat fertility. Front Genet 2023; 14:1195480. [PMID: 37547465 PMCID: PMC10400778 DOI: 10.3389/fgene.2023.1195480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Background: There is growing interest in the genetic improvement of fertility traits in female goats. With high-throughput genotyping, single-cell RNA sequencing (scRNA-seq) is a powerful tool for measuring gene expression profiles. The primary objective was to investigate comparative transcriptome profiling of granulosa cells (GCs) of high- and low-fertility goats, using scRNA-seq. Methods: Thirty samples from Ji'ning Gray goats (n = 15 for high fertility and n = 15 for low fertility) were retrieved from publicly available scRNA-seq data. Functional enrichment analysis and a literature mining approach were applied to explore modules and hub genes related to fertility. Then, interactions between types of RNAs identified were predicted, and the ceRNA regulatory network was constructed by integrating these interactions with other gene regulatory networks (GRNs). Results and discussion: Comparative transcriptomics-related analyses identified 150 differentially expressed genes (DEGs) between high- and low-fertility groups, based on the fold change (≥5 and ≤-5) and false discovery rate (FDR <0.05). Among these genes, 80 were upregulated and 70 were downregulated. In addition, 81 mRNAs, 58 circRNAs, 8 lincRNAs, 19 lncRNAs, and 55 miRNAs were identified by literature mining. Furthermore, we identified 18 hub genes (SMAD1, SMAD2, SMAD3, SMAD4, TIMP1, ERBB2, BMP15, TGFB1, MAPK3, CTNNB1, BMPR2, AMHR2, TGFBR2, BMP4, ESR1, BMPR1B, AR, and TGFB2) involved in goat fertility. Identified biological networks and modules were mainly associated with ovary signature pathways. In addition, KEGG enrichment analysis identified regulating pluripotency of stem cells, cytokine-cytokine receptor interactions, ovarian steroidogenesis, oocyte meiosis, progesterone-mediated oocyte maturation, parathyroid and growth hormone synthesis, cortisol synthesis and secretion, and signaling pathways for prolactin, TGF-beta, Hippo, MAPK, PI3K-Akt, and FoxO. Functional annotation of identified DEGs implicated important biological pathways. These findings provided insights into the genetic basis of fertility in female goats and are an impetus to elucidate molecular ceRNA regulatory networks and functions of DEGs underlying ovarian follicular development.
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Affiliation(s)
- Farzad Ghafouri
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mostafa Sadeghi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Masoumeh Naserkheil
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Animal Breeding and Genetics Division, National Institute of Animal Science, Cheonan-si, Republic of Korea
| | - Vahid Dehghanian Reyhan
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Arash Javanmard
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Seyed Reza Miraei-Ashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Soheila Ghahremani
- Department of Animal Science, Faculty of Agriculture, University of Tarbiat Modares, Tehran, Iran
| | - Herman W. Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Rostam Abdollahi-Arpanahi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - John P. Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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Xue H, Xu J, Wu M, Chen L, Xu L. Identification and sequence analysis of prolactin receptor and its differential expression profile at various developmental stages in striped hamsters. ACTA ACUST UNITED AC 2021; 54:e10274. [PMID: 33729390 PMCID: PMC7959167 DOI: 10.1590/1414-431x202010274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/16/2020] [Indexed: 11/22/2022]
Abstract
Prolactin (PRL) plays critical roles in regulation of biological functions with the binding of specific prolactin receptor (PRLR). Revealing the expression patterns of PRLR at different developmental stages is beneficial to better understand the role of PRL and its mechanism of action in striped hamsters. In this study, the cDNA sequence of PRLR (2866-base-pairs) was harvested from the pituitary of mature female striped hamsters (Cricetulus barabensis) that contains an 834-base-pair 5′-untranslated region (1-834 bp), a 1848-base-pair open reading frame (835-2682 bp), and a 184-base-pair 3′-untranslated region (2683-2866). The 1848-base-pair open reading frame encodes a mature prolactin-binding protein of 592 amino acids. In the mature PRLR, two prolactin-binding motifs, 12 cysteines, and five potential Asn-linked glycosylation sites were detected. Our results showed that the PRLR mRNA quantity in the hypothalamus, pituitary, ovaries, or testis was developmental-stage-dependent, with the highest level at sub-adult stage and the lowest level at old stage. We also found that PRLR mRNAs were highest in pituitary, medium level in hypothalamus, and lowest in ovaries or testis. PRLR mRNAs were significantly higher in males than in females, except in the hypothalamus and pituitary from 7-week-old striped hamsters. Moreover, the PRLR mRNAs in the hypothalamus, pituitary, and ovaries or testis were positively correlated with the expression levels of GnRH in the hypothalamus. These results indicated that the PRLR has conserved domain in striped hamster, but also possesses specific character. PRLR has multiple biological functions including positively regulating reproduction in the striped hamster.
