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Lorenzatti A, Piga EJ, Gismondi M, Binolfi A, Margarit E, Calcaterra N, Armas P. Genetic variations in G-quadruplex forming sequences affect the transcription of human disease-related genes. Nucleic Acids Res 2023; 51:12124-12139. [PMID: 37930868 PMCID: PMC10711447 DOI: 10.1093/nar/gkad948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023] Open
Abstract
Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4s). G4s folded in proximal promoter regions (PPR) are associated either with positive or negative transcriptional regulation. Given that single nucleotide variants (SNVs) affecting G4 folding (G4-Vars) may alter gene transcription, and that SNVs are associated with the human diseases' onset, we undertook a novel comprehensive study of the G4-Vars genome-wide (G4-variome) to find disease-associated G4-Vars located into PPRs. We developed a bioinformatics strategy to find disease-related SNVs located into PPRs simultaneously overlapping with putative G4-forming sequences (PQSs). We studied five G4-Vars disturbing in vitro the folding and stability of the G4s located into PPRs, which had been formerly associated with sporadic Alzheimer's disease (GRIN2B), a severe familiar coagulopathy (F7), atopic dermatitis (CSF2), myocardial infarction (SIRT1) and deafness (LHFPL5). Results obtained in cultured cells for these five G4-Vars suggest that the changes in the G4s affect the transcription, potentially contributing to the development of the mentioned diseases. Collectively, data reinforce the general idea that G4-Vars may impact on the different susceptibilities to human genetic diseases' onset, and could be novel targets for diagnosis and drug design in precision medicine.
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Affiliation(s)
- Agustín Lorenzatti
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Ernesto J Piga
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Mauro Gismondi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Andrés Binolfi
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, Rosario S200EZP, Santa Fe, Argentina
| | - Ezequiel Margarit
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
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Moise-Silverman J, Silverman LA. A review of the genetics and epigenetics of central precocious puberty. Front Endocrinol (Lausanne) 2022; 13:1029137. [PMID: 36531492 PMCID: PMC9757059 DOI: 10.3389/fendo.2022.1029137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Gonadotrophin dependent sexual precocity, commonly referred to as central precocious puberty (CPP), results from a premature reactivation of the hypothalamic-pituitary-gonadal (HPG) axis before the normal age of pubertal onset. CPP is historically described as girls who enter puberty before the age of eight, and boys before the age of nine. Females are more likely to be diagnosed with idiopathic CPP; males diagnosed with CPP have a greater likelihood of a defined etiology. These etiologies may include underlying CNS congenital defects, tumors, trauma, or infections as well as environmental, genetic, and epigenetic factors. Recently, genetic variants and mutations which may cause CPP have been identified at both the level of the hypothalamus and the pituitary. Single nucleotide polymorphisms (SNPs), monogenetic mutations, and modifications of the epigenome have been evaluated in relationship to the onset of puberty; these variants are thought to affect the development, structure and function of GnRH neurons which may lead to either precocious, delayed, or absent pubertal reactivation. This review will describe recent advances in the field of the genetic basis of puberty and provide a clinically relevant approach to better understand these varying etiologies of CPP.
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Affiliation(s)
| | - Lawrence A. Silverman
- Division of Pediatric Endocrinology Goyreb Children’s Hospital – Atlantic Health System, Morristown, NJ, United States
- *Correspondence: Lawrence A. Silverman,
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Berthon A, Settas N, Delaney A, Giannakou A, Demidowich A, Faucz FR, Seminara SB, Chen ME, Stratakis CA. Kisspeptin deficiency leads to abnormal adrenal glands and excess steroid hormone secretion. Hum Mol Genet 2021; 29:3443-3450. [PMID: 33089319 DOI: 10.1093/hmg/ddaa215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 01/14/2023] Open
Abstract
Knockout mice for the kisspeptin receptor, Kiss1r (Kiss1r-/-) and its ligand kisspeptin, Kiss1 (Kiss1-/-) replicate the phenotype of isolated hypogonadotropic hypogonadism (IHH) associated with variants of these genes in humans. A recent report suggests that kisspeptin may be involved in human fetal adrenocortical development and function. Herein, we characterized the adrenal function and morphology in Kiss1-/- mice that do not go through normal puberty. Two fetal markers were expressed in eosinophilic cells potentially derived from the X-zone that should disappear at puberty in male mice and during the first pregnancy in female animals. Although the hypercorticosteronism observed in Kiss1-/- females corrected overtime, hyperaldosteronism persisted at 14 months and correlated with the overexpression of Star. To determine if KISS1 and KISS1R genes are involved in the development of primary aldosteronism (PA) and hypercortisolism [Cushing's syndrome (CS)] in humans, we sequenced these 2 genes in 65 patients with PA and/or CS. Interestingly, a patient with CS presented with a germline KISS1 variant (p.H90D, rs201073751). We also found three rare variants in the KISS1R gene in three patients with PA: p.C95W (rs141767649), p.A189T (rs73507527) and p.R229R (rs115335009). The two missense variants have been previously associated with IHH. Our findings suggest that KISS1 may play a role in adrenal function in mice and possibly adrenocortical steroid hormone secretion in humans, beyond its recently described role in human fetal adrenocortical development.
