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Atrian-Afiani F, Berger B, Draxl C, Sölkner J, Mészáros G. Selective Sweeps in the Austrian Turopolje and Other Commercial Pig Populations. Animals (Basel) 2023; 13:3749. [PMID: 38136787 PMCID: PMC10741191 DOI: 10.3390/ani13243749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
The goal of our study was to identify signatures of selection in the Turopolje pigs and other commercial pig breeds. We conducted a comprehensive analysis of five datasets, including one local pig breed (Turopolje) and four commercial pig breeds (Large White, Landrace, Pietrain, and Duroc), using strict quality control measures. Our final dataset consisted of 485 individuals and 54,075 single nucleotide polymorphisms (SNPs). To detect selection signatures within these pig breeds, we utilized the XP-EHH and XP-nSL methodologies, which allowed us to identify candidate genes that have been subject to positive selection. Our analysis consistently highlighted the PTBP2 and DPYD genes as commonly targeted by selection in the Turopolje breed. DPYD is associated with muscular development in pigs and other species and PTBP2 emerges as one of the potential genes linked to seminal characteristics. Furthermore, in the Large White breed, a number of genes were detected with the two methods, such as ATP1A1, CASQ2, CD2, IGSF3, MAB21L3, NHLH2, SLC22A15, VANGL1. In the Duroc breed, a different set of genes was detected, such as ARSB, BHMT, BHMT2, DMGDH, JMY. The function of these genes was related to body weight, production efficiency and meat quality, average daily gain, and other similar traits. Overall, our results have identified a number of genomic regions that are under selective pressure between local and commercial pig breeds. This information can help to improve our understanding of the mechanisms underlying pig breeding, and ultimately contribute to the development of more efficient and sustainable pig production practices. Our study highlights the power of using multiple genomic methodologies to detect genetic signatures of selection, and provides important insights into the genetic diversity of pig breeds.
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Affiliation(s)
- Farzad Atrian-Afiani
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; (F.A.-A.); (J.S.)
| | - Beate Berger
- Institut für Biologische Landwirtschaft und Biodiversität der Nutztiere, HBLFA Raumberg-Gumpenstein 2, 4600 Thalheim bei Wels, Austria;
| | - Christian Draxl
- Österreichische Schweineprüfanstalt GmbH, 2004 Streitdorf, Austria;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; (F.A.-A.); (J.S.)
| | - Gábor Mészáros
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; (F.A.-A.); (J.S.)
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In Silico Examination of Single Nucleotide Missense Mutations in NHLH2, a Gene Linked to Infertility and Obesity. Int J Mol Sci 2023; 24:ijms24043193. [PMID: 36834605 PMCID: PMC9968165 DOI: 10.3390/ijms24043193] [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: 12/29/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Continual advances in our understanding of the human genome have led to exponential increases in known single nucleotide variants. The characterization of each of the variants lags behind. For researchers needing to study a single gene, or multiple genes in a pathway, there must be ways to narrow down pathogenic variants from those that are silent or pose less pathogenicity. In this study, we use the NHLH2 gene which encodes the nescient helix-loop-helix 2 (Nhlh2) transcription factor in a systematic analysis of all missense mutations to date in the gene. The NHLH2 gene was first described in 1992. Knockout mice created in 1997 indicated a role for this protein in body weight control, puberty, and fertility, as well as the motivation for sex and exercise. Only recently have human carriers of NHLH2 missense variants been characterized. Over 300 missense variants for the NHLH2 gene are listed in the NCBI single nucleotide polymorphism database (dbSNP). Using in silico tools, predicted pathogenicity of the variants narrowed the missense variants to 37 which were predicted to affect NHLH2 function. These 37 variants cluster around the basic-helix-loop-helix and DNA binding domains of the transcription factor, and further analysis using in silico tools provided 21 SNV resulting in 22 amino acid changes for future wet lab analysis. The tools used, findings, and predictions for the variants are discussed considering the known function of the NHLH2 transcription factor. Overall use of these in silico tools and analysis of these data contribute to our knowledge of a protein which is both involved in the human genetic syndrome, Prader-Willi syndrome, and in controlling genes involved in body weight control, fertility, puberty, and behavior in the general population, and may provide a systematic methodology for others to characterize variants for their gene of interest.
