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Antonczyk C, Ratert C, Schwennen C, Kamphues J, Abd El-Wahab A. Chemical Composition of Newborn Piglets with Different Weights at Birth in Sows with a High Reproductive Performance. Animals (Basel) 2024; 14:1380. [PMID: 38731384 PMCID: PMC11082942 DOI: 10.3390/ani14091380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
The present study aimed to quantify and update the data on the body composition (energy nutrients) of newborn piglets of different body weights at the time of birth, as well as of the placenta mass. Data were collected from newborn piglets (n = 25) from modern genetic lines which were stillborn or died within the first 24 h of life after being crushed to death with various body weights at birth (<0.8 kg (n = 5); 0.8-1.2 kg (n = 5); >1.2-1.6 kg (common birth weight, n = 10) and >1.6 kg (n = 5)). The placenta (n = 20) of sows from a conventional breeding farm were collected, too. The body composition of newborns of "normal" (>1.2-1.6 kg) and even lighter (0.8-1.2) weights still indicated a "normal" composition. In the case of a lower body weight of piglets <0.8 kg at birth, the crude ash (24.1%) and crude protein (8.21%) contents were higher, but the crude fat (16.1%), carbohydrate (57.4%), and gross energy (3.60%) contents were lower. The placental composition in comparison to the piglet body composition was characterized by higher crude protein contents (24.3%) and lower crude ash (31.6%), crude fat (9.08%), and carbohydrate (55.6%) contents. In conclusion, the energy and protein accumulation in the total mass of fetuses and placentas increased by 75% and 64%, respectively, in comparison to times in which the litter size varied around 10-12 piglets, essentially as a result of the larger fetal mass and not of a different body composition.
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Affiliation(s)
- Carina Antonczyk
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany (C.S.); (J.K.)
| | - Christine Ratert
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany (C.S.); (J.K.)
| | - Cornelia Schwennen
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany (C.S.); (J.K.)
| | - Josef Kamphues
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany (C.S.); (J.K.)
| | - Amr Abd El-Wahab
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany (C.S.); (J.K.)
- Department of Nutrition and Nutritional Deficiency Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
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2
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Mármol-Sánchez E, Cirera S, Zingaretti LM, Jacobsen MJ, Ramayo-Caldas Y, Jørgensen CB, Fredholm M, Cardoso TF, Quintanilla R, Amills M. Modeling microRNA-driven post-transcriptional regulation using exon-intron split analysis in pigs. Anim Genet 2022; 53:613-626. [PMID: 35811409 DOI: 10.1111/age.13238] [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: 10/22/2021] [Revised: 04/23/2022] [Accepted: 06/16/2022] [Indexed: 11/27/2022]
Abstract
The contribution of microRNAs (miRNAs) to mRNA post-transcriptional regulation has often been explored by the post hoc selection of downregulated genes and determining whether they harbor binding sites for miRNAs of interest. This approach, however, does not discriminate whether these mRNAs are also downregulated at the transcriptional level. Here, we have characterized the transcriptional and post-transcriptional changes in mRNA expression in two porcine tissues: gluteus medius muscle of fasted and fed Duroc gilts and adipose tissue of lean and obese Duroc-Göttingen minipigs. Exon-intron split analysis of RNA-seq data allowed us to identify downregulated mRNAs with high post-transcriptional signals in fed or obese states, and we assessed whether they harbor binding sites for upregulated miRNAs in any of these two physiological states. We found 26 downregulated mRNAs with high post-transcriptional signals in the muscle of fed gilts and 21 of these were predicted targets of miRNAs upregulated in fed pigs. For adipose tissue, 44 downregulated mRNAs in obese minipigs displayed high post-transcriptional signals, and 25 of these were predicted targets of miRNAs upregulated in the obese state. These results suggest that the contribution of miRNAs to mRNA repression is more prominent in the skeletal muscle system. Finally, we identified several genes that may play relevant roles in the energy homeostasis of the pig skeletal muscle (DKK2 and PDK4) and adipose (SESN3 and ESRRG) tissues. By differentiating transcriptional from post-transcriptional changes in mRNA expression, exon-intron split analysis provides a valuable view of the regulation of gene expression, complementary to canonical differential expression analyses.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Susanna Cirera
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Mette Juul Jacobsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture, Barcelona, Spain
