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Qu L, Shen M, Guo J, Wang X, Dou T, Hu Y, Li Y, Ma M, Wang K, Liu H. Identification of potential genomic regions and candidate genes for egg albumen quality by a genome-wide association study. Arch Anim Breed 2019; 62:113-123. [PMID: 31807621 PMCID: PMC6853030 DOI: 10.5194/aab-62-113-2019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 03/05/2019] [Indexed: 11/17/2022] Open
Abstract
Albumen
quality is a leading economic trait in the chicken industry. Major studies have paid
attention to genetic architecture underlying albumen quality. However, the putative
quantitative trait locus (QTL) for this trait is still unclear. In this genome-wide
association study, we used an F2 resource population to study longitudinal albumen
quality. Seven single-nucleotide polymorphism (SNP) loci were found to be significantly
(p<8.43×10-7) related to albumen quality by univariate analysis,
while 11 SNPs were significantly (p<8.43×10-7) associated with
albumen quality by multivariate analysis. A QTL on GGA4 had a pervasive function on
albumen quality, including a SNP at the missense of NCAPG, and a SNP at the
intergenic region of FGFPB1. It was further found that the putative QTLs at
GGA1, GGA2, and GGA7 had the strongest effects on albumen height (AH) at 32 weeks, Haugh
units (HU) at 44 weeks, and AH at 55 weeks. Moreover, novel SNPs on GGA5 and GGA3 were
associated with AH and HU at 32, 44, and 48 weeks of age. These results confirmed the
regions for egg weight that were detected in a previous study and were similar with QTL
for albumen quality. These results showed that GGA4 had the strongest effect on albumen
quality. Only a few significant loci were detected for most characteristics probably
reflecting the attributes of a pleiotropic gene and a minor-polygene in quantitative
traits.
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Affiliation(s)
- Liang Qu
- College of Animal Science & Technology, Nanjing Agricultural University, Nanjing, China.,Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Manman Shen
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, China.,College of Animal Science & Technology, Yangzhou University, Yangzhou, China
| | - Jun Guo
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Xingguo Wang
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Taocun Dou
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Yuping Hu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Yongfeng Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Meng Ma
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Kehua Wang
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Honglin Liu
- College of Animal Science & Technology, Nanjing Agricultural University, Nanjing, China
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Guo T, Duan Z, Chen J, Xie C, Wang Y, Chen P, Wang X. Pull-down combined with proteomic strategy reveals functional diversity of synaptotagmin I. PeerJ 2017; 5:e2973. [PMID: 28194317 PMCID: PMC5301975 DOI: 10.7717/peerj.2973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/10/2017] [Indexed: 12/05/2022] Open
Abstract
Synaptotagmin I (Syt I) is most abundant in the brain and is involved in multiple cellular processes. Its two C2 domains, C2A and C2B, are the main functional regions. Our present study employed a pull-down combined with proteomic strategy to identify the C2 domain-interacting proteins to comprehensively understand the biological roles of the C2 domains and thus the functional diversity of Syt I. A total of 135 non-redundant proteins interacting with the C2 domains of Syt I were identified. Out of them, 32 and 64 proteins only bound to C2A or C2B domains, respectively, and 39 proteins bound to both of them. Compared with C2A, C2B could bind to many more proteins particularly those involved in synaptic transmission and metabolic regulation. Functional analysis indicated that Syt I may exert impacts by interacting with other proteins on multiple cellular processes, including vesicular membrane trafficking, synaptic transmission, metabolic regulation, catalysis, transmembrane transport and structure formation, etc. These results demonstrate that the functional diversity of Syt I is higher than previously expected, that its two domains may mediate the same and different cellular processes cooperatively or independently, and that C2B domain may play even more important roles than C2A in the functioning of Syt I. This work not only further deepened our understanding of the functional diversity of Syt I and the functional differences between its two C2 domains, but also provided important clues for the further related researches.
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Affiliation(s)
- Tianyao Guo
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University , Changsha , Hunan , P. R. of China
| | - Zhigui Duan
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University , Changsha , Hunan , P. R. of China
| | - Jia Chen
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University , Changsha , Hunan , P. R. of China
| | - Chunliang Xie
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University , Changsha , Hunan , P. R. of China
| | - Ying Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University , Changsha , Hunan , P. R. of China
| | - Ping Chen
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University , Changsha , Hunan , P. R. of China
| | - Xianchun Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University , Changsha , Hunan , P. R. of China
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Lorenzetti* S, Narciso L. Nuclear Receptors: Connecting Human Health to the Environment. COMPUTATIONAL APPROACHES TO NUCLEAR RECEPTORS 2012. [DOI: 10.1039/9781849735353-00001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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4
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Yimthaing S, Plant N, Plant K. Regulation of nuclear import pathways by vitamin D signalling: Potential biological implications. Toxicology 2011. [DOI: 10.1016/j.tox.2011.09.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Ghosh S, Vassilev AP, Zhang J, Zhao Y, DePamphilis ML. Assembly of the human origin recognition complex occurs through independent nuclear localization of its components. J Biol Chem 2011; 286:23831-41. [PMID: 21555516 DOI: 10.1074/jbc.m110.215988] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Initiation of eukaryotic genome duplication begins when a six-subunit origin recognition complex (ORC) binds to DNA. However, the mechanism by which this occurs in vivo and the roles played by individual subunits appear to differ significantly among organisms. Previous studies identified a soluble human ORC(2-5) complex in the nucleus, an ORC(1-5) complex bound to chromatin, and an Orc6 protein that binds weakly, if at all, to other ORC subunits. Here we show that stable ORC(1-6) complexes also can be purified from human cell extracts and that Orc6 and Orc1 each contain a single nuclear localization signal that is essential for nuclear localization but not for ORC assembly. The Orc6 nuclear localization signal, which is essential for Orc6 function, is facilitated by phosphorylation at its cyclin-dependent kinase consensus site and by association with Kpna6/1, nuclear transport proteins that did not co-purify with other ORC subunits. These and other results support a model in which Orc6, Orc1, and ORC(2-5) are transported independently to the nucleus where they can either assemble into ORC(1-6) or function individually.