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Topaloglu AK, Simsek E, Kocher MA, Mammadova J, Bober E, Kotan LD, Turan I, Celiloglu C, Gurbuz F, Yuksel B, Good DJ. Inactivating NHLH2 variants cause idiopathic hypogonadotropic hypogonadism and obesity in humans. Hum Genet 2022; 141:295-304. [PMID: 35066646 DOI: 10.1007/s00439-021-02422-9] [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: 11/05/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022]
Abstract
Metabolism has a role in determining the time of pubertal development and fertility. Nonetheless, molecular/cellular pathways linking metabolism/body weight to puberty/reproduction are unknown. The KNDy (Kisspeptin/Neurokinin B/Dynorphin) neurons in the arcuate nucleus of the hypothalamus constitute the GnRH (gonadotropin-releasing hormone) pulse generator. We previously created a mouse model with a whole-body targeted deletion of nescient helix-loop-helix 2 (Nhlh2; N2KO), a class II member of the basic helix-loop-helix family of transcription factors. As this mouse model features pubertal failure and late-onset obesity, we wanted to study whether NHLH2 represents a candidate molecule to link metabolism and puberty in the hypothalamus. Exome sequencing of a large Idiopathic Hypogonadotropic Hypogonadism cohort revealed obese patients with rare sequence variants in NHLH2, which were characterized by in-silico protein analysis, chromatin immunoprecipitation, and luciferase reporter assays. In vitro heterologous expression studies demonstrated that the variant p.R79C impairs Nhlh2 binding to the Mc4r promoter. Furthermore, p.R79C and other variants show impaired transactivation of the human KISS1 promoter. These are the first inactivating human variants that support NHLH2's critical role in human puberty and body weight control. Failure to carry out this function results in the absence of pubertal development and late-onset obesity in humans.
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Affiliation(s)
- A Kemal Topaloglu
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Mississippi Medical Center, Jackson, MS, USA.
- Department of Neurobiology and Anatomical Sciences, University of Mississippi Medical Center, Jackson, MS, USA.
| | - Enver Simsek
- Division of Pediatric Endocrinology, Faculty of Medicine, Eskisehir Osman Gazi University, Eskisehir, Turkey
| | - Matthew A Kocher
- Translational Biology, Medicine and Health Graduate Program, Virginia Tech, Roanoke, VA, USA
| | - Jamala Mammadova
- Division of Pediatric Endocrinology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Ece Bober
- Division of Pediatric Endocrinology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Leman Damla Kotan
- Division of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Ihsan Turan
- Division of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Can Celiloglu
- Division of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Fatih Gurbuz
- Division of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Bilgin Yuksel
- Division of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Deborah J Good
- Translational Biology, Medicine and Health Graduate Program, Virginia Tech, Roanoke, VA, USA
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
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Kocher MA, Huang FW, Le E, Good DJ. Snord116 Post-transcriptionally Increases Nhlh2 mRNA Stability: Implications for Human Prader-Willi Syndrome. Hum Mol Genet 2021; 30:1101-1110. [PMID: 33856031 DOI: 10.1093/hmg/ddab103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/25/2022] Open
Abstract
The smallest genomic region causing Prader-Willi Syndrome (PWS) deletes the non-coding RNA SNORD116 cluster; however, the function of SNORD116 remains a mystery. Previous work in the field revealed the tantalizing possibility that expression of NHLH2, a gene previously implicated in both obesity and hypogonadism, was downregulated in PWS patients and differentiated stem cells. In silico RNA: RNA modeling identified several potential interaction domains between SNORD116 and NHLH2 mRNA. One of these interaction domains was highly conserved in most vertebrate NHLH2 mRNAs examined. A construct containing the Nhlh2 mRNA, including its 3'-UTR, linked to a c-myc tag was transfected into a hypothalamic neuron cell line in the presence and absence of exogenously-expressed Snord116. Nhlh2 mRNA expression was upregulated in the presence of Snord116 dependent on the length and type of 3'UTR used on the construct. Furthermore, use of actinomycin D to stop new transcription in N29/2 cells demonstrated that the upregulation occurred through increased stability of the Nhlh2 mRNA in the 45 minutes immediately following transcription. In silico modeling also revealed that a single nucleotide variant (SNV) in the NHLH2 mRNA could reduce the predicted interaction strength of the NHLH2:SNORD116 diad. Indeed, use of an Nhlh2 mRNA construct containing this SNV significantly reduces the ability of Snord116 to increase Nhlh2 mRNA levels. For the first time, these data identify a motif and mechanism for SNORD116-mediated regulation of NHLH2, clarifying the mechanism by which deletion of the SNORD116 snoRNAs locus leads to PWS phenotypes.
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Affiliation(s)
- Matthew A Kocher
- Translational Biology, Medicine and Health Graduate Program, 1 Riverside Circle, Virginia Tech, Roanoke, VA 24016
| | - Fenix W Huang
- Biocomplexity Institute & Initiative, University of Virginia, 995 Research Park Blvd, Town Center III, 4th Floor, Charlottesville, VA 22911
| | - Erin Le
- Department of Human Nutrition, Foods, and Exercise, 1981 Kraft Drive (0913), Integrated Life Sciences Building, Virginia Tech, Blacksburg, VA 24060
| | - Deborah J Good
- Translational Biology, Medicine and Health Graduate Program, 1 Riverside Circle, Virginia Tech, Roanoke, VA 24016.,Department of Human Nutrition, Foods, and Exercise, 1981 Kraft Drive (0913), Integrated Life Sciences Building, Virginia Tech, Blacksburg, VA 24060
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Good DJ, Zhang H, Grange RW, Braun T. Pro-opiomelanocortin Neurons and the Transcriptional Regulation of Motivated Exercise. Exerc Sport Sci Rev 2020; 48:74-82. [DOI: 10.1249/jes.0000000000000219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Senba E, Kami K. A new aspect of chronic pain as a lifestyle-related disease. NEUROBIOLOGY OF PAIN 2017; 1:6-15. [PMID: 31194049 PMCID: PMC6550110 DOI: 10.1016/j.ynpai.2017.04.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 04/14/2017] [Indexed: 12/22/2022]
Abstract
Activation of mesolimbic dopamine system underlies exercise-induced hypoalgesia. Interaction between mesolimbic system and hypothalamus determines physical activity. Changing the lifestyle inactive to active may attenuate and prevent chronic pain.