| | - Claus B Jørgensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Tainã Figueiredo Cardoso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, Brazil
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture, Barcelona, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Spain
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3
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Aymerich P, Soldevila C, Bonet J, Gasa J, Coma J, Solà-Oriol D. Increasing Dietary Lysine Impacts Differently Growth Performance of Growing Pigs Sorted by Body Weight. Animals (Basel) 2020; 10:E1032. [PMID: 32545783 PMCID: PMC7341301 DOI: 10.3390/ani10061032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/02/2020] [Accepted: 06/10/2020] [Indexed: 01/10/2023] Open
Abstract
An experiment was conducted analyzing whether growing pigs classified in different initial body weight categories (BWCAT) have a different response to increasing standardized ileal digestible lysine to net energy ratio (SID Lys:NE), to assess whether light pigs might benefit from being differentially fed. A total of 1170 pigs in pens of 13 were individually weighed, classified in 3 BWCAT (Lp: 32.1 ± 2.8 kg, Mp: 27.5 ± 2.3 kg, and Sp: 23.4 ± 2.9 kg), and afterwards pens were randomly allocated to 5 dietary SID Lys:NE treatments (3.25 to 4.88 g/Mcal) fed over 47 days. Results reported a greater linear improvement of growth and feed efficiency of Sp compared to Lp when increasing SID Lys:NE. Modelling the response to SID Lys:NE using quadratic polynomial models showed that the levels to reach 98% of maximum growth from day 0-47 were 3.67, 3.88, 4.06 g SID Lys/Mcal NE for Lp, Mp, and Sp, respectively. However, due to the overlapping SID Lys:NE confidence intervals at maximum performance, it was not possible to determine if requirements were different between BWCAT. Summarizing, the results suggested that feeding small pigs greater SID Lys:NE than large pigs can improve their performance and increase the efficiency of the overall production system.
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Affiliation(s)
- Pau Aymerich
- Vall Companys Group, 25191 Lleida, Spain; (C.S.); (J.B.); (J.C.)
- Animal Nutrition and Welfare Service, Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (J.G.); (D.S.-O.)
| | - Carme Soldevila
- Vall Companys Group, 25191 Lleida, Spain; (C.S.); (J.B.); (J.C.)
| | - Jordi Bonet
- Vall Companys Group, 25191 Lleida, Spain; (C.S.); (J.B.); (J.C.)
| | - Josep Gasa
- Animal Nutrition and Welfare Service, Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (J.G.); (D.S.-O.)
| | - Jaume Coma
- Vall Companys Group, 25191 Lleida, Spain; (C.S.); (J.B.); (J.C.)
| | - David Solà-Oriol
- Animal Nutrition and Welfare Service, Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (J.G.); (D.S.-O.)
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4
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Hu L, Peng X, Han F, Wu F, Chen D, Wu D, Feyera T, Zhang K, Che L. Effects of Birth Weight and Postnatal Nutritional Restriction on Skeletal Muscle Development, Myofiber Maturation, and Metabolic Status of Early-Weaned Piglets. Animals (Basel) 2020; 10:E156. [PMID: 31963382 PMCID: PMC7022288 DOI: 10.3390/ani10010156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
Piglets with light weaning weight commonly have a slow post-weaning growth rate due to impaired skeletal muscle development. Therefore, the present study aimed to investigate the impact of birth weight and nutrient intake on skeletal muscle development, myofiber maturation, and metabolic status of early-weaned piglets. Twelve pairs of normal birth weight and intrauterine growth-retarded (IUGR) piglets (seven days old) were randomly assigned to receive adequate nutrient intake or restricted nutrient intake for 21 days. Serum and muscle samples were collected for further analysis. The results indicated that muscle weight, cross-sectional areas, and muscular glycogen were lower (p < 0.05) in both IUGR and restricted fed piglets. Nutrient restriction decreased the contents of RNA, the RNA to DNA ratio, and the percentages of myosin heavy chain (MyHC) IIx (p < 0.05), whereas increased the activity of β-hydroxy-acyl-CoA-dehydrogenase (HAD), the ratio of HAD to citrate synthase, as well as the percentages of MyHC I (p < 0.05). In addition, nutrient restriction significantly decreased muscular glycogen, mRNA levels of fatty acid transport protein 1, cationic amino acid transporter 1, and glucose transporter 4 in IUGR piglets compared with the other groups (p < 0.05). The results of the present study showed that IUGR impaired skeletal muscle growth and disturbed the hormone and mRNA expression of genes related to energy metabolism, which led to a more severe energy deficit when receiving postnatal nutritional restriction. Postnatal nutritional restriction resulted in delayed myofiber maturation of the piglets, which may be associated with the transformation of MyHC isoform and the change of metabolic status.