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Affiliation(s)
- Annabel Berthon
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), Bethesda, MD 20892, USA.,Institut Cochin, Centre National de la Recherche Scientifique (CNRS), INSERM, Université Paris Descartes, 75014 Paris, France
| | - Nikolaos Settas
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), Bethesda, MD 20892, USA
| | - Angela Delaney
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), Bethesda, MD 20892, USA.,Endocrinology Inter-Institute Training Programs, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Andreas Giannakou
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), Bethesda, MD 20892, USA
| | - Andrew Demidowich
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), Bethesda, MD 20892, USA
| | - Fabio R Faucz
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), Bethesda, MD 20892, USA
| | - Stephanie B Seminara
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA02114, USA
| | - Margaret E Chen
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA02114, USA
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics (SEGEN), Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), Bethesda, MD 20892, USA.,Endocrinology Inter-Institute Training Programs, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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Li X, Xiao J, Li K, Zhou Y. MiR-199-3p modulates the onset of puberty in rodents probably by regulating the expression of Kiss1 via the p38 MAPK pathway. Mol Cell Endocrinol 2020; 518:110994. [PMID: 32818586 DOI: 10.1016/j.mce.2020.110994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022]
Abstract
The Kiss1 gene plays an indispensable role in modulating the onset of puberty and fertility in mammals. Although an increasing number of genetic and environmental factors that influence reproduction through Kiss1 have been identified, the function of microRNAs, a class of posttranscriptional regulators, in regulating Kiss1 expression remains poorly understood. This study aimed at investigating the mechanism by which Kiss1 expression is regulated by microRNAs. A simplified miRNome screen by a dual-fluorescence reporter system based on Kiss1 was performed to identify microRNAs that affect the expression of Kiss1. The expression patterns of the identified microRNAs during the period of murine sexual development were investigated, and only miR-199-3p was studied further. Aided by bioinformatics algorithms, miR-199-3p was demonstrated to be a repressor of Kiss1 expression, as it blocked the expression of Kiss1 through the p38 MAPK pathway by simultaneously inhibiting several targets in both GT1-7 cells and primary hypothalamic neurons. Both the inhibition of the p38 MAPK pathway by the intracerebroventricular administration of chemical agents in rats and the ectopic expression of miR-199-3p by lentivirus injection in the hypothalamus in mice delayed puberty onset and gonad development. Our results presented a novel regulatory mechanism of puberty onset which the sustained downregulation of miR-199-3p might gradually release the inhibition of the p38 MAPK/Fos/CREB/Kiss1 pathway during puberty development.
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Affiliation(s)
- Xiaoning Li
- Key Laboratory of Science & Technology of Eco-Textile, Ministry of Education, Donghua University, Shanghai, China; College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China
| | - Junhua Xiao
- College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China
| | - Kai Li
- College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China
| | - Yuxun Zhou
- Key Laboratory of Science & Technology of Eco-Textile, Ministry of Education, Donghua University, Shanghai, China; College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China.
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Genome-wide association analysis reveals the genetic locus for high reproduction trait in Chinese Arbas Cashmere goat. Genes Genomics 2020; 42:893-899. [PMID: 32506265 DOI: 10.1007/s13258-020-00937-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Litter size is the most important reproductive trait which plays a crucial role in goat production. Therefore, improvement of litter size trait has been of increasing interest in goat industry as small improvement in litter size may lead to large profit. The recent Cashmere goat breeding program produced a high-reproductive genetic line of Arbas Cashmere goat. But the genetic mechanism of high reproduction rate remains largely unknown in this Chinese native goat breed. To address this question, we performed a genome-wide association studies (GWAS) using two groups of goats varying in fecundity. OBJECTIVES Our study was aimed to investigate the significant SNPs and genes associated with high reproduction trait in Inner Mongolia Arbas Cashmere Goat. METHODS We used logistic model association to perform GWAS using 47 goats from high fecundity group (~ 190%) and 314 goats from low fecundity group (~ 130%) of the Arbas Cashmere goat breed. RESULTS We identified 66 genomic regions associated with genome wide significant level wherein six loci were found to be associated with reproduction traits. Further analysis showed that five key candidate genes including KISS1, KHDRBS2, WNT10B, SETDB2 and PPP3CA genes are involved in goat fecundity trait. Gene ontology enrichment analysis revealed that several biological pathways could be involved in the variation of fecundity in female goats. CONCLUSIONS The identified significant SNPs or genes provide useful information about the underlying genetic control of fecundity trait which will be helpful to use them in goat breeding programs for improving the reproductive efficiency of goats.