Physical exercise has been established as a low-cost, safe, and effective way to manage chronic intractable pain. We investigated the underlying mechanisms of exercise-induced hypoalgesia (EIH) using a mouse model of neuropathic pain (NPP). Epigenetic changes in activated microglia and maintained GABA synthesis in the spinal dorsal horn may contribute to EIH. Voluntary exercise (VE), a strong reward for animals, also induced EIH, which may be due in part to the activation of dopamine (DA) neurons in the ventral tegmental area (VTA). VE increases the expression of pCREB in dopaminergic neurons in the VTA, which would enhance dopamine production, and thereby contributes to the activation of the mesolimbic reward system in NPP model mice. We demonstrated that neurons in the laterodorsal tegmental and pedunculopontine tegmental nuclei, a major input source of rewarding stimuli to the VTA, were activated by exercise. Chronic pain is at least partly attributed to sedentary and inactive lifestyle as indicated by the Fear-avoidance model. Therefore, chronic pain could be recognized as a lifestyle-related disease. Physical activity/inactivity may be determined by genetic/epigenetic and neural factors encoded in our brain. The hypothalamus and reward system is closely related in the axis of food intake, energy metabolism and physical activity. Understanding the interactions between the mesolimbic DA system and the hypothalamus that sense and regulate energy balance is thus of significant importance. For example, proopiomelanocortin neurons and melanocortin 4 receptors may play a role in connecting these two systems. Therefore, in a certain sense, chronic pain and obesity may share common behavioral and neural pathology, i.e. physical inactivity, as a result of inactivation of the mesolimbic DA system. Exercise and increasing physical activity in daily life may be important in treating and preventing chronic pain, a life-style related disease.
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Key Words
- CBP, chronic low back pain
- Chronic pain
- DA, dopamine
- Dopamine
- Exercise-induced hypoalgesia
- FM, fibromyalgia
- GABA, gamma-aminobutyric acid
- HDAC, histone deacetylase
- LDT, laterodorsal tegmental nucleus
- LH, lateral hypothalamus
- LHb, lateral habenula
- Laterodorsal tegmental nucleus
- NAc, nucleus accumbens
- NPP, neuropathic pain
- PPTg, pedunculopontine tegmental nucleus
- PSL, partial sciatic nerve ligation
- Physical activity/inactivity
- RMTg, rostromedial tegmental nucleus
- TH, tyrosine hydroxylase
- TMD, temporomandibular disorder
- VTA, ventral tegmental area
- VWR, voluntary wheel running
- Ventral tegmental area
- delta FosB, delta FBJ murine osteosarcoma viral
- mPFC, medial prefrontal cortex
- pCREB, phosphorylated cyclic AMP response element-binding protein
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Affiliation(s)
- Emiko Senba
- Department of Physical Therapy, Osaka Yukioka College of Health Science, 1-1-41 Sojiji, Ibaraki-City, Osaka 567-0801, Japan.,Department of Rehabilitation Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama City, Wakayama 641-8509, Japan
| | - Katsuya Kami
- Department of Rehabilitation Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama City, Wakayama 641-8509, Japan
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Analysis of g.265T>C SNP of fatty acid synthase gene and expression study in skeletal muscle and backfat tissues of Italian Large White and Italian Duroc pigs. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Good DJ, Braun T. NHLH2: at the intersection of obesity and fertility. Trends Endocrinol Metab 2013; 24:385-90. [PMID: 23684566 PMCID: PMC3732504 DOI: 10.1016/j.tem.2013.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/15/2013] [Accepted: 04/17/2013] [Indexed: 11/28/2022]
Abstract
Nescient helix-loop-helix 2 (NHLH2/NSCL2) is a neuronal transcription factor originally thought to be involved in neuronal development and childhood neuroblastomas. Accumulating evidence has since identified roles for NHLH2 in adult phenotypes of obesity and fertility. We summarize these findings here and attempt to link genotype with phenotype in mouse models and humans. In particular, NHLH2 (Nhlh2 in mice) is one of only two genes that are genetically linked to physical activity levels. Nhlh2 also controls obesity and fertility, with strong sexual dimorphism for both phenotypes in Nhlh2 mutant animals. We propose that Nhlh2 might function as a molecular sensor in different adult hypothalamic neurons to regulate energy balance, leading to normal body weight and reproduction.
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Affiliation(s)
- Deborah J Good
- Department of Human Nutrition, Foods and Exercise, Virginia Tech University, Blacksburg, VA 24061, USA.
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