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Affiliation(s)
- Liang Hu
- Institute of Animal Nutrition, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China
| | - Xie Peng
- Institute of Animal Nutrition, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China
| | - Fei Han
- Institute of Animal Nutrition, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China
| | - Fali Wu
- Institute of Animal Nutrition, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China
| | - De Wu
- Institute of Animal Nutrition, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China
| | - Takele Feyera
- Department of Animal Science, Aarhus University, DK-8830 Tjele, Denmark
| | - Keying Zhang
- Institute of Animal Nutrition, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China
| | - Lianqiang Che
- Institute of Animal Nutrition, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China
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5
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Li L, Cheng X, Chen L, Li J, Luo W, Li C. Long Noncoding Ribonucleic Acid MSTRG.59589 Promotes Porcine Skeletal Muscle Satellite Cells Differentiation by Enhancing the Function of PALLD. Front Genet 2019; 10:1220. [PMID: 31850071 PMCID: PMC6887656 DOI: 10.3389/fgene.2019.01220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/05/2019] [Indexed: 01/08/2023] Open
Abstract
Skeletal muscle satellite cells are a class of undifferentiated mononuclear myogenic stem cells distributed between the myofibroblast and membrane basement. Since their development determines the development of skeletal muscles, knowledge of their proliferation, differentiation, and fate is vital for understanding skeletal muscle development. Increasing evidence have shown that long noncoding RNA (lncRNA) plays an important role in regulating the development process of satellite cells. Based on the results of our previous studies, we screened lncRNA MSTRG.59589, which is highly expressed in skeletal muscle tissue. In the present study, knockdown of MSTRG.59589 significantly inhibited satellite cell differentiation at various time points, whereas overexpression of MSTRG.59589 demonstrated opposite effects. An MSTRG.59589 knockdown cell model was constructed for transcriptome sequencing, and RNA sequencing analysis screened out a large number of differentially expressed genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of these differentially expressed genes revealed that they are mainly enriched in actin cytoskeleton, muscle contraction, and other pathways related to muscle development. Mechanistic analyses showed that MSTRG.59589 could promote the differentiation process of skeletal muscle satellite cells by positively regulating the expression level of the target gene PALLD. This experiment lays a theoretical foundation for deeper studies on the mechanism of MSTRG.59589 in the differentiation of porcine skeletal muscle satellite cells.
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Affiliation(s)
- Long Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xiaofang Cheng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Ling Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Jingxuan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Wenzhe Luo
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
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6
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Chen L, Shi G, Chen G, Li J, Li M, Zou C, Fang C, Li C. Transcriptome Analysis Suggests the Roles of Long Intergenic Non-coding RNAs in the Growth Performance of Weaned Piglets. Front Genet 2019; 10:196. [PMID: 30936891 PMCID: PMC6431659 DOI: 10.3389/fgene.2019.00196] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/25/2019] [Indexed: 11/19/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) have been considered to play a key regulatory role in various biological processes. An increasing number of studies have utilized transcriptome analysis to obtain lincRNAs with functions related to cancer, but lincRNAs affecting growth rates in weaned piglets are rarely described. Although lincRNAs have been systematically identified in various mouse tissues and cell lines, studies of lincRNA in pigs remain rare. Therefore, identifying and characterizing novel lincRNAs affecting the growth performance of weaned piglets is of great importance. Here, we reconstructed 101,988 lincRNA transcripts and identified 1,078 lincRNAs in two groups of longissimus dorsi muscle (LDM) and subcutaneous fat (SF) based on published RNA-seq datasets. These lincRNAs exhibit typical characteristics, such as shorter lengths and lower expression relative to protein-encoding genes. Gene ontology analysis revealed that some lincRNAs could be involved in weaned piglet related processes, such as insulin resistance and the AMPK signaling pathway. We also compared the positional relationship between differentially expressed lincRNAs (DELs) and quantitative trait loci (QTL) and found that some of DELs may play an important role in piglet growth and development. Our work details part of the lincRNAs that may affect the growth performance of weaned piglets and promotes future studies of lincRNAs for molecular-assisted development in weaned piglets.