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Sahoo SS, Mishra C, Kaushik R, Rout PK, Singh MK, Bhusan S, Dige MS. Association of a SNP in KISS 1 gene with reproductive traits in goats. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1608730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Siddhant Sekhar Sahoo
- Department of Animal Breeding and Genetics, College of Veterinary Science and Animal Husbandry, OUAT, Bhubaneswar, India
| | - Chinmoy Mishra
- Department of Animal Breeding and Genetics, College of Veterinary Science and Animal Husbandry, OUAT, Bhubaneswar, India
| | - Rakesh Kaushik
- Animal Genetics and Breeding Division, ICAR- Central Institute for Research on Goats, Mathura, India
| | - Pramod Kumar Rout
- Animal Genetics and Breeding Division, ICAR- Central Institute for Research on Goats, Mathura, India
| | - Manoj Kumar Singh
- Animal Genetics and Breeding Division, ICAR- Central Institute for Research on Goats, Mathura, India
| | - Saket Bhusan
- Animal Genetics and Breeding Division, ICAR- Central Institute for Research on Goats, Mathura, India
| | - Mahesh Shivanand Dige
- Animal Genetics and Breeding Division, ICAR- Central Institute for Research on Goats, Mathura, India
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Chen T, Chen L, Wu H, Xie R, Wang F, Chen X, Sun H, Xiao F. Low Frequency of MKRN3 and DLK1 Variants in Chinese Children with Central Precocious Puberty. Int J Endocrinol 2019; 2019:9879367. [PMID: 31687022 PMCID: PMC6794979 DOI: 10.1155/2019/9879367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/20/2019] [Accepted: 09/18/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Central precocious puberty (CPP) is defined by gonadotropin-dependent development of secondary sexual characteristics before the age of 8 years in girls and 9 years in boys. MKRN3 and DLK1 are two genes, disease-causing variants of which have recently been discovered to cause idiopathic CPP. METHODS We screened 173 Chinese patients (9 males and 164 females; 9 familial and 164 sporadic) with ICPP and 43 patients (9 males and 34 females; 3 familial and 40 sporadic) with early puberty for variants in MKRN3. We also screened 19 patients with ICPP and early puberty for variants of DLK1 (17 males and 2 females; 5 familial and 14 sporadic). RESULTS We identified four novel missense variants of MKRN3, c.1138G > A (p.Glu380Lys), c.1420T > A (p.Leu474Met), c.673C > G (p.Leu225Val), and c.1071C > G (p.Ile357Met) in two sporadic cases and three familial cases. According to ACMG standards, two MKRN3 variant (p.Glu380Lys and p.Ile357Met) are likely pathogenic, and two others are of uncertain significance. We also performed bioinformatic analysis to evaluate the impact of variants on MKRN3 protein structures, which showed that Ile357Met locates at the zinc-binding region (C3HC4 RING finger motif), while Glu380Lys is spatially extremely close to the C3HC4 RING finger, MKRN-specific Cys-His domain, and the third C3H1 zinc-finger motif region. Per Glu380Lys, Glu with negative charges has been changed into Lys with positive charges, which may affect the hydrogen bond formation between amino acids and the stability of the local structure, thus affecting the binding of zinc iron to MKRN3 protein. Besides, we did not identify any variants of DLK1 gene in our patients. CONCLUSIONS In this study, we report four novel MKRN3 variants in patients with ICPP. Moreover, we did not find any variants of DLK1 gene. Variants of MKRN3 are relatively uncommon in Chinese ICPP patients.
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Affiliation(s)
- Ting Chen
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Linqi Chen
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haiying Wu
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Rongrong Xie
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Fengyun Wang
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiuli Chen
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hui Sun
- Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Fei Xiao
- School of Basic Medicine & Biological Sciences, Medical College of Soochow University, Soochow University, Suzhou, Jiangsu, China
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Zhao Y, Wu J, Wang X, Jia H, Chen DN, Li JD. Prokineticins and their G protein-coupled receptors in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 161:149-179. [PMID: 30711026 DOI: 10.1016/bs.pmbts.2018.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prokineticins are two conserved small proteins (~8kDa), prokineticin 1 (PROK1; also called EG-VEGF) and prokineticin 2 (PROK2; also called Bv8), with an N-terminal AVITGA sequence and 10 cysteines forming 5 disulfide bridges. PROK1 and PROK2 bind to two highly related G protein-coupled receptors (GPCRs), prokineticin receptor 1 (PROKR1) and prokineticin receptor 2 (PROKR2). Prokineticins and their receptors are widely expressed. PROK1 is predominantly expressed in peripheral tissues, especially steroidogenic organs, whereas PROK2 is mainly expressed in the central nervous system and nonsteroidogenic cells of the testes. Prokineticins signaling has been implicated in several important physiological functions, including gastrointestinal smooth muscle contraction, circadian rhythm regulation, neurogenesis, angiogenesis, pain perception, mood regulation, and reproduction. Dysregulation of prokineticins signaling has been observed in a variety of diseases, such as cancer, ischemia, and neurodegeneration, in which prokineticins signaling seems to be a promising therapeutic target. Based on the phenotypes of knockout mice, PROKR2 and PROK2 have recently been identified as causative genes for idiopathic hypogonadotropic hypogonadism, a developmental disorder characterized by impaired development of gonadotropin-releasing hormone neurons and infertility. In vitro functional studies with these disease-associated PROKR2 mutations uncovered some novel features for this receptor, such as biased signaling, which may be used to understand GPCR signaling regulation in general.
