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Chen Z, Li J, Bai Y, Liu Z, Wei Y, Guo D, Jia X, Shi B, Zhang X, Zhao Z, Hu J, Han X, Wang J, Liu X, Li S, Zhao F. Unlocking the Transcriptional Control of NCAPG in Bovine Myoblasts: CREB1 and MYOD1 as Key Players. Int J Mol Sci 2024; 25:2506. [PMID: 38473754 DOI: 10.3390/ijms25052506] [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: 01/18/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Muscle formation directly determines meat production and quality. The non-SMC condensin I complex subunit G (NCAPG) is strongly linked to the growth features of domestic animals because it is essential in controlling muscle growth and development. This study aims to elucidate the tissue expression level of the bovine NCAPG gene, and determine the key transcription factors for regulating the bovine NCAPG gene. In this study, we observed that the bovine NCAPG gene exhibited high expression levels in longissimus dorsi and spleen tissues. Subsequently, we cloned and characterized the promoter region of the bovine NCAPG gene, consisting of a 2039 bp sequence, through constructing the deletion fragment double-luciferase reporter vector and site-directed mutation-identifying core promoter region with its key transcription factor binding site. In addition, the key transcription factors of the core promoter sequence of the bovine NCAPG gene were analyzed and predicted using online software. Furthermore, by integrating overexpression experiments and the electrophoretic mobility shift assay (EMSA), we have shown that cAMP response element binding protein 1 (CREB1) and myogenic differentiation 1 (MYOD1) bind to the core promoter region (-598/+87), activating transcription activity in the bovine NCAPG gene. In conclusion, these findings shed important light on the regulatory network mechanism that underlies the expression of the NCAPG gene throughout the development of the muscles in beef cattle.
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Affiliation(s)
- Zongchang Chen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jingsheng Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanbin Bai
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhanxin Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yali Wei
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Dashan Guo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xue Jia
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaolan Zhang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiangmin Han
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Use of a graph neural network to the weighted gene co-expression network analysis of Korean native cattle. Sci Rep 2022; 12:9854. [PMID: 35701465 PMCID: PMC9197844 DOI: 10.1038/s41598-022-13796-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
In the general framework of the weighted gene co-expression network analysis (WGCNA), a hierarchical clustering algorithm is commonly used to module definition. However, hierarchical clustering depends strongly on the topological overlap measure. In other words, this algorithm may assign two genes with low topological overlap to different modules even though their expression patterns are similar. Here, a novel gene module clustering algorithm for WGCNA is proposed. We develop a gene module clustering network (gmcNet), which simultaneously addresses single-level expression and topological overlap measure. The proposed gmcNet includes a “co-expression pattern recognizer” (CEPR) and “module classifier”. The CEPR incorporates expression features of single genes into the topological features of co-expressed ones. Given this CEPR-embedded feature, the module classifier computes module assignment probabilities. We validated gmcNet performance using 4,976 genes from 20 native Korean cattle. We observed that the CEPR generates more robust features than single-level expression or topological overlap measure. Given the CEPR-embedded feature, gmcNet achieved the best performance in terms of modularity (0.261) and the differentially expressed signal (27.739) compared with other clustering methods tested. Furthermore, gmcNet detected some interesting biological functionalities for carcass weight, backfat thickness, intramuscular fat, and beef tenderness of Korean native cattle. Therefore, gmcNet is a useful framework for WGCNA module clustering.
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Muniz MMM, Fonseca LFS, Dos Santos Silva DB, de Oliveira HR, Baldi F, Chardulo AL, Ferro JA, Cánovas A, de Albuquerque LG. Identification of novel mRNA isoforms associated with meat tenderness using RNA sequencing data in beef cattle. Meat Sci 2020; 173:108378. [PMID: 33248741 DOI: 10.1016/j.meatsci.2020.108378] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/24/2022]
Abstract
The Warner-Bratzler shear force (WBSF) and myofibrillar fragmentation index (MFI) are complementary methodologies used to measure beef tenderness. Longissimus thoracis samples from the 20 most extreme bulls (out of 80 bulls set) for WBSF (tender (n = 10) and tough (n = 10)) and MFI (high (n = 10) and low (n = 10)) traits were collected to perform transcriptomic analysis using RNA-Sequencing. All analysis were performed through CLC Genomics Workbench. A total of 39 and 27 transcripts for WBSF and MFI phenotypes were DE, respectively. The possible DE novel mRNA isoforms, for WBSF and MFI traits, are myosin encoders (e.g. MYL1 and MYL6). In addition, we identified potential mRNA isoforms related to genes affecting the speed fibers degradation during the meat aging process. The DE novel transcripts are transcripted by genes with biological functions related to oxidative process, energy production and striated muscle contraction. The results suggest that the identified mRNA isoforms could be used as potential candidate to select animals in order to improve meat tenderness.
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Affiliation(s)
- Maria Malane Magalhães Muniz
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada.
| | | | | | - Hinayah Rojas de Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil; National Council for Scientific and Technological Development (CNPq), Brazil
| | - Artur Loyola Chardulo
- National Council for Scientific and Technological Development (CNPq), Brazil; São Paulo State University (Unesp), College of Veterinary and Animal Science, Botucatu, SP, Brazil
| | - Jesus Aparecido Ferro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil; National Council for Scientific and Technological Development (CNPq), Brazil
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Lucia Galvão de Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil; National Council for Scientific and Technological Development (CNPq), Brazil.
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Chardulo LAL, Baldassini WA, Curi RA, Pereira GL, Machado Neto OR, Dal-Pai M, Vechetti-Júnior IJ, Malheiros JM, Enriquez-Valencia CE. Gene and protein expression of myosin heavy chain in Nellore cattle comparing growth or meat tenderness traits. Anim Biotechnol 2019; 32:300-309. [PMID: 31702438 DOI: 10.1080/10495398.2019.1688168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The objective was to investigate gene and protein expression of myosin heavy chain (MyHC) in Nellore cattle slaughtered at different weights (BW) or degrees of meat tenderness. Ninety animals with initial BW 370 ± 37 kg, 24 months of age, were slaughtered after 95 days on feed. We evaluated shear force (SF), myofibrillar fragmentation index, ribeye area, backfat thickness, marbling, color, and cooking losses. Subsequently, 24 animals were selected and divided into four contrasting groups, in which light (BW = 504.58 ± 32.36 kg) versus heavy animals (BW = 604.83 ± 42.97 kg) and animals with tender (SF = 3.88 ± 0.57 kg) versus tough meat (SF = 7.95 ± 1.04 kg) were compared. The MYH7, MYH2 and MYH1 genes were analyzed by real-time PCR. The MyHC isoforms (MyHC-I, MyHC-IIa, and MyHC-IIx) were quantified by SDS-PAGE electrophoresis. We found lower expression of MYH2 and MYH1 genes in heavy compared to light animals and a higher amount of MyHC-I isoform in the tough meat group compared to the tender meat group. Protein expression of MyHC-IIa was higher in the tender meat group. A negative correlation was found of this protein and SF (tenderness), suggesting MyHC-IIa as a biomarker of meat quality.
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Affiliation(s)
- L A L Chardulo
- College of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - W A Baldassini
- College of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - R A Curi
- College of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - G L Pereira
- College of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - O R Machado Neto
- College of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - M Dal-Pai
- Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - I J Vechetti-Júnior
- Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
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