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Affiliation(s)
- Lin Chen
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gaoli Shi
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingxuan Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mengxun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zou
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Changchun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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7
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Zou C, Li S, Deng L, Guan Y, Chen D, Yuan X, Xia T, He X, Shan Y, Li C. Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig. Genes (Basel) 2017; 8:genes8080203. [PMID: 28820450 PMCID: PMC5575666 DOI: 10.3390/genes8080203] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/12/2017] [Accepted: 08/14/2017] [Indexed: 01/28/2023] Open
Abstract
There are major differences between Yorkshire (lean-type) and Wannanhua pig (fat-type) in terms of growth performance and meat quality. Long intergenic noncoding RNAs (lincRNAs) are a class of regulators that are involved in numerous biological processes and widely identified in many species. However, the role of lincRNAs in pig is largely unknown, and the mechanisms by which they affect growth and meat quality are elusive. In this study, we used published data to identify 759 lincRNAs in porcine longissimus dorsi muscle. These putative lincRNAs shared many features with mammalian lincRNAs, such as shorter length and fewer exons. Gene ontology and pathway analysis indicated that many potential target genes (PTGs) of lincRNAs were involved in muscle growth-related and meat quality-related biological processes. Moreover, we constructed a co-expression network between differentially expressed lincRNAs (DELs) and their PTGs, and found a potential mechanism that most DELs can use to upregulate their PTGs, which may finally contribute to the growth and meat quality differences between the two breeds through an unknown manner. This work details some lincRNAs and their PTGs related to muscle growth or meat quality, and facilitates future research on the roles of lincRNAs in these two types of pig, as well as molecular-assisted breeding for pig.
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Affiliation(s)
- Cheng Zou
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Sha Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lulu Deng
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yang Guan
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dake Chen
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiongkun Yuan
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Tianrui Xia
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xinglin He
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yawei Shan
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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8
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Wang H, Li R, Zhou X, Xue L, Xu X, Liu B. Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data. Sci Rep 2016; 6:36388. [PMID: 27812017 PMCID: PMC5095665 DOI: 10.1038/srep36388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/14/2016] [Indexed: 12/05/2022] Open
Abstract
Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3′ end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3′UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS.
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Affiliation(s)
- Hongyang Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Rui Li
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Xiang Zhou
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Liyao Xue
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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9
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Yu P, Ji L, Lee KJ, Yu M, He C, Ambati S, McKinney EC, Jackson C, Baile CA, Schmitz RJ, Meagher RB. Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine. PLoS One 2016; 11:e0154949. [PMID: 27171244 PMCID: PMC4865362 DOI: 10.1371/journal.pone.0154949] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/21/2016] [Indexed: 12/11/2022] Open
Abstract
The reprogramming of cellular memory in specific cell types, and in visceral adipocytes in particular, appears to be a fundamental aspect of obesity and its related negative health outcomes. We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We developed fluorescence nuclear cytometry (FNC) and fluorescence activated nuclear sorting (FANS) of cellular nuclei from visceral adipose tissue (VAT) using the levels of the pan-adipocyte protein, peroxisome proliferator-activated receptor gamma-2 (PPARg2), to distinguish classes of PPARg2-Positive (PPARg2-Pos) adipocyte nuclei from PPARg2-Negative (PPARg2-Neg) leukocyte and endothelial cell nuclei. PPARg2-Pos nuclei were 10-fold enriched for most adipocyte marker transcripts relative to PPARg2-Neg nuclei. PPARg2-Pos nuclei showed 2- to 50-fold higher levels of transcripts encoding most of the chromatin-remodeling factors assayed, which regulate the methylation of histones and DNA cytosine (e.g., DNMT1, TET1, TET2, KDM4A, KMT2C, SETDB1, PAXIP1, ARID1A, JMJD6, CARM1, and PRMT5). PPARg2-Pos nuclei were large with decondensed chromatin. TAB-seq demonstrated 5-hydroxymethylcytosine (5hmC) levels were remarkably dynamic in gene bodies of various classes of VAT nuclei, dropping 3.8-fold from the highest quintile of expressed genes to the lowest. In short, VAT-derived adipocytes appear to be more actively remodeling their chromatin than non-adipocytes.
