1
|
Gong X, Zheng M, Zhang J, Ye Y, Duan M, Chamba Y, Wang Z, Shang P. Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs. Front Vet Sci 2022; 9:919904. [PMID: 35754534 PMCID: PMC9218471 DOI: 10.3389/fvets.2022.919904] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Fat deposition traits are one of the key factors in pig production and breeding. The fat deposition capacity of pigs mainly affects the quality of pork and pig productivity. The aim of this study was to analyze the differential expression of mRNA levels in dorsal adipose tissue of Tibetan and York pigs at different growth stages using transcriptomic data to estimate key genes that regulate fat deposition in pigs. The results showed that a total of 32,747 positively expressed genes were present in the dorsal adipose tissue of the two breeds. Differentially expressed gene (DEG) screening of multiple combinations between the two breeds yielded 324 DEGS. Gene ontology (GO) biofunctional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGS were mainly involved in lipid metabolic pathways, steroid biosynthetic pathways and lipid biosynthetic processes, sterol biosynthetic processes, brown adipocyte differentiation, and other pathways related to lipid deposition and metabolism. The results showed that ACACA, SLC2A4 and THRSP genes positively regulated the lipid deposition ability and CHPT1 gene negatively regulated the lipid deposition ability in pigs. The results of this experiment suggest a theoretical basis for further studies on the regulatory mechanisms of fat deposition in pigs.
Collapse
Affiliation(s)
- Xinglong Gong
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Min Zheng
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Jian Zhang
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Yourong Ye
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Mengqi Duan
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Zhongbin Wang
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Peng Shang
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| |
Collapse
|
2
|
Gubanova NV, Orlova NG, Dergilev AI, Oparina NY, Orlov YL. Glioblastoma gene network reconstruction and ontology analysis by online bioinformatics tools. J Integr Bioinform 2021; 18:jib-2021-0031. [PMID: 34783229 PMCID: PMC8709738 DOI: 10.1515/jib-2021-0031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma is the most aggressive type of brain tumors resistant to a number of antitumor drugs. The problem of therapy and drug treatment course is complicated by extremely high heterogeneity in the benign cell populations, the random arrangement of tumor cells, and polymorphism of their nuclei. The pathogenesis of gliomas needs to be studied using modern cellular technologies, genome- and transcriptome-wide technologies of high-throughput sequencing, analysis of gene expression on microarrays, and methods of modern bioinformatics to find new therapy targets. Functional annotation of genes related to the disease could be retrieved based on genetic databases and cross-validated by integrating complementary experimental data. Gene network reconstruction for a set of genes (proteins) proved to be effective approach to study mechanisms underlying disease progression. We used online bioinformatics tools for annotation of gene list for glioma, reconstruction of gene network and comparative analysis of gene ontology categories. The available tools and the databases for glioblastoma gene analysis are discussed together with the recent progress in this field.
Collapse
Affiliation(s)
- Natalya V Gubanova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Nina G Orlova
- Financial University under the Government of the Russian Federation, 119991 Moscow, Russia.,Moscow State Technical University of Civil Aviation, 125993 Moscow, Russia
| | | | | | - Yuriy L Orlov
- Novosibirsk State University, 630090 Novosibirsk, Russia.,The Digital Health Institute, I.M.Sechenov First Moscow State Medical University of the Russian Ministry of Health, 119991 Moscow, Russia
| |
Collapse
|
3
|
Hou X, Wang L, Zhao F, Liu X, Gao H, Shi L, Yan H, Wang L, Zhang L. Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds. Animals (Basel) 2021; 11:ani11113169. [PMID: 34827901 PMCID: PMC8614396 DOI: 10.3390/ani11113169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Variation exists in muscle-related traits, such as muscle growth and meat quality, between obese and lean pigs. In this study, the transcriptome profiles of skeletal muscle between Beijing Blackand Yorkshire pigs were characterized to explore the molecular mechanism underlying skeletal muscle-relatedtraits. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that differentially expressed mRNAs, lncRNAs, and circRNAs involved in skeletal muscle development and fatty acid metabolism played a key role in the determination of muscle-related traits between different pig breeds. These results provide candidate genes responsible for muscle phenotypic variation and are valuable for pig breeding. Abstract RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.