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Affiliation(s)
- Yaguang Zhao
- School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China; Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Jiayu Wu
- School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China; Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Xinying Wang
- School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China; Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Hong Jia
- School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China; Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Dan-Na Chen
- Department of Basic Medical Sciences, Changsha Medical University, Changsha, China.
| | - Jia-Da Li
- School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China; Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China.
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Leka-Emiri S, Chrousos GP, Kanaka-Gantenbein C. The mystery of puberty initiation: genetics and epigenetics of idiopathic central precocious puberty (ICPP). J Endocrinol Invest 2017; 40:789-802. [PMID: 28251550 DOI: 10.1007/s40618-017-0627-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 01/25/2017] [Indexed: 01/04/2023]
Abstract
Puberty is a major developmental stage. Damaging mutations, considered as "mistakes of nature", have contributed to the unraveling of the networks implicated in the normal initiation of puberty. Genes involved in the abnormal hypothalamic-pituitary-gonadal (HPG) axis development, in the normosmic idiopathic hypogonadotropic hypogonadism (nIHH), in the X-linked or autosomal forms of Kallmann syndrome and in precocious puberty have been identified (GNRH1, GNRHR, KISS1, GPR54, FGFR1, FGF8, PROK2, PROKR2, TAC3, TACR3, KAL1, PROK2, PROKR2, CHD7, LEP, LEPR, PC1, DAX1, SF-1, HESX-1, LHX3, PROP-1). Most of them were found to play critical roles in HPG axis development and regulation, the embryonic GnRH neuronal migration and secretion, the regulation and action of the hypothalamic GnRH. However, the specific neural and molecular mechanisms triggering GnRH secretion remain one of the scientific enigmas. Although GnRH neurons are probably capable of autonomously generating oscillations, many gonadal steroid-dependent and -independent mechanisms have also been proposed. It is now well proven that the secretion of GnRH is regulated by kisspeptin as well as by permissive or opposing signals mediated by neurokinin B and dynorphin. These three supra-GnRH regulators compose the kisspeptin-neurokinin B-dynorphin neuronal (KNDy) system, a key player in pubertal onset and progression. Moreover, an ongoing increasing number of inhibitory, stimulatory and permissive networks acting upstream on GnRH neurons, such as GABA, NPY, LIN28B, MKRN3 and others integrate diverse hormonal and peripheral signals and have been proposed as the "gate-keepers" of puberty, while epigenetic modifications play also an important role in puberty initiation.
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Affiliation(s)
- Sofia Leka-Emiri
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, Faculty of Medicine, National and Kapodistrian University of Athens, Medical School, "Aghia Sofia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, Faculty of Medicine, National and Kapodistrian University of Athens, Medical School, "Aghia Sofia" Children's Hospital, Athens, Greece
| | - Christina Kanaka-Gantenbein
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, Faculty of Medicine, National and Kapodistrian University of Athens, Medical School, "Aghia Sofia" Children's Hospital, Athens, Greece.
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Zeydabadi Nejad S, Ramezani Tehrani F, Zadeh-Vakili A. The Role of Kisspeptin in Female Reproduction. Int J Endocrinol Metab 2017; 15:e44337. [PMID: 29201072 PMCID: PMC5702467 DOI: 10.5812/ijem.44337] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/20/2017] [Accepted: 03/09/2017] [Indexed: 02/05/2023] Open
Abstract
CONTEXT Kisspeptin (KISS1), a recently discovered neuropeptide that acts upstream of gonadotropin-releasing hormone (GnRH) neurons, is critical for maturation and function of the reproductive axis. This review aimed at providing comprehensive and up-to-date information on Kisspeptin and its role in female reproduction. EVIDENCE ACQUISITION A literature review was performed using PubMed for all English language articles published between 1999 and 2016. RESULTS The kisspeptin system (KISS1/G protein-coupled receptor-54,GPR54) has recently been addressed as an essential gatekeeper of puberty onset and gonadotropin secretion. Compelling evidence has documented that hypothalamic Kisspeptin mediates steroid feedback and metabolic cues at different developmental stages throughout lifespan. Furthermore, in pre/postnatally androgenized animal models, which exhibit many of the characteristics of Polycystic Ovarian Syndrome (PCOS), the hypothalamic expression of KISS1 and GnRH is abnormal, which might lead to multiple tissue abnormalities observed in this disorder. CONCLUSIONS Kisspeptin, a principal activator of GnRH neurons and the target of endocrine and metabolic cues, is a prerequisite for the onset of puberty and maintenance of normal reproductive function, as abnormal KISS1/GPR54 system has been reported in both animal models and patients with certain forms of infertility, e.g. Idiopathic Hypogonadotropic hypogonadism (IHH) and PCOS. The information suggests that kisspeptin or its receptor represents a potential therapeutic target in the treatment of patients with fertility disorders.