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Affiliation(s)
- Soma Ghosh
- NICHD, National Institutes of Health, Bethesda, Maryland 20892-2753, USA
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A PXR-mediated negative feedback loop attenuates the expression of CYP3A in response to the PXR agonist pregnenalone-16α-carbonitrile. PLoS One 2011; 6:e16703. [PMID: 21311750 PMCID: PMC3032768 DOI: 10.1371/journal.pone.0016703] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 12/27/2010] [Indexed: 01/24/2023] Open
Abstract
The nuclear receptor superfamily of ligand-activated transcription factors plays a central role in the regulation of cellular responses to chemical challenge. Nuclear receptors are activated by a wide range of both endogenous and exogenous chemicals, and their target genes include those involved in the metabolism and transport of the activating chemical. Such target gene activation, thus, acts to remove the stimulating xenobiotic or to maintain homeostatic levels of endogenous chemicals. Given the dual nature of this system it is important to understand how these two roles are balanced, such that xenobiotics are efficiently removed while not impacting negatively on homeostasis of endogenous chemicals. Using DNA microarray technology we have examined the transcriptome response of primary rat hepatocytes to two nuclear receptor ligands: Pregnenalone-16α-carbonitrile (PCN), a xenobiotic PXR agonist, and lithocholic acid, an endogenous mixed PXR/VDR/FXR agonist. We demonstrate that despite differences in the profile of activated nuclear receptors, transcriptome responses for these two ligands are broadly similar at lower concentrations, indicating a conserved general response. However, as concentrations of stimulating ligand rises, the transcriptome responses diverge, reflecting a need for specific responses to the two stimulating chemicals. Finally, we demonstrate a novel feed-back loop for PXR, whereby ligand-activation of PXR suppresses transcription of the PXR gene, acting to attenuate PXR protein expression levels at higher ligand concentrations. Through in silico simulation we demonstrate that this feed-back loop is an important factor to prevent hyperexpression of PXR target genes such as CYP3A and confirm these findings in vitro. This novel insight into the regulation of the PXR-mediated regulatory signal networks provides a potential mechanistic rationale for the robustness in steroid homeostasis within the cell.
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Plant N, Aouabdi S. Nuclear receptors: the controlling force in drug metabolism of the liver? Xenobiotica 2009; 39:597-605. [PMID: 19622002 DOI: 10.1080/00498250903098218] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The body is in a constant battle to achieve homeostasis; indeed, the robustness with which it can respond to moves away from homeostasis is a vital part in the survival of the organism as a whole. There thus exists a need for a network of sensors that are able to capture, interpret, and respond to alterations in chemical levels that move the body away from homeostasis and this applies to both endogenous and exogenous chemicals. With respect to external chemicals (xenobiotics), this xenosensing is often carried out through specific interactions with cellular receptors. The phenomenon of 'xenosensing' has attracted much interest of late, whereby xenobiotics interact with receptors resulting in the activation of a battery of genes mediating oxidative drug metabolism, conjugation, and transport, thereby enhancing the elimination of the xenobiotic by the organism. However, this beneficial response is counterbalanced by the increasingly recognized role of nuclear receptors in mediating drug-drug interactions via enzyme induction or the production of toxicity through interaction with endogenous pathways. This review will focus on the role of nuclear receptors in mediating these effects, and how such knowledge will contribute to a mechanism-based risk assessment for xenobiotics.
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Affiliation(s)
- N Plant
- Centre for Toxicology, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU27XH, UK.
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8
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Cheema MS, Gibson GG, Plant N, Plant KE. Cyproterone acetate represses the human karyopherin α2 promoter by antagonism of the glucocorticoid receptor. Toxicology 2008. [DOI: 10.1016/j.tox.2008.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Plant N. Can systems toxicology identify common biomarkers of non-genotoxic carcinogenesis? Toxicology 2008; 254:164-9. [PMID: 18674585 DOI: 10.1016/j.tox.2008.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 06/30/2008] [Accepted: 07/01/2008] [Indexed: 10/25/2022]
Abstract
For the rapid development of safe, efficacious chemicals it is important that any potential liabilities are identified as early as possible in the discovery/development pipeline. Once identified it is then possible to make rational decisions on whether to progress a chemical and/or series further; one such liability is chemical carcinogenesis, a highly undesirable characteristic in a novel chemical entity. Chemical carcinogens may be roughly divided into two classes, those that elicit their actions through direct damage to DNA (genotoxic carcinogens) and those that cause carcinogenesis through mechanisms that involve direct damage of the DNA by the agent (non-genotoxic carcinogens). Whereas the former group can be identified by in vitro screens to a good degree of accuracy, the latter group are far more problematic due to their diverse modes of action. This review will focus on the latter class of chemical carcinogens, examining how modern '-omic' technologies have begun to identify signatures that may represent sensitive, early markers for these processes. In addition to their use in signature generation the role of -omic level approaches to delineating molecular mechanisms of action will also be discussed.
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Affiliation(s)
- Nick Plant
- Centre for Toxicology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.
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Cheema MS, Plant NJ, Gibson GG, Plant KE. Response of nuclear import factor encoding genes to xenobiotics: Analysis of the human karyopherin α2 promoter. Toxicology 2007. [DOI: 10.1016/j.tox.2007.06.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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