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Affiliation(s)
- Huiliang Xue
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Jinhui Xu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Ming Wu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Lei Chen
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Laixiang Xu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
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Wang H, Khoradmehr A, Jalali M, Salehi MS, Tsutsui K, Jafarzadeh Shirazi MR, Tamadon A. The roles of RFamide-related peptides (RFRPs), mammalian gonadotropin-inhibitory hormone (GnIH) orthologues in female reproduction. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2018; 21:1210-1220. [PMID: 30627363 PMCID: PMC6312679 DOI: 10.22038/ijbms.2018.30520.7355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/21/2018] [Indexed: 01/12/2023]
Abstract
OBJECTIVES To benefit from reproduction and deal with challenges in the environmental conditions, animals must adapt internal physiology to maximize the reproduction rate. Maladaptive variations in the neurochemical systems and reproductive system can lead to manifestation of several significant mammalian reprocesses, including mammalian ovarian lifespan. RFamide-related peptide (RFRP, Rfrp), mammalian orthologues of gonadotropin-inhibitory hormone (GnIH), which is a regulator to prevent the gonadotropin-releasing hormone (GnRH) neural activity, is known to be related to reproductive traits. This review aimed to summarize recent five-year observations to outline historic insights and novel perspectives into the functions of RFRPs in coding the mammalian reproductive physiology, especially highlight recent advances in the impact on RFRPs in regulating mammalian ovary lifespan. MATERIALS AND METHODS We reviewed the recent five-year important findings of RFRP system involved in mammalian ovary development. Data for this review were collected from Google Scholar and PubMed using the RFRP keyword combined with the keywords related to physiological or pathological reproductive functions. RESULTS Recent discoveries are focused on three major fronts in research on RFRP role in female reproduction including reproductive functions, energy balance, and stress regulation. The roles of RFRPs in various development phases of mammal reproduction including prepuberty, puberty, estrous cycle, pregnancy, milking, menopause, and/or ovarian diseases have been shown. CONCLUSION Overall, these recent advances demonstrate that RFRPs serve as critical mediators in mammalian ovarian development.
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Affiliation(s)
- Huimei Wang
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences; Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Arezoo Khoradmehr
- Research and Clinical Center for Infertility, Yazd Reproduction Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Jalali
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad Saied Salehi
- Department of Physiology, Faculty of Biological Sciences and Technology, Shahid Beheshti University, Tehran, Iran
| | - Kazuyoshi Tsutsui
- Laboratory of Integrative Brain Sciences, Department of Biology and Center for Medical Life Science, Waseda University, Tokyo, Japan
| | | | - Amin Tamadon
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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Wang K, Yan H, Xu H, Yang Q, Zhang S, Pan C, Chen H, Zhu H, Liu J, Qu L, Lan X. A novel indel within goat casein alpha S1 gene is significantly associated with litter size. Gene 2018; 671:161-169. [PMID: 29864495 DOI: 10.1016/j.gene.2018.05.119] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 01/08/2023]
Abstract
The ruminant casein gene family (CSNs, link as CSN1S1-CSN2-CSN1S2-CSN3) is characterized by diverse variations and has been extensively studied for ruminant milk traits, however, studies on insertion/deletion (indel) mutations within this gene family and their effects on prolificacy are extremely limited. This study aimed to detect possible novel indels within CSNs in an indigenous Chinese goat breed-Shaanbei White Cashmere goat (SBWC, n = 3047) and four other Chinese goat breeds (n = 1136) with varied litter size rates (105%-283%) and different estrus types (seasonal vs. perennial), as well as exploring the association between these potential indels and litter size. Only one novel 11-bp indel within the CSN1S1 gene was found. The association analyses uncovered that this novel indel was related to the first-birth litter size of SBWC population (n = 2690) (P < 1.0 E-8). Individuals with the II genotype (n = 676) had the best litter size when compared with those ID genotype (n = 1098) and DD genotype (n = 916) individuals. Animals with the II genotype were found to have higher relative expression level of CSN1S1 gene in the ovary (P < 0.01). Besides, Chi-square tests for different litter size and estrous cycle breeds showed that perennial-estrus breeds and multi-kids breeds had higher "I" allelic frequencies and "II" genotypic frequencies. These findings suggest the 11-bp indel within the CSN1S1 gene is significantly associated with reproduction traits and can be an effective molecular marker for litter size of goat breeding.