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Affiliation(s)
- Sareh Zeydabadi Nejad
- Reproductive Endocrinology Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, IR Iran
| | - Fahimeh Ramezani Tehrani
- Reproductive Endocrinology Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, IR Iran
| | - Azita Zadeh-Vakili
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, IR Iran
- Corresponding author: Azita Zadeh-Vakili, PhD, Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, IR Iran. Tel: +98-2122432513, Fax: +98-2122402463, E-mail:
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El-Tarabany MS, Zaglool AW, El-Tarabany AA, Awad A. Association analysis of polymorphism in KiSS1 gene with reproductive traits in goats. Anim Reprod Sci 2017; 180:92-99. [PMID: 28336267 DOI: 10.1016/j.anireprosci.2017.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 03/09/2017] [Accepted: 03/12/2017] [Indexed: 01/23/2023]
Abstract
Understanding the genetic information of related genes is helpful for the selection and breeding course through marker assisted selection. The aim of the current study was to detect polymorphisms of the KiSS1 gene in 137 animals, including Baladi, Zaraibi and Damascus goat breeds by PCR-RFLP, and DNA sequencing and to investigate the association between these variants and reproductive traits. Comparison of the nucleotide sequence indicated the substitution of T with A at position 121 (T121A) in the intron 1 of the KiSS1 gene in all goat breeds. This substitution distorts the restriction site of the XmnI restriction enzyme and consequently two genotypes were detected (TA and TT). The T121A SNP is associated significantly with litter size in Damascus and Zaribi breeds (p=0.025 and 0.001, respectively). The animals with the TT genotype in Damascus and Zaribi breeds had a significantly higher estradiol17β level than that recorded in TA genotype at estrus phase (p=0.013 and 0.028, respectively) and late-luteal phase (p=0.067 and 0.041, respectively) of the estrus cycle. Furthermore, animals with the TT genotype in Damascus and Zaribi breeds had significant higher progesterone level at mid-luteal (p=0.037 and 0.045, respectively) phase. Meanwhile, there were no significant differences in progesterone level in late-luteal phase between both genotypes in Zaribi breed (p=0.267). The current trial indicated that the prolific TT genotype in both Damascus and Zaribi breeds had superior estradiol17β level at estrus phase and an eminent progesterone level at both early and mid-luteal phases of the estrous cycle.
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Affiliation(s)
- Mahmoud S El-Tarabany
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Zagazig University, Sharkia, Egypt.
| | - Asmaa W Zaglool
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Zagazig University, Sharkia, Egypt
| | - Akram A El-Tarabany
- Biological Applications Department, Radioisotopes Applications Division, NRC, Atomic Energy Authority, Inshas, Cairo, Egypt
| | - Ashraf Awad
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Zagazig University, Sharkia, Egypt
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Ortiz-Cabrera NV, Riveiro-Álvarez R, López-Martínez MÁ, Pérez-Segura P, Aragón-Gómez I, Trujillo-Tiebas MJ, Soriano-Guillén L. Clinical Exome Sequencing Reveals MKRN3 Pathogenic Variants in Familial and Nonfamilial Idiopathic Central Precocious Puberty. Horm Res Paediatr 2016; 87:88-94. [PMID: 27931036 DOI: 10.1159/000453262] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/04/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Idiopathic central precocious puberty (ICPP) is the premature activation of the hypothalamic-pituitary-gonadal axis in the absence of organic disease. Up to now, just gain-of-function mutations of KISS1/KISS1R and loss-of-function mutations of the maternally imprinted gene MKRN3 are the known genetic causes of ICPP. Our intention is to evaluate variants present in genes related to the pubertal onset pathway that could act as disease-causing or predisposing variants. METHODS We studied the clinical exome of 20 patients diagnosed with ICPP using the Illumina platform. The bioinformatics analysis was performed using 2 different programs, and the variants were filtered according to a list of genes related to the gonadotropin-releasing hormone pathway. RESULTS In a "sporadic case," we found a missense variant in MKRN3 NM_005664.3: c.203G>A, causing the protein change NP_005655.1:p.Arg68His, predicted as pathogenic by 2 informatics tools. The proband carrying this variant was diagnosed with ICPP at 7.75 years of age. We did not find any pathogenic variants in KISS1, KISS1R, LIN28, GNRH, GNRHR, TACR3, and TAC3. CONCLUSION MKRN3 is the most frequent genetic cause of familial ICPP, so it is wise to screen for MKRN3 mutations in all patients with familial ICPP and in patients with an unclear paternal pubertal history.