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Affiliation(s)
- Ping Yu
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Kevin J. Lee
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
- GRU-UGA Medical Partnership, University of Georgia Health Sciences Campus, Prince Avenue, Athens, GA, 30602, United States of America
| | - Miao Yu
- Department of Chemistry, University of Chicago, 5735 S Ellis Ave, Chicago, IL, 60637 USA
| | - Chuan He
- Department of Chemistry, University of Chicago, 5735 S Ellis Ave, Chicago, IL, 60637 USA
| | - Suresh Ambati
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Elizabeth C. McKinney
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Crystal Jackson
- Abeome Corporation, Athens, GA, 111 Riverbend Road, 30602, United States of America
| | - Clifton A. Baile
- Department of Foods and Nutrition, University of Georgia, 305 Sanford Dr, Athens, GA, 30602, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Richard B. Meagher
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
- * E-mail:
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Wang Z, Li Q, Chamba Y, Zhang B, Shang P, Zhang H, Wu C. Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue. PLoS One 2015; 10:e0141138. [PMID: 26505482 PMCID: PMC4624711 DOI: 10.1371/journal.pone.0141138] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/04/2015] [Indexed: 01/25/2023] Open
Abstract
Transcriptome profiles established using high-throughput sequencing can be effectively used for screening genome-wide differentially expressed genes (DEGs). RNA sequences (from RNA-seq) and microRNA sequences (from miRNA-seq) from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small-ear pig [DSP] and Tibetan pig [TP]) and two introduced pig breeds (Landrace [LL] and Yorkshire [YY]) were examined using HiSeq 2000 to identify and compare the differential expression of functional genes related to muscle growth and lipid deposition. We obtained 27.18 G clean data through the RNA-seq and detected that 18,208 genes were positively expressed and 14,633 of them were co-expressed in the muscle tissues of the four samples. In all, 315 DEGs were found between the Chinese pig group and the introduced pig group, 240 of which were enriched with functional annotations from the David database and significantly enriched in 27 Gene Ontology (GO) terms that were mainly associated with muscle fiber contraction, cadmium ion binding, response to organic substance and contractile fiber part. Based on functional annotation, we identified 85 DEGs related to growth traits that were mainly involved in muscle tissue development, muscle system process, regulation of cell development, and growth factor binding, and 27 DEGs related to lipid deposition that were mainly involved in lipid metabolic process and fatty acid biosynthetic process. With miRNA-seq, we obtained 23.78 M reads and 320 positively expressed miRNAs from muscle tissues, including 271 known pig miRNAs and 49 novel miRNAs. In those 271 known miRNAs, 20 were higher and 10 lower expressed in DSP-TP than in LL-YY. The target genes of the 30 miRNAs were mainly participated in MAPK, GnRH, insulin and Calcium signaling pathway and others involved cell development, growth and proliferation, etc. Combining the DEGs and the differentially expressed (DE) miRNAs, we drafted a network of 46 genes and 18 miRNAs for regulating muscle growth and a network of 15 genes and 16 miRNAs for regulating lipid deposition. We identified that CAV2, MYOZ2, FRZB, miR-29b, miR-122, miR-145-5p and miR-let-7c, etc, were key genes or miRNAs regulating muscle growth, and FASN, SCD, ADORA1, miR-4332, miR-182, miR-92b-3p, miR-let-7a and miR-let-7e, etc, were key genes or miRNAs regulating lipid deposition. The quantitative expressions of eight DEGs and seven DE miRNAs measured with real-time PCR certified that the results of differential expression genes or miRNAs were reliable. Thus, 18,208 genes and 320 miRNAs were positively expressed in porcine longissimus dorsi muscle. We obtained 85 genes and 18 miRNAs related to muscle growth and 27 genes and 16 miRNAs related to lipid deposition, which provided new insights into molecular mechanism of the economical traits in pig.
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Affiliation(s)
- Zhixiu Wang
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
| | - Qinggang Li
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, People’s Republic of China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, People’s Republic of China
| | - Bo Zhang
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
| | - Peng Shang
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
| | - Hao Zhang
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
- * E-mail:
| | - Changxin Wu
- National Engineering Laboratory For Animal Breeding, China Agricultural University, Beijing, People’s Republic of China
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