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Affiliation(s)
- Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China; Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Han Xu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Qing Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China.
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Jinwang Liu
- Station of Veterinary and Animal Husbandry of Tong town of Jiaxian County, Jiaxian, Shaanxi, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China.
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Quillet R, Ayachi S, Bihel F, Elhabazi K, Ilien B, Simonin F. RF-amide neuropeptides and their receptors in Mammals: Pharmacological properties, drug development and main physiological functions. Pharmacol Ther 2016; 160:84-132. [PMID: 26896564 DOI: 10.1016/j.pharmthera.2016.02.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RF-amide neuropeptides, with their typical Arg-Phe-NH2 signature at their carboxyl C-termini, belong to a lineage of peptides that spans almost the entire life tree. Throughout evolution, RF-amide peptides and their receptors preserved fundamental roles in reproduction and feeding, both in Vertebrates and Invertebrates. The scope of this review is to summarize the current knowledge on the RF-amide systems in Mammals from historical aspects to therapeutic opportunities. Taking advantage of the most recent findings in the field, special focus will be given on molecular and pharmacological properties of RF-amide peptides and their receptors as well as on their implication in the control of different physiological functions including feeding, reproduction and pain. Recent progress on the development of drugs that target RF-amide receptors will also be addressed.
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Affiliation(s)
- Raphaëlle Quillet
- Biotechnologie et Signalisation Cellulaire, UMR 7242 CNRS, Université de Strasbourg, Illkirch, France
| | - Safia Ayachi
- Biotechnologie et Signalisation Cellulaire, UMR 7242 CNRS, Université de Strasbourg, Illkirch, France
| | - Frédéric Bihel
- Laboratoire Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, Illkirch, France
| | - Khadija Elhabazi
- Biotechnologie et Signalisation Cellulaire, UMR 7242 CNRS, Université de Strasbourg, Illkirch, France
| | - Brigitte Ilien
- Biotechnologie et Signalisation Cellulaire, UMR 7242 CNRS, Université de Strasbourg, Illkirch, France
| | - Frédéric Simonin
- Biotechnologie et Signalisation Cellulaire, UMR 7242 CNRS, Université de Strasbourg, Illkirch, France.
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Genome-wide transcriptome analysis in the ovaries of two goats identifies differentially expressed genes related to fecundity. Gene 2016; 582:69-76. [PMID: 26851539 DOI: 10.1016/j.gene.2016.01.047] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/06/2016] [Accepted: 01/28/2016] [Indexed: 12/20/2022]
Abstract
The goats are widely kept as livestock throughout the world. Two excellent domestic breeds in China, the Laiwu Black and Jining Grey goats, have different fecundities and prolificacies. Although the goat genome sequences have been resolved recently, little is known about the gene regulations at the transcriptional level in goat. To understand the molecular and genetic mechanisms related to the fecundities and prolificacies, we performed genome-wide sequencing of the mRNAs from two breeds of goat using the next-generation RNA-Seq technology and used functional annotation to identify pathways of interest. Digital gene expression analysis showed 338 genes were up-regulated in the Jining Grey goats and 404 were up-regulated in the Laiwu Black goats. Quantitative real-time PCR verified the reliability of the RNA-Seq data. This study suggests that multiple genes responsible for various biological functions and signaling pathways are differentially expressed in the two different goat breeds, and these genes might be involved in the regulation of goat fecundity and prolificacy. Taken together, our study provides insight into the transcriptional regulation in the ovaries of 2 species of goats that might serve as a key resource for understanding goat fecundity, prolificacy and genetic diversity between species.
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Zhao L, Zhong M, Xue HL, Ding JS, Wang S, Xu JH, Chen L, Xu LX. Effect of RFRP-3 on reproduction is sex- and developmental status-dependent in the striped hamster (Cricetulus barabensis). Gene 2014; 547:273-9. [DOI: 10.1016/j.gene.2014.06.054] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 06/07/2014] [Accepted: 06/24/2014] [Indexed: 10/25/2022]
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