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Polymorphism and DNA methylation in the promoter modulate KISS1 gene expression and are associated with litter size in goats. Anim Reprod Sci 2015; 155:36-41. [DOI: 10.1016/j.anireprosci.2015.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/26/2015] [Accepted: 01/30/2015] [Indexed: 12/22/2022]
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Polymorphisms rs12998 and rs5780218 in KiSS1 suppressor metastasis gene in Mexican patients with breast cancer. DISEASE MARKERS 2015; 2015:365845. [PMID: 25810563 PMCID: PMC4355114 DOI: 10.1155/2015/365845] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 01/26/2015] [Accepted: 02/04/2015] [Indexed: 01/30/2023]
Abstract
AIMS KiSS1 is a metastasis suppressor gene associated with inhibition of cellular chemotaxis and invasion attenuating the metastasis in melanoma and breast cancer cell lines. Along the KiSS-1 gene at least 294 SNPs have been described; however the association of these polymorphisms as genetic markers for metastasis in breast cancer studies has not been investigated. Here we describe two simple PCR-RFLPs protocols to identify the rs5780218 (9DelT) and the rs12998 (E20K) KiSS1 polymorphisms and the allelic, genotypic, and haplotypic frequencies in Mexican general population (GP) and patients with benign breast disease (BBD) or breast cancer (BC). RESULTS The rs5780218 polymorphism was individually associated with breast cancer (P = 0.0332) and the rs12998 polymorphism shows statistically significant differences when GP versus case (BC and BBD) groups were compared (P < 0.0001). The H1 Haplotype (G/-) occurred more frequently in BC group (0.4256) whereas H2 haplotype (G/T) was the most prevalent in BBD group (0.4674). CONCLUSIONS Our data indicated that the rs5780218 polymorphism individually confers susceptibility for development of breast cancer in Mexican population and a possible role as a genetic marker in breast cancer metastasis for H1 haplotype (Wt/variant) in KiSS1 gene must be analyzed in other populations.
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Leka-Emiri S, Louizou E, Kambouris M, Chrousos G, De Roux N, Kanaka-Gantenbein C. Absence of GPR54 and TACR3 mutations in sporadic cases of idiopathic central precocious puberty. Horm Res Paediatr 2014; 81:177-81. [PMID: 24434351 DOI: 10.1159/000356913] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Kisspeptin (KISS1)/GPR54 (KISSR) signaling complex and neurokinin B (NKB)/NKB receptor (TACR3) signaling have been proposed as an integral part of the network coordinating GnRH release. GPR54 (KISS1R) and TACR3 gene mutations have been described in cases of idiopathic hypogonadotrophic hypogonadism, while limited data exist on gain-of-function mutation in GPR54 (KISS1R) gene causing idiopathic central precocious puberty (ICPP). No data on TACR3 mutations in ICPP have been described so far. The aim of this study was to elucidate the possible impact of GPR54 (KISS1R) and TACR3 mutations in ICPP. METHODS PCR-amplified genomic DNA of 38 girls with ICPP was analyzed for GPR54 and TACR3 gene mutations. RESULTS No GPR54 or TACR3 mutations were found. The A/G coding sequence single nucleotide polymorphism (SNP) on the GPR54 gene (dbSNP ID: rs10407968) was found in 2 patients with ICPP. CONCLUSION Our data indicate that GPR54 and TACR3 gene mutations are not a frequent cause of ICPP. The identified A/G synonymous SNP (dbSNP ID: rs10407968) located in exon 1 of the gene is not likely to have a pathogenic role in exon splicing and therefore in the premature initiation of puberty.