Collapse
|
4
|
The involvement of NR4A1 and NR4A2 in the regulation of the luteal function in rats. Acta Histochem 2018; 120:713-719. [PMID: 30097186 DOI: 10.1016/j.acthis.2018.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/29/2018] [Accepted: 07/30/2018] [Indexed: 11/23/2022]
Abstract
The nuclear receptor 4A (NR4A) members play important roles in cellular proliferation, differentiation and apoptosis. The current study first evaluate the expression of ovarian NR4A1 during different luteal stages in rats. Immature rats aged 28 days were treated with sequential Pregnant mare serum gonadotropin (PMSG) (D -2) / human chorionic gonadotropin (hCG) (D 0) to induce pseudopregnancy. Serum progesterone (P4) and ovarian expression of NR4A1 were detected by RIA and WB, respectively, at follicle stage (D 0), early (D 2), middle (D 7) and late (D 14 and D 20) luteal stages. To confirm the role of NR4A1 during the luteal regression, rats were treated with prostaglandin F2α analog (PGF) for 0-8 h on D 7 to detect the expressions of NR4A1 and NR4A2. RIA result showed that serum P4 reached highest level on D 7 and then declined. WB results showed that there were two types of NR4A1 (NR4A1-L and NR4A1-S) expressed in the ovary. The ovarian NR4A1-L decreased at the late luteal stage (D 20). However, the NR4A1-S increased at the late luteal stage (D 14). After PGF treatment on D 7, the expression of NR4A1-S increased which peaked at 0.5-1 h and then declined; while NR4A1-L expression did not change within 8 h. Real-time PCR results showed that the ovarian NR4A1 mRNA increased within 0.5 h, maintained high at 1 h and then declined. The NR4A2 mRNA expression exhibited a similar pattern to that of NR4A1 mRNA, though its abundance was not as high as NR4A1. IHC results revealed that NR4A1-L was expressed mainly in the cytoplasm of luteal steroidogenic cells, faintly expressed in the follicle theca cells, oocytes and the pericytes; while NR4A2 was primarily localized in the cytoplasm of luteal steroidogenic cells. In conclusion, all these results demonstrate that NR4A2 as well as NR4A1 might be involved in the luteal development and luteolysis in rats.
Collapse
|
5
|
Miao Z, Wei P, Khan MA, Zhang J, Guo L, Liu D, Zhang X, Bai Y, Wang S. Transcriptome analysis reveals differential gene expression in intramuscular adipose tissues of Jinhua and Landrace pigs. J Vet Med Sci 2018; 80:953-959. [PMID: 29709900 PMCID: PMC6021883 DOI: 10.1292/jvms.18-0074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Meat is a rich source of protein, fatty acids and carbohydrates for human needs. In
addition to necessary nutrients, high fat contents in pork increase the tenderness and
juiciness of the meat, featuring diverse application in various dishes. This study
investigated the transcriptomic profiles of intramuscular adipose tissues in Jinhua and
Landrace pigs by employing advanced RNA sequencing. Results showed significant interesting
to note that there were significant differences in the expression of genes. 1,632 genes
showed significant differential expression, 837 genes were up-regulated and 195 genes were
down-regulated. Variations in genes responsible for cell aggregation, extracellular matrix
formation, cellular lipid catabolic process, and fatty acid binding strongly supported
that both pig breeds feature variable fat and muscle metabolism. Certain differentially
expressed genes are included in the pathway of mitogen-activated protein kinase signaling
pathway, Ras signaling pathway and insulin pathway. Results from real-time quantitative
polymerase chain reaction also validated the differential expression of 17 mRNAs between
meats of the two pig breeds. Overall, these findings reveal significant differences in fat
and protein metabolism of intramuscular adipose tissues of two pig breeds at the
transcriptomic level and suggest diversification at the genetic level between breeds of
the same species.
