Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies
Maternal nutrition has the ability of influence critical processes in fetal life, including muscle development. Also, in this period, epigenetic sensitivity to external stimuli is higher and produces long-lasting effects. Thus, the aim of this study was to investigate epigenetic mechanisms, includin...
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MDPI AG
2024-02-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/14/4/652 |
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| author | Roberta Cavalcante Cracco Pamela Almeida Alexandre Guilherme Henrique Gebim Polizel Arícia Christofaro Fernandes Miguel Henrique de Almeida Santana |
| author_facet | Roberta Cavalcante Cracco Pamela Almeida Alexandre Guilherme Henrique Gebim Polizel Arícia Christofaro Fernandes Miguel Henrique de Almeida Santana |
| author_sort | Roberta Cavalcante Cracco |
| collection | DOAJ |
| description | Maternal nutrition has the ability of influence critical processes in fetal life, including muscle development. Also, in this period, epigenetic sensitivity to external stimuli is higher and produces long-lasting effects. Thus, the aim of this study was to investigate epigenetic mechanisms, including the identification and characterization of long non-coding RNA (lncRNA) from animals that had undergone different strategies of prenatal supplementation. A group of Nellore cows (n = 126) were separated into three nutritional plans: NP (control)—Not Programmed, without protein–energy supplementation; PP—Partially Programmed, protein–energy supplementation in the final third of pregnancy; and CP—Complete Programming, protein–energy supplementation during the full period of gestation. A total of 63 male offspring were used in this study, of which 15 (5 per treatment) had <i>Longissimus thoracis</i> muscle at 15 (biopsy) and 22 months (slaughter). Biopsy samples were subjected to RNA extraction and sequencing. Differential expression (DE) of remodeling factors and chromatin-modifying enzyme genes were performed. For the identification and characterization of lncRNA, a series of size filters and protein coding potential tests were performed. The lncRNAs identified had their differential expression and regulatory potential tested. Regarding DE of epigenetic mechanisms, no differentially expressed gene was found (<i>p</i> > 0.1). Identification of potential lncRNA was successful, identifying 1823 transcripts at 15 months and 1533 at 22 months. Among these, four were considered differentially expressed between treatments at 15 months and 6 were differentially expressed at 22 months. Yet, when testing regulatory potential, 13 lncRNAs were considered key regulators in the PP group, and 17 in the CP group. PP group lncRNAs possibly regulate fat-cell differentiation, in utero embryonic development, and transforming growth factor beta receptor, whereas lncRNA in the CP group regulates in utero embryonic development, fat-cell differentiation and vasculogenesis. Maternal nutrition had no effect on differential expression of epigenetic mechanisms; however, it seems to impair lncRNA regulation of epigenetics. |
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| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-07T22:46:03Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-dbb7c65c26f347da8d8ad2c513a9ca662024-02-23T15:04:56ZengMDPI AGAnimals2076-26152024-02-0114465210.3390/ani14040652Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional StrategiesRoberta Cavalcante Cracco0Pamela Almeida Alexandre1Guilherme Henrique Gebim Polizel2Arícia Christofaro Fernandes3Miguel Henrique de Almeida Santana4Department of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, BrazilMicrobiomes for One Systems Health (MOSH), CSIRO Agriculture & Food, 306 Carmody Rd, St Lucia, QLD 4067, AustraliaDepartment of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, BrazilDepartment of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, BrazilDepartment of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, BrazilMaternal nutrition has the ability of influence critical processes in fetal life, including muscle development. Also, in this period, epigenetic sensitivity to external stimuli is higher and produces long-lasting effects. Thus, the aim of this study was to investigate epigenetic mechanisms, including the identification and characterization of long non-coding RNA (lncRNA) from animals that had undergone different strategies of prenatal supplementation. A group of Nellore cows (n = 126) were separated into three nutritional plans: NP (control)—Not Programmed, without protein–energy supplementation; PP—Partially Programmed, protein–energy supplementation in the final third of pregnancy; and CP—Complete Programming, protein–energy supplementation during the full period of gestation. A total of 63 male offspring were used in this study, of which 15 (5 per treatment) had <i>Longissimus thoracis</i> muscle at 15 (biopsy) and 22 months (slaughter). Biopsy samples were subjected to RNA extraction and sequencing. Differential expression (DE) of remodeling factors and chromatin-modifying enzyme genes were performed. For the identification and characterization of lncRNA, a series of size filters and protein coding potential tests were performed. The lncRNAs identified had their differential expression and regulatory potential tested. Regarding DE of epigenetic mechanisms, no differentially expressed gene was found (<i>p</i> > 0.1). Identification of potential lncRNA was successful, identifying 1823 transcripts at 15 months and 1533 at 22 months. Among these, four were considered differentially expressed between treatments at 15 months and 6 were differentially expressed at 22 months. Yet, when testing regulatory potential, 13 lncRNAs were considered key regulators in the PP group, and 17 in the CP group. PP group lncRNAs possibly regulate fat-cell differentiation, in utero embryonic development, and transforming growth factor beta receptor, whereas lncRNA in the CP group regulates in utero embryonic development, fat-cell differentiation and vasculogenesis. Maternal nutrition had no effect on differential expression of epigenetic mechanisms; however, it seems to impair lncRNA regulation of epigenetics.https://www.mdpi.com/2076-2615/14/4/652cattleepigeneticsfetal programminggene expressionmuscle |
| spellingShingle | Roberta Cavalcante Cracco Pamela Almeida Alexandre Guilherme Henrique Gebim Polizel Arícia Christofaro Fernandes Miguel Henrique de Almeida Santana Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies Animals cattle epigenetics fetal programming gene expression muscle |
| title | Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies |
| title_full | Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies |
| title_fullStr | Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies |
| title_full_unstemmed | Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies |
| title_short | Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies |
| title_sort | evaluation of muscle long non coding rna profile during rearing and finishing phase of bulls subjected to different prenatal nutritional strategies |
| topic | cattle epigenetics fetal programming gene expression muscle |
| url | https://www.mdpi.com/2076-2615/14/4/652 |
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