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Affiliation(s)
- Sofia Leka-Emiri
- Division of Endocrinology, Metabolism and Diabetes, 1st Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens, Greece
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Association analysis of polymorphisms in caprine KiSS1 gene with reproductive traits. Anim Reprod Sci 2014; 151:71-7. [DOI: 10.1016/j.anireprosci.2014.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 09/01/2014] [Accepted: 09/16/2014] [Indexed: 11/19/2022]
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Frees S, Menendez C, Crum M, Bagga PS. QGRS-Conserve: a computational method for discovering evolutionarily conserved G-quadruplex motifs. Hum Genomics 2014; 8:8. [PMID: 24885782 PMCID: PMC4017754 DOI: 10.1186/1479-7364-8-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 04/21/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Nucleic acids containing guanine tracts can form quadruplex structures via non-Watson-Crick base pairing. Formation of G-quadruplexes is associated with the regulation of important biological functions such as transcription, genetic instability, DNA repair, DNA replication, epigenetic mechanisms, regulation of translation, and alternative splicing. G-quadruplexes play important roles in human diseases and are being considered as targets for a variety of therapies. Identification of functional G-quadruplexes and the study of their overall distribution in genomes and transcriptomes is an important pursuit. Traditional computational methods map sequence motifs capable of forming G-quadruplexes but have difficulty in distinguishing motifs that occur by chance from ones which fold into G-quadruplexes. RESULTS We present Quadruplex forming 'G'-rich sequences (QGRS)-Conserve, a computational method for calculating motif conservation across exomes and supports filtering to provide researchers with more precise methods of studying G-quadruplex distribution patterns. Our method quantitatively evaluates conservation between quadruplexes found in homologous nucleotide sequences based on several motif structural characteristics. QGRS-Conserve also efficiently manages overlapping G-quadruplex sequences such that the resulting datasets can be analyzed effectively. CONCLUSIONS We have applied QGRS-Conserve to identify a large number of G-quadruplex motifs in the human exome conserved across several mammalian and non-mammalian species. We have successfully identified multiple homologs of many previously published G-quadruplexes that play post-transcriptional regulatory roles in human genes. Preliminary large-scale analysis identified many homologous G-quadruplexes in the 5'- and 3'-untranslated regions of mammalian species. An expectedly smaller set of G-quadruplex motifs was found to be conserved across larger phylogenetic distances. QGRS-Conserve provides means to build datasets that can be filtered and categorized in a variety of biological dimensions for more targeted studies in order to better understand the roles that G-quadruplexes play.
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Affiliation(s)
- Scott Frees
- Department of Computer Science, Ramapo College of New Jersey, 505 Ramapo Valley Road, Mahwah, NJ 08807, USA
| | - Camille Menendez
- Department of Bioinformatics, Ramapo College of New Jersey, 505 Ramapo Valley Road, Mahwah, NJ 08807, USA
| | - Matt Crum
- Department of Bioinformatics, Ramapo College of New Jersey, 505 Ramapo Valley Road, Mahwah, NJ 08807, USA
| | - Paramjeet S Bagga
- Department of Bioinformatics, Ramapo College of New Jersey, 505 Ramapo Valley Road, Mahwah, NJ 08807, USA
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Bagga JS, D’Antonio LA. Role of conserved cis-regulatory elements in the post-transcriptional regulation of the human MECP2 gene involved in autism. Hum Genomics 2013; 7:19. [PMID: 24040966 PMCID: PMC3844687 DOI: 10.1186/1479-7364-7-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/04/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The MECP2 gene codes for methyl CpG binding protein 2 which regulates activities of other genes in the early development of the brain. Mutations in this gene have been associated with Rett syndrome, a form of autism. The purpose of this study was to investigate the role of evolutionarily conserved cis-elements in regulating the post-transcriptional expression of the MECP2 gene and to explore their possible correlations with a mutation that is known to cause mental retardation. RESULTS A bioinformatics approach was used to map evolutionarily conserved cis-regulatory elements in the transcribed regions of the human MECP2 gene and its mammalian orthologs. Cis-regulatory motifs including G-quadruplexes, microRNA target sites, and AU-rich elements have gained significant importance because of their role in key biological processes and as therapeutic targets. We discovered in the 5'-UTR (untranslated region) of MECP2 mRNA a highly conserved G-quadruplex which overlapped a known deletion in Rett syndrome patients with decreased levels of MeCP2 protein. We believe that this 5'-UTR G-quadruplex could be involved in regulating MECP2 translation. We mapped additional evolutionarily conserved G-quadruplexes, microRNA target sites, and AU-rich elements in the key sections of both untranslated regions. Our studies suggest the regulation of translation, mRNA turnover, and development-related alternative MECP2 polyadenylation, putatively involving interactions of conserved cis-regulatory elements with their respective trans factors and complex interactions among the trans factors themselves. We discovered highly conserved G-quadruplex motifs that were more prevalent near alternative splice sites as compared to the constitutive sites of the MECP2 gene. We also identified a pair of overlapping G-quadruplexes at an alternative 5' splice site that could potentially regulate alternative splicing in a negative as well as a positive way in the MECP2 pre-mRNAs. CONCLUSIONS A Rett syndrome mutation with decreased protein expression was found to be associated with a conserved G-quadruplex. Our studies suggest that MECP2 post-transcriptional gene expression could be regulated by several evolutionarily conserved cis-elements like G-quadruplex motifs, microRNA target sites, and AU-rich elements. This phylogenetic analysis has provided some interesting and valuable insights into the regulation of the MECP2 gene involved in autism.