Collapse
Affiliation(s)
- Zhiguo Miao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Panpeng Wei
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Muhammad Akram Khan
- Department of Pathobiology, Faculty of Veterinary and Animal Sciences, PMAS- Arid Agriculture University Rawalpindi, 46000, Pakistan
| | - Jinzhou Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Liping Guo
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Dongyang Liu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Xiaojian Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Yueyu Bai
- Animal Health Supervision of Henan Province, Bureau of Animal Husbandry of Henan province, Zhengzhou, 450000, P.R. China
| | - Shan Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| |
Collapse
|
6
|
Talbott H, Hou X, Qiu F, Zhang P, Guda C, Yu F, Cushman RA, Wood JR, Wang C, Cupp AS, Davis JS. Early transcriptome responses of the bovine midcycle corpus luteum to prostaglandin F2α includes cytokine signaling. Mol Cell Endocrinol 2017; 452:93-109. [PMID: 28549990 PMCID: PMC7388008 DOI: 10.1016/j.mce.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/17/2017] [Accepted: 05/18/2017] [Indexed: 12/16/2022]
Abstract
In ruminants, prostaglandin F2alpha (PGF2α)-mediated luteolysis is essential prior to estrous cycle resumption, and is a target for improving fertility. To deduce early PGF2α-provoked changes in the corpus luteum a short time-course (0.5-4 h) was performed on cows at midcycle. A microarray-determined transcriptome was established and examined by bioinformatic pathway analysis. Classic PGF2α effects were evident by changes in early response genes (FOS, JUN, ATF3) and prediction of active pathways (PKC, MAPK). Several cytokine transcripts were elevated and NF-κB and STAT activation were predicted by pathway analysis. Self-organizing map analysis grouped differentially expressed transcripts into ten mRNA expression patterns indicative of temporal signaling cascades. Comparison with two analogous datasets revealed a conserved group of 124 transcripts similarly altered by PGF2α treatment, which both, directly and indirectly, indicated cytokine activation. Elevated levels of cytokine transcripts after PGF2α and predicted activation of cytokine pathways implicate inflammatory reactions early in PGF2α-mediated luteolysis.
Collapse
Affiliation(s)
- Heather Talbott
- Olson Center for Women's Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA; Biochemistry and Molecular Biology Department, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA.
| | - Xiaoying Hou
- Olson Center for Women's Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA.
| | - Fang Qiu
- Biostatistics Department, University of Nebraska Medical Center, 984375 Nebraska Medical Center, Omaha, NE 68198-4375, USA.
| | - Pan Zhang
- Olson Center for Women's Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA.
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE 68198-5805, USA.
| | - Fang Yu
- Biostatistics Department, University of Nebraska Medical Center, 984375 Nebraska Medical Center, Omaha, NE 68198-4375, USA.
| | - Robert A Cushman
- Nutrition and Environmental Management Research Unit, United States Department of Agriculture, P.O. Box 166 (State Spur 18D)/USDA-ARS-PA-USMARC, Clay Center, NE 68933, USA.
| | - Jennifer R Wood
- Animal Science Department, University of Nebraska-Lincoln, P.O. Box 830908, C203 ANSC, Lincoln, NE 68583-0908, USA.
| | - Cheng Wang
- Olson Center for Women's Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA.
| | - Andrea S Cupp
- Animal Science Department, University of Nebraska-Lincoln, P.O. Box 830908, C203 ANSC, Lincoln, NE 68583-0908, USA.
| | - John S Davis
- Olson Center for Women's Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA; Biochemistry and Molecular Biology Department, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA; Veterans Affairs Medical Center, 4101 Woolworth Ave, Omaha, NE 68105, USA.
| |
Collapse
|