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Affiliation(s)
- Joetsaroop S Bagga
- John P. Stevens High School, 855 Grove Ave., Edison, NJ 08820, USA
- Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, USA
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An X, Ma T, Hou J, Fang F, Han P, Yan Y, Zhao H, Song Y, Wang J, Cao B. Association analysis between variants in KISS1 gene and litter size in goats. BMC Genet 2013; 14:63. [PMID: 23915023 PMCID: PMC3734198 DOI: 10.1186/1471-2156-14-63] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 07/25/2013] [Indexed: 12/20/2022] Open
Abstract
Background Kisspeptins are the peptide products of KISS1 gene, which operate via the G - protein-coupled receptor GPR54. These peptides have emerged as essential upstream regulators of neurons secreting gonadotropin-releasing hormone (GnRH), the major hypothalamic node for the stimulatory control of the hypothalamic–pituitary– gonadal (HPG) axis. The present study detected the polymorphisms of caprine KISS1 gene in three goat breeds and investigated the associations between these genetic markers and litter size. Results Three goat breeds (n = 680) were used to detect single nucleotide polymorphisms (SNPs) in the coding regions with their intron–exon boundaries and the proximal flanking regions of KISS1 gene by DNA sequencing and PCR–RFLP. Eleven novel SNPs (g.384G>A, g.1147T>C, g.1417G>A, g.1428_1429delG, g.2124C>T, g.2270C>T, g.2489T>C, g.2510G>A, g.2540C>T, g.3864_3865delCA and g.3885_3886insACCCC) were identified. It was shown that Xinong Saanen and Guanzhong goat breeds were in Hardy-Weinberg disequilibrium at g.384G>A locus (P < 0.05). Both g.2510G>A and g.2540C>T loci were closely linked in Xinong Saanen (SN), Guanzhong (GZ) and Boer (BG) goat breeds (r2 > 0.33). The g.384G>A, g.2489T>C, g.2510G>A and g.2540C>T SNPs were associated with litter size (P<0.05). Individuals with AATTAATT combinative genotype of SN breed (SC) and TTAATT combinative genotype of BG breed (BC) had higher litter size than those with other combinative genotypes in average parity. The results extend the spectrum of genetic variation of the caprine KISS1 gene, which might contribute to goat genetic resources and breeding. Conclusions This study explored the genetic polymorphism of KISS1 gene, and indicated that four SNPs may play an important role in litter size. Their genetic mechanism of reproduction in goat breeds should be further investigated. The female goats with SC1 (AATTAATT) and BC7 (TTAATT) had higher litter size than those with other combinative genotypes in average parity and could be used for the development of new breeds of prolific goats. Further research on a large number of animals is required to confirm the link with increased prolificacy in goats.
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Affiliation(s)
- Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
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Menendez C, Frees S, Bagga PS. QGRS-H Predictor: a web server for predicting homologous quadruplex forming G-rich sequence motifs in nucleotide sequences. Nucleic Acids Res 2012; 40:W96-W103. [PMID: 22576365 PMCID: PMC3394323 DOI: 10.1093/nar/gks422] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Naturally occurring G-quadruplex structural motifs, formed by guanine-rich nucleic acids, have been reported in telomeric, promoter and transcribed regions of mammalian genomes. G-quadruplex structures have received significant attention because of growing evidence for their role in important biological processes, human disease and as therapeutic targets. Lately, there has been much interest in the potential roles of RNA G-quadruplexes as cis-regulatory elements of post-transcriptional gene expression. Large-scale computational genomics studies on G-quadruplexes have difficulty validating their predictions without laborious testing in 'wet' labs. We have developed a bioinformatics tool, QGRS-H Predictor that can map and analyze conserved putative Quadruplex forming 'G'-Rich Sequences (QGRS) in mRNAs, ncRNAs and other nucleotide sequences, e.g. promoter, telomeric and gene flanking regions. Identifying conserved regulatory motifs helps validate computations and enhances accuracy of predictions. The QGRS-H Predictor is particularly useful for mapping homologous G-quadruplex forming sequences as cis-regulatory elements in the context of 5'- and 3'-untranslated regions, and CDS sections of aligned mRNA sequences. QGRS-H Predictor features highly interactive graphic representation of the data. It is a unique and user-friendly application that provides many options for defining and studying G-quadruplexes. The QGRS-H Predictor can be freely accessed at: http://quadruplex.ramapo.edu/qgrs/app/start.
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Affiliation(s)
- Camille Menendez
- Bioinformatics and Computer Science, School of Theoretical and Applied Science, Ramapo College of New Jersey, Mahwah, NJ 